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(dA)230*(dT,dU)230
?
-
-
-
-
?
(pT)7(p(2,3-dihydroxy-5-oxopentyl phosphate))(pT)6
?
-
-
-
-
?
12-mer oligodeoxyribonucleotide containing a 2'-deoxyguanosine at the natural AP site
?
-
-
-
-
?
12-mer oligodeoxyribonucleotide containing a natural AP site
?
-
the minimal kinetic model for the natural AP site incision consists of four stages corresponding to three different transient states of APE1. When the enzyme is complexed with the AP-substrate, the catalytic cycle is completed within 3 s
-
-
?
12-mer oligodeoxyribonucleotide containing a tetrahydrofuran analogue at the natural AP site
?
-
-
-
-
?
18-mer containing P33-labeled tetrahydrofuran
?
-
-
-
-
?
21 bp double-stranded DNA containing an apurinic/apyrimidinic-site analogue
?
-
the affinity of EndoIV for the substrate analogue is very high and its dissociation constant is less than 0.01 microM. A C-terminal DNA-recognition loop at residues 265-269 that is only present in the long type enzymes contributes to its high affinity for apurinic/apyrimidinic sites
-
?
26-bp-oligonucleotide
5'-hexachloro-fluorescein phosphoramidite-labeled 13-mer fragment + ?
oligonucleotide containing a 5'-hexachloro-fluorescein phosphoramidite-labeled tetrahydrofuranyl residue in the middle
-
-
?
3'-fluorescein-labeled '-AGTAGACAAG(dU)TACCATGCCTGCACGAAGTT-3'
?
-
-
-
?
3'-fluorescein-labeled 5'-AACTTCGTGCAGGCATGGTAG(dU)TTGTCTACT-3'
?
-
-
-
?
3'-fluorescein-labeled 5'-AGTAGACAAGCTACCATGCCTGCACGAAGTT-3'
?
-
-
-
?
30-mer oligonucleotide duplex DNa containing a tetrahydrofuran analogue
?
-
-
-
-
?
31mer oligonucleotide duplex
?
34-mer dsDNA containing an internal tetrahydrofuran
18-mer ds DNA + ?
-
-
-
-
?
34-mer ssDNA containing an internal tetrahydrofuran
18-mer ssDNA + ?
-
-
-
-
?
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite A
?
-
-
-
-
?
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite G
?
-
-
-
-
?
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite A
?
-
-
-
-
?
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite G
?
-
-
-
-
?
37mer with AP/A
?
-
-
-
-
?
37mer with AP/C
?
-
-
-
-
?
37mer with AP/G
?
-
-
-
-
?
37mer with AP/T
?
-
-
-
-
?
37mer with dihydrouridine
?
-
-
-
-
?
43-mer oligonucleotide containing apurinic/apyrimidinic sites
fragments of DNA
-
-
-
?
43-mer oligonucleotide containing the AP-site analog tetrahydrofuran at nt 31
?
-
-
-
-
?
43-mer oligonucleotide containing the AP-site analog THF at nt 31
?
-
-
-
-
?
5'-AACTTCGTGCAGGCATGGG(m6A)TCTTGTCTACT-3'
?
-
-
-
?
5'-AGTAGACAAGATCCCATGCCTGCACGAAGTT-3'
?
-
-
-
?
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
?
-
-
-
?
5'-CTCTCCCTTC-8-oxo-7,8-dihydroguanine-CTCCTTTCCTCT-3'
?
-
-
-
?
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
?
5'-Cy3-CAAGGTAGTTATCCTTG-1-Black Hole Quencher1-3'
?
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
?
-
-
-
?
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
?
-
-
-
?
5'-TCGAGGATCCTGAGCTCGAGTCGACGXTCGCGAATTCTGCGGATCCAAGC-3'
?
alkylated-depurinated DNA
?
-
-
-
-
?
AP DNA
fragments of DNA
-
AP sites
-
-
?
AP-DNA-DNA
?
-
synthetic DNA-DNA hybrid
-
-
?
AP-DNA-RNA
?
-
synthetic DNA-RNA hybrids that simulate a transcription intermediate
-
-
?
c-myc coding region determinant mRNA
?
CAAXACCTTCATCCTTTCC
?
-
X: AP site
-
-
?
CAXAACCTTCATCCTTTCC
?
-
X: AP site
-
-
?
CTAGTCAXCACTGTCTGTGGATAC
?
-
X: AP site
-
-
?
CXAAACCTTCATCCTTTCC
?
-
X: AP site
-
-
?
cytosine-labeled DNA
?
-
-
-
-
?
DNA containing 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine/C
?
DNA containing 5,6-dihydrothymidine/A
?
DNA containing 5-hydroxy-2'-deoxyuridine/G
?
DNA containing 5-OH-C/A
?
-
-
-
-
?
DNA containing 5-OH-C/G
?
-
-
-
-
?
DNA containing an abasic site
?
-
45-mer oligomer
-
-
?
DNA containing apurinic site
?
DNA containing apurinic sites
?
DNA containing apurinic/apyrimidinic site
?
-
-
-
-
?
DNA containing apurinic/apyrimidinic site
DNA fragments
-
-
-
-
?
DNA containing apurinic/apyrimidinic sites
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
DNA containing dihydrouracil
?
-
-
-
?
DNA containing dihydrouridine/G
?
-
-
-
-
?
DNA containing O-benzylhydroxylamine
?
-
-
-
-
?
DNA containing O-methylhydroxylamine
?
-
-
-
-
?
DNA containing tamdem dihydrouracil
?
-
the human AP endonuclease APE1 can process the 3' termini generated by human endonuclease III (hNTH) and endonuclease VIII. Both human endonuclease III and endonuclease VIII cannot completely remove both dihydrouracil lesions. With the participation of APE1 and polynucleotide kinase, the 3'-lesions remaining in the products of the reaction with human endonuclease III and endonuclease VIII can efficiently removed. The resulting products can be utilized by repair DNA polymerases as primers for repair synthesis
-
-
?
DNA containing tandem dihydrouracil
?
-
the human AP endonuclease APE1 can process the 3' termini generated by human endonuclease III (hNTH) and endonuclease VIII. Both human endonuclease III and endonuclease VIII cannot completely remove both dihydrouracil lesions. With the participation of APE1 and polynucleotide kinase, the 3'-lesions remaining in the products of the reaction with human endonuclease III and endonuclease VIII can efficiently removed. The resulting products can be utilized by repair DNA polymerases as primers for repair synthesis
-
-
?
DNA containing tetrahydrofuranyl/G
?
DNA containing thymine glycol
?
-
-
-
-
?
DNA containing urea
?
-
-
-
-
?
DNA with 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine/C
?
-
-
-
-
?
DNA with 2-deoxyribonolactone
?
-
-
-
-
?
DNA with 5,6-dihydrothymidine/A
?
-
-
-
-
?
DNA with 5,6-dihydrothymine
?
-
-
-
-
?
DNA with 5,6-dihydrouracil
?
-
-
-
-
?
DNA with 5-hydroxy-2'-deoxyuridine/G
?
-
-
-
-
?
DNA with 5-hydroxy-5-methylhydantoin
?
-
-
-
-
?
DNA with 5-hydroxy-6-hydrothymine
?
-
-
-
-
?
DNA with 5-hydroxy-6-hydrouracil
?
-
-
-
-
?
DNA with alloxan
?
-
-
-
-
?
DNA with an abasic site
?
DNA with an abasic site
DNA with 5'-phosphate terminus + DNA with 3'-alpha,beta-unsaturated aldehyde
DNA with dihydrouridine/G
?
-
-
-
-
?
DNA with tetrahydrofuranyl/G
?
-
-
-
-
?
DNA with thymine glycol
?
-
-
-
-
?
DNA with uracil glycol
?
-
-
-
-
?
double-stranded DNA with abasic sites
?
-
-
-
-
?
duplex oligonucleotide containing a 5,6-dihydro-2'-deoxyuridine*G pair
?
-
nucleotide incison repair activity
-
-
?
duplex oligonucleotide containing a alpha-2'-deoxyadenosine*T pair
?
-
nucleotide incison repair activity
-
-
?
duplex oligonucleotide containing a tetrahydrofuran*G pair
?
-
nucleotide incison repair activity
-
-
?
GTACGTAXCCACAGACAGTGATGA
?
-
X: AP site
-
-
?
linear 31-mer duplex oligonucleotide (3'-32P-labeled top strand contains an abasic site at position 17)
3'-32P-labeled 14-mer oligonucleotide
-
cleavage 3' to the apurinic/apyrimidinic site
-
-
?
N1 duplex DNA substrate + H2O
?
oligodeoxynucleotide with abasic site 2,3-dihydroxy-5-oxopentyl phosphate
?
-
-
-
-
?
oligomer with G/U pair
?
-
-
-
-
?
Reactive Blue 2
?
-
-
-
-
?
single-stranded DNA with abasic sites
?
-
catalytic efficiency is 20fold less than the activity against double-stranded DNA with abasic sites
-
-
?
THF-containing oligonucleotide
?
thymidine-labeled DNA
?
-
-
-
-
?
additional information
?
-
30mer THF-T duplex
?
5'-[32P]labeled 30mer THF-T duplex
-
-
?
30mer THF-T duplex
?
5'-[32P]labeled 30mer THF-T duplex
-
-
?
31mer oligonucleotide duplex
?
3'-[alpha-32P]-dAMP-labeled 31mer oligonucleotide duplex
-
-
?
31mer oligonucleotide duplex
?
3'-[alpha-32P]-dAMP-labeled 31mer oligonucleotide duplex
-
-
?
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
?
-
the fluorogenic substrate OligoI is based on the sequence immediately surrounding the stem V-loop region (OligoI) and incorporating a fluorescent tag, Cy3, at the 5' end and a fluorescence Black Hole Quencher at the 3' end of the oligonucleotide
-
-
?
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
?
-
the fluorogenic substrate OligoI is based on the sequence immediately surrounding the stem V-loop region (OligoI) and incorporating a fluorescent tag, Cy3, at the 5' end and a fluorescence Black Hole Quencher at the 3' end of the oligonucleotide
-
-
?
5'-Cy3-CAAGGTAGTTATCCTTG-1-Black Hole Quencher1-3'
?
-
the fluorogenic substrate DNAOligoI is based on the sequence immediately surrounding the stem Vloop region (OligoI) and incorporating a fluorescent tag, Cy3, at the 5' end and a fluorescence Black Hole Quencher at the 3' end of the oligonucleotide, DNAOligoI has an identical sequence to OligoI except that deoxythymidylate is substituted for 2' hydroxyl uridine
-
-
?
5'-Cy3-CAAGGTAGTTATCCTTG-1-Black Hole Quencher1-3'
?
-
the fluorogenic substrate DNAOligoI is based on the sequence immediately surrounding the stem Vloop region (OligoI) and incorporating a fluorescent tag, Cy3, at the 5' end and a fluorescence Black Hole Quencher at the 3' end of the oligonucleotide, DNAOligoI has an identical sequence to OligoI except that deoxythymidylate is substituted for 2' hydroxyl uridine
-
-
?
5'-TCGAGGATCCTGAGCTCGAGTCGACGXTCGCGAATTCTGCGGATCCAAGC-3'
?
a synthetic stable AP-site analog where X represents tetrahydrofuran
-
-
?
5'-TCGAGGATCCTGAGCTCGAGTCGACGXTCGCGAATTCTGCGGATCCAAGC-3'
?
a synthetic stable AP-site analog where X represents tetrahydrofuran
-
-
?
AP-DNA
fragments of DNA
-
-
-
-
?
AP-DNA
fragments of DNA
-
-
-
-
?
AP-DNA
fragments of DNA
Base excision repair pathway, enzyme cleaves the 5'-phosphodiester bond, generating 3'-OH and 5'-dRP termini
-
-
?
c-myc coding region determinant mRNA
?
-
APE1 preferentially cleaves in between UA and CA dinucleotides of c-myc coding region determinant RNA
-
-
?
c-myc coding region determinant mRNA
?
-
APE1 preferentially cleaves in between UA and CA dinucleotides of c-myc coding region determinant RNA
-
-
?
c-myc RNA
?
-
APE1 cleaves at the UA, CA, and UG sites of c-myc RNA in vitro
-
-
?
c-myc RNA
?
-
APE1 cleaves at the UA, CA, and UG sites of c-myc RNA in vitro
-
-
?
DNA
fragments of DNA
-
AP endonuclease pE296R has strong preference for mispaired and oxidative base lesions at the 3'-termini of single-strand breaks, the 3'-terminal damaged pyrimidines (uracil, 5,6-dihydrouracil, and 5-hydroxycytosine) are removed with higher efficiency than damaged purines inosine and 7,8-dihydro-8-oxoguanine
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
exhibits DNA-glycosylase activity on different types of DNA substrates with pyrimidine damage, being able to release both urea and thymine glycol from double-stranded polydeoxyribonucleotides, also possesses an apurinic/apyrimidinic lyase activity on UV- or gamma-irradiated DNA substrates
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
hydrolyzes phosphodiester bond near heat-induced apruinic sites in double or single strand DNA
-
?
DNA
fragments of DNA
-
hydrolyzes phosphodiester bond near heat-induced apruinic sites in double or single strand DNA
-
?
DNA
fragments of DNA
-
specific for apurinic sites
-
?
DNA
fragments of DNA
-
specific for apurinic sites
-
?
DNA
fragments of DNA
-
breaks strand on the 3'-side of apurinic sugar residues giving a 3'-OH and a 5'-phosphate
-
?
DNA
fragments of DNA
-
The latter lesions are processed by AP endonucleases, which are important components of the base excision repair pathway
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
removes UV light and osmium tetroxide damaged bases via an N-glycosylase activity followed by a 3'-purinic/apyrimidinic endonuclease activity, product is a nucleoside-free site flanked by 3'- and 5'-terminal phosphate groups
-
?
DNA
fragments of DNA
-
incises DNA damaged with UV light, ionizing radiation, OsO4, KMnO4 and H2O2 at cytosine and thymine sites
-
?
DNA
fragments of DNA
-
specific for DNA containing either apurinic or apyrimidinic sites
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
specific for DNA containing either apurinic or apyrimidinic sites
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
dU)230 (ratio dT:dU is 15) partially depyrimidinated by uracil-DNA glycosylase
-
?
DNA
fragments of DNA
-
alkylated-depurinated DNA
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
specific for apurinic sites
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
AP endonuclease I forms deoxyribose 3'-phosphate and 5'-OH termini upon cleaving depurinated DNA
-
?
DNA
fragments of DNA
-
cleaves the phosphodiester bond 3' to the apurinic/apyrimidinic site
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
cleavage at abasic sites in duplexes with paired lesions is slower than in duplexes with single lesions. Double strand breaks are readily generated in duplexes with abasic sites positioned 3' to each other. In duplexes containing abasic sites set 1 base pair apart, 5' to each other, both enzymes slowly cleave the abasic site on one strand only and are unable to incise the other stand
-
?
DNA
fragments of DNA
-
removes 5-hydroxy-2'-deoxycytidine and 5-hydroxy-2'-deoxyuridine via a N-glycosylase/beta-elimination reaction
-
?
DNA
fragments of DNA
-
cuts the DNA strands on the 5' side of the apurinic sites giving a 3'-OH and a 5'-phosphate
-
?
DNA
fragments of DNA
-
endonucleolytic cleavage near apurinic or apyrimidinic sites to products with 5'-phosphates, e.g. UV-irradiated poly(dA)*poly(dT)
-
?
DNA
fragments of DNA
-
catalyzes phosphodiester bond cleavage via a lyase- rather than a hydrolase mechanism
-
?
DNA
fragments of DNA
-
synthetic oligodeoxynucleotides containing abasic sites
-
?
DNA
fragments of DNA
-
specific for apurinic sites
-
?
DNA
fragments of DNA
-
endonuclease III: excision of a number of thymine- and cytosine-derived lesions from DNA, no purine-derived lesions excised by endonuclease III
-
?
DNA
fragments of DNA
-
endonucleolytic activity against apurinic and apyrimidinic sites and a dose-dependent response to DNA that has been X-irradiated, UV-irradiated or treated with OsO4
-
?
DNA
fragments of DNA
-
cleaves the phosphodiester bond 3' to the apurinic/apyrimidinic site
-
?
DNA
fragments of DNA
-
cleaves the phosphodiester bond 3' to the apurinic/apyrimidinic site
-
?
DNA
fragments of DNA
-
cleaves the phosphodiester bond 3' to the apurinic/apyrimidinic site
-
?
DNA
fragments of DNA
-
duplex oligonucleotides containing the base lesion analogs O-methylhydoxylamine or O-benzylhydroxylamine, N-glycosylase activity generates intermediary AP site which is subsequently cleaved by the enzyme -associated AP lyase activity, O-alkoxyamine-modified AP sites are poorer substrates than the presumed physiological substrates
-
?
DNA
fragments of DNA
-
enzyme generates only single-strand breaks when the base damage is set one and three base-pairs apart, and only slowly introduces double-strand breaks in substrates where base damage is set five or seven base-pairs apart. Treatment of an abasic site-containing DNA readily yields double-strand breaks.
-
?
DNA
fragments of DNA
-
DNA containing dihydrouridine, 5,3-dihydrothymidine, 5-hydroxy-2'-deoxyuridine, 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine or tetrahydrofuranyl
-
?
DNA
fragments of DNA
-
the beta-elimination reaction breaking the C3'-O-P bond 3' to an AP site can be followed by a delta-elimination reaction breaking the C5'-O-P bond 5' to the AP site, with the release of an unsaturated derivative of the base-free sugar and the generation of a gap flanked by 3'-phosphate and 5'-phosphate ends
-
?
DNA
fragments of DNA
-
recognizes urea, an oxidative ring fragmentation product of thymine
-
?
DNA
fragments of DNA
-
when DNA containing thymine glycol is used as substrate the combined N-glycosylase/AP endonuclease activity is about 2fold higher than the AP endonuclease activity
-
?
DNA
fragments of DNA
-
KsgA has al DNA glycosylase/AP lyase activity for C mispaired with oxidized T
-
-
?
DNA
fragments of DNA
-
KsgA has al DNA glycosylase/AP lyase activity for C mispaired with oxidized T
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
specific for apurinic sites
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
648685, 648686, 648687, 694298, 701749, 702317, 702939, 703032, 703960, 704663, 704731, 704948, 705736, 706019, 706429 -
-
?
DNA
fragments of DNA
-
-
?
DNA
fragments of DNA
-
-
?
DNA
fragments of DNA
-
-
?
DNA
fragments of DNA
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
cleavage of apyrimidinic DNA both 5' and 3' to the site of damage in a ratio of 60:40, respectively, even though it can cleave on both sides of an internal apyrimidinic site, it does not release deoxyribose 5-phosphate from terminal apyrimidinic sites
-
?
DNA
fragments of DNA
-
acts on specific adenines in single-stranded DNA
-
?
DNA
fragments of DNA
-
cleaves single- and double-stranded oligonucleotides lacking one or two bases
-
?
DNA
fragments of DNA
enzyme reveals glycosylase activity and apurinic/apyrimidinic lyase activity on duplex DNA containing 8-OH-G, DNA containing 8-OH-G/A is not cleaved, DNA containing 8-OH-G/T and 8-OH-G/G is slightly cleaved
-
?
DNA
fragments of DNA
-
cleavage at abasic sites in duplexes with paired lesions is slower than in duplexes with single lesions. Double strand breaks are readily generated in duplexes with abasic sites positioned 3' to each other. In duplexes containing abasic sites set 1 base pair apart, 5' to each other, both enzymes slowly cleave the abasic site on one strand only and are unable to incise the other stand
-
?
DNA
fragments of DNA
-
acts on both 5-hydroxycytosine and abasic sites, preferentially when these are situated opposite guanines
-
?
DNA
fragments of DNA
-
catalyzes incision at the C4-keto-C-1-aldehyde site, hydrolyzes 3'-phosphoglycolates 25fold more slowly than C-4-keto-C-1-aldehydes
-
?
DNA
fragments of DNA
-
cleaves the DNA phosphodiester backbone immediately 5' to an AP site, also shows 3'-phosphodiesterase activity, 3'-phosphatase activity, RNaseH and significant 3'-5'-exonuclease activity
-
?
DNA
fragments of DNA
-
catalyzes 5'-incision of 2-deoxyribonolactone, but acts at least 10fold less effectively to remove the 3'-phosphates at direct strand breaks
-
?
DNA
fragments of DNA
cleaves thymine glycol-containing form I plasmid DNA and a dihydrouracil-containing oligonucleotide duplex
-
?
DNA
fragments of DNA
-
rate of AP lyase-mediated strand cleavage is much slower than the rate of DNA N-glycoxsylase-mediated base release
-
?
DNA
fragments of DNA
-
specific for DNA containing either apurinic or apyrimidinic sites
-
?
DNA
fragments of DNA
-
endonuclease A: activity for UV-irradiated DNA, gamma-irradiated DNA and OsO4-treated DNA
-
?
DNA
fragments of DNA
base excision repair (BERa) pathway is initiated by lesion-specific glycosylases that excise the damaged base from the sugar-phosphate backbone, resulting in a potentially cytotoxic apurinic/apyrimidinic (AP) site intermediate that becomes the substrate for the major human AP endonuclease
-
-
?
DNA
fragments of DNA
-
bifunctional enzyme is involved in base excision repair, it is a bifunctional DNA glycosylase/apurinic/apyrimidinic lyase which removes hydrated, reduced, or oxidized bases from the DNA backbone as the initial step of base excision repair
-
-
?
DNA
fragments of DNA
-
DNA single-strand breaks containing 3'-blocking groups are generated from attack of the sugar backbone by reactive oxygen species or after base excision by DNA glycosylase/apurinic/apyrimidinic (AP) lyases
-
-
?
DNA
fragments of DNA
-
5'-deoxyribose-5-phosphate and apurinic/apyrimidinic sites are excised with half-lives of 2.7 and 7.0 min, respectively
-
-
?
DNA
fragments of DNA
-
Ape1 cleaves the phosphodiester backbone 5' to the AP site generating 3'-hydroxyl and 5'-deoxyribosephosphate termini, Ape1 exhibits a prominent 5' hydrolytic AP endonuclease, a weak 3'-diesterase and a 3'-5'-exonuclease activity
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
at low concentrations the enzyme is specific for depurinated native DNA, at higher concentrations it degrades DNA in a non-specific manner
-
?
DNA
fragments of DNA
-
DNA single-strand breaks containing 3'-blocking groups are generated from attack of the sugar backbone by reactive oxygen species or after base excision by DNA glycosylase, apurinic, apyrimidinic (AP) lyases
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
acts specifically on pyrimidine dimers, preferring those in double-stranded DNA to those in singes-stranded DNA, enzyme has glycosylase and apyrimidinic/apurinic endonuclease activity, cleaves 3' to the AP site generating a 3'-deoxyribose moiety and a 5'-phosphate
-
?
DNA
fragments of DNA
-
phage-T4 and Micrococcus luteus enzyme nick the C(3')-O-P-bond 3' to the apurinic/apyrimidinic sites in DNA, the phage enzyme can also subsequently nick the C(5')-O-P bond 5' to the apurinic/apyrimidinic site
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
supercoiled DNA
-
?
DNA
fragments of DNA
-
specific for apurinic sites
-
?
DNA
fragments of DNA
-
enzyme recognizes apurinic and apyrimidinic sites induced by acid and gamma-rays, as well as lesions which are introduced into DNA by UV irradiation and OsO4
-
?
DNA
fragments of DNA
thymine glycol DNA glycosylase, urea DNA glycosylase and AP lyase activity
-
?
DNA
fragments of DNA
-
no activity with methylated or OsO4-treated DNA
-
?
DNA
fragments of DNA
-
enzyme plays an important role in oxidative signalling, transcription factor regulation, and cell cycle control
-
-
ir
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
specific for apurinic sites
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
cleaves phosphodiester bridge wihich is the immediate neighbor of the AP site on its 5' side leaving 3'-OH and 5'-phosphate ends
-
?
DNA
fragments of DNA
-
PM2 phage DNA
-
?
DNA
fragments of DNA
-
DNA repair enzyme is involved in base excision repair of apurinic/apyrimidinic sites after oxidative DNA damage
-
-
?
DNA
fragments of DNA
-
multifunctional enzyme involved in DNA base excision repair of oxidative DNA damage and in redox regulation of a number of transcription factors
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
cleaves all four types of abasic site-containing substrates: AP/G, AP/A, AP/C, AP/T, with a moderate preference for AP/T sites
-
?
DNA
fragments of DNA
-
cuts the DNA strands on the 5' side of the apurinic sites giving a 3'-OH and a 5'-phosphate
-
?
DNA
fragments of DNA
-
catalyzes the hydrolysis of the 5'-phosphodiester bond at the abasic site
-
?
DNA
fragments of DNA
-
recognizes and cleaves DNA substrates containing dihydrouracil, 2,6-diamino-4-hydroxy-5N-methylformamidopyrimidine and abasic sites, but not DNA substrates containing uracil or 8-oxoguanine
-
?
DNA
fragments of DNA
-
DNA containing dihydrouridine, 5,3-dihydrothymidine, 5-hydroxy-2'-deoxyuridine, 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine or tetrahydrofuranyl
-
?
DNA
fragments of DNA
-
oxidative DNA damage is primarily reversed by the base excision repair pathway, initiated by N-glycosylase apurinic/apyrimidinic lyase proteins
-
-
ir
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
enzyme has a 3' to 5' exonuclease activity and shows additional functional similarities to DNA repair enzymes
-
?
DNA
fragments of DNA
-
specific for apurinic sites
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
enzyme has a 3' to 5' exonuclease activity and shows additional functional similarities to DNA repair enzymes
-
?
DNA
fragments of DNA
-
specific for apurinic sites
-
?
DNA
fragments of DNA
Tequatrovirus T4
-
-
-
-
?
DNA
fragments of DNA
Tequatrovirus T4
-
-
-
?
DNA
fragments of DNA
Tequatrovirus T4
-
-
-
?
DNA
fragments of DNA
Tequatrovirus T4
-
-
-
-
?
DNA
fragments of DNA
Tequatrovirus T4
-
endonucleolytic cleavage near apurinic or apyrimidinic sites to products with 5'-phosphates, e.g. UV-irradiated poly(dA)*poly(dT)
-
?
DNA
fragments of DNA
Tequatrovirus T4
-
catalyzes phosphodiester bond cleavage via a lyase- rather than a hydrolase mechanism
-
?
DNA
fragments of DNA
Tequatrovirus T4
-
duplex oligonucleotides containing the base lesion analogs O-methylhydoxylamine or O-benzylhydroxylamine, N-glycosylase activity generates intermediary AP site which is subsequently cleaved by the enzyme -associated AP lyase activity, O-alkoxyamine-modified AP sites are poorer substrates than the presumed physiological substrates
-
?
DNA
fragments of DNA
Tequatrovirus T4
-
phage-T4 and Micrococcus luteus enzyme nick the C(3')-O-P-bond 3' to the apurinic/apyrimidinic sites in DNA, the phage enzyme can also subsequently nick the C(5')-O-P bond 5' to the apurinic/apyrimidinic site
-
?
DNA containing 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine/C
?
-
-
-
-
?
DNA containing 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine/C
?
-
-
-
-
?
DNA containing 5,6-dihydrothymidine/A
?
-
-
-
-
?
DNA containing 5,6-dihydrothymidine/A
?
-
-
-
-
?
DNA containing 5-hydroxy-2'-deoxyuridine/G
?
-
-
-
-
?
DNA containing 5-hydroxy-2'-deoxyuridine/G
?
-
-
-
-
?
DNA containing apurinic site
?
-
-
-
-
?
DNA containing apurinic site
?
-
-
-
-
?
DNA containing apurinic sites
?
-
-
-
-
?
DNA containing apurinic sites
?
-
-
-
-
?
DNA containing apurinic/apyrimidinic sites
?
-
-
-
?
DNA containing apurinic/apyrimidinic sites
?
-
-
-
-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
-
apurinic/apyrimidinic endonuclease Nfo protects Bacillus subtilis spores from DNA damage accumulated during spore dormancy
-
-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
-
specificity
-
-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
-
C4'-oxidized abasic sites are efficiently excised via intermediate Schiff-base formation. Activity is 100fold less efficient than repair by exonuclease III
-
-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
-
endonuclease III plays an important cellular role by removing premutagenic pyrimidine damages produced by reactive oxygen species. EcoNth is a bifunctional enzyme that has DNA glycosylase and apurinic/apyrimidinic lyase activity
-
-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
-
the enzyme forms a Schiff base-type intermediate with the substrate after the damaged base is removed
-
-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
hydrogen bonds to phosphate groups 3' to the cleavage site is essential for the binding of the enzyme to the product DNA, which may be necessary for efficient functioning of the base excision rapair pathway
-
-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
inducible enzyme, the enzyme exhibits endonucleolytic activity and is regulated as part of the acid-adaptive response of the organism. Smx is likely the primary, if not the sole, AP endonuclease induced during growth at low pH values, loss of Smx activity renders the mutant strain sensitive to hydrogen peroxide treatment but relatively unaffected by acid-mediated damage or near-UV irradiation
-
-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
inducible enzyme, the enzyme exhibits endonucleolytic activity and is regulated as part of the acid-adaptive response of the organism. Smx is likely the primary, if not the sole, AP endonuclease induced during growth at low pH values, loss of Smx activity renders the mutant strain sensitive to hydrogen peroxide treatment but relatively unaffected by acid-mediated damage or near-UV irradiation
-
-
?
DNA containing tetrahydrofuranyl/G
?
-
-
-
-
?
DNA containing tetrahydrofuranyl/G
?
-
-
-
-
?
DNA with an abasic site
?
the enzyme has little specificity for the base opposite 8-oxoguanine. The enzyme has both DNA glycosylase and DNA lyase (beta-elimination) activity, and the combined glycosylase/lyase activity occurs at a rate comparable with the glycosylase activity alone
-
-
?
DNA with an abasic site
?
the enzyme has little specificity for the base opposite 8-oxoguanine. The enzyme has both DNA glycosylase and DNA lyase (beta-elimination) activity, and the combined glycosylase/lyase activity occurs at a rate comparable with the glycosylase activity alone
-
-
?
DNA with an abasic site
?
-
-
-
?
DNA with an abasic site
?
the enzyme is part of the base excision repair (BER) pathway. It protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine, from single- and double-stranded DNA substrates
-
-
?
DNA with an abasic site
?
the substrate specificity for 8-oxoguanine/guanine sites is higher than that for 8-oxoguanine/cytosine sites. apurinic-lyase activity of this enzyme cleaved only 20% of these apurinic-sites at the same time point
-
-
?
DNA with an abasic site
?
-
-
-
?
DNA with an abasic site
?
the enzyme is part of the base excision repair (BER) pathway. It protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine, from single- and double-stranded DNA substrates
-
-
?
DNA with an abasic site
?
the substrate specificity for 8-oxoguanine/guanine sites is higher than that for 8-oxoguanine/cytosine sites. apurinic-lyase activity of this enzyme cleaved only 20% of these apurinic-sites at the same time point
-
-
?
DNA with an abasic site
DNA with 5'-phosphate terminus + DNA with 3'-alpha,beta-unsaturated aldehyde
the enzyme excises an oxidatively-damaged form of guanine. Bifunctional enzyme with both DNA glycosylase and apurinic/apyrimidinic lyase activities
-
-
?
DNA with an abasic site
DNA with 5'-phosphate terminus + DNA with 3'-alpha,beta-unsaturated aldehyde
bifunctional enzyme with both DNA glycosylase and apurinic/apyrimidinic lyase activities. The specificity of DNA glycosylase activity of is compared using 39-mer DNA duplexes containing an 8-oxoG residue opposite each of the four natural DNA bases (A, T, G and C). The enzyme efficiently cleaves oligomers containing 8-oxoG:C and 8-oxoG:G base pairs, less effective on oligomers containing 8-oxoG:T and 8-oxoG:A mispairs. The enzyme catalyzes a beta-elimination reaction at the apurinic site produced by excision of the 8-oxoguanine and thus generates a 5'-phosphate terminus and a 3'-alpha,beta-unsaturated aldehyde sugar terminus at the incision site. Bifunctional enzyme with both DNA glycosylase and apurinic/apyrimidinic lyase activities
-
-
?
N1 duplex DNA substrate + H2O
?
5'-FAM peptide-labelled AP DNA duplex substrate
-
-
?
N1 duplex DNA substrate + H2O
?
5'-FAM peptide-labelled AP DNA duplex substrate
-
-
?
N1 duplex DNA substrate + H2O
?
5'-FAM peptide-labelled AP DNA duplex substrate
-
-
?
THF-containing oligonucleotide
?
-
AP endonuclease activity
-
-
?
THF-containing oligonucleotide
?
-
AP endonuclease activity
-
-
?
additional information
?
-
major role in plant defence against oxidative DNA damage
-
-
?
additional information
?
-
-
major role in plant defence against oxidative DNA damage
-
-
?
additional information
?
-
-
no substrate: alkylated sites
-
-
?
additional information
?
-
-
no substrate: alkylated sites
-
-
?
additional information
?
-
-
no substrate: native DNA
-
-
?
additional information
?
-
-
no substrate: native DNA
-
-
?
additional information
?
-
-
DNA polymerase X, along with polymerization and 3'-5'-exonuclease activities, possesses an intrinsic abasic endonuclease activity. Both, abasic endonuclease and 3'-5'-exonuclease activities are genetically linked and governed by the same metal ligands located at the C-terminal polymerase and histidinol phosphatase domain of the polymerase
-
-
?
additional information
?
-
-
enzyme also has DNA N-glycosylase activity
-
-
?
additional information
?
-
-
important role in repair of oxidative DNA damage
-
-
?
additional information
?
-
enzyme plays an important role in repair of DNA damages
-
-
?
additional information
?
-
-
enzyme plays an important role in repair of DNA damages
-
-
?
additional information
?
-
-
no activity with DNA that has been damaged by UV light, methyl methanesulfonate, osmium teroxide or sodium bisulfite
-
-
?
additional information
?
-
-
enzyme has an essential base excision repair (BER) activity and a redox activity that regulates expression of a number of genes through reduction of their transcription factors, AP-1, NFkappaB, HIF-1alpha, CREB, p53 and others
-
-
?
additional information
?
-
-
no substrate: alkylated sites
-
-
?
additional information
?
-
-
no substrate: native DNA
-
-
?
additional information
?
-
-
enzyme also has DNA N-glycosylase activity
-
-
?
additional information
?
-
-
enzyme also has DNA N-glycosylase activity
-
-
?
additional information
?
-
-
enzyme also has DNA N-glycosylase activity
-
-
?
additional information
?
-
-
enzyme also has DNA N-glycosylase activity
-
-
?
additional information
?
-
-
all known bacterial AP lyases and some at least of the mammalian ones, also acts as DNA glycosylases
-
-
?
additional information
?
-
-
bacteriophage T4 endonuclease V and Escherichia coli endonuclease II catalyze N-glycosylase and 3'-abasic endonuclease reaction, beta-elimination reaction
-
-
?
additional information
?
-
-
no substrate: alkylated sites
-
-
?
additional information
?
-
-
no substrate: native DNA
-
-
?
additional information
?
-
-
pdT8d(-)dTn is cleaved by endonuclease III yielding two products which have the same electrophoretic behaviour as the doublet obtained by alkaline beta-elimination, thus the enzyme is a beta-elimination catalyst
-
-
?
additional information
?
-
-
KsgA does not remove C opposite normal bases, 7,8-dihydro-8-oxoguanine and 2-hydroxyadenine, KsgA does not excise thymine glycol, 5-formyluracil, and 5-hydroxymethyluracil opposite cytosine from double-stranded oligonucleotides
-
-
?
additional information
?
-
Escherichia coli endonuclease III is a DNA glycosylase with a broad substrate specificity for oxidized or reduced pyrimidine bases. Endo III possesses two types of activities: N-glycosylase (hydrolysis of the N-glycosidic bond) and AP lyase (elimination of the 3'-phosphate of the AP-site)
-
-
?
additional information
?
-
-
Escherichia coli endonuclease III is a DNA glycosylase with a broad substrate specificity for oxidized or reduced pyrimidine bases. Endo III possesses two types of activities: N-glycosylase (hydrolysis of the N-glycosidic bond) and AP lyase (elimination of the 3'-phosphate of the AP-site)
-
-
?
additional information
?
-
analysis of structural rearrangements of the DNA substrates and uncleavable ligands during their interaction with Endo III using oligonucleotide duplexes containing 5,6-dihydrouracil, a natural abasic site, its tetrahydrofuran analogue, and undamaged duplexes carried fluorescent DNA base analogues 2-aminopurine and 1,3-diaza-2-oxophenoxazine as environment-sensitive reporter groups, pre-steady-state kinetic analysis, overview. Endo III induces several fast sequential conformational changes in DNA during binding, lesion recognition, and adjustment to a catalytically competent conformation. The glycosylase uses a multistep mechanism of damage recognition, which likely involves Gln41 and Leu81 as DNA lesion sensors
-
-
?
additional information
?
-
-
analysis of structural rearrangements of the DNA substrates and uncleavable ligands during their interaction with Endo III using oligonucleotide duplexes containing 5,6-dihydrouracil, a natural abasic site, its tetrahydrofuran analogue, and undamaged duplexes carried fluorescent DNA base analogues 2-aminopurine and 1,3-diaza-2-oxophenoxazine as environment-sensitive reporter groups, pre-steady-state kinetic analysis, overview. Endo III induces several fast sequential conformational changes in DNA during binding, lesion recognition, and adjustment to a catalytically competent conformation. The glycosylase uses a multistep mechanism of damage recognition, which likely involves Gln41 and Leu81 as DNA lesion sensors
-
-
?
additional information
?
-
-
enzymatic repair of abasic sites, key intermediate step in base excision repair pathway
-
-
?
additional information
?
-
-
KsgA does not remove C opposite normal bases, 7,8-dihydro-8-oxoguanine and 2-hydroxyadenine, KsgA does not excise thymine glycol, 5-formyluracil, and 5-hydroxymethyluracil opposite cytosine from double-stranded oligonucleotides
-
-
?
additional information
?
-
-
no substrate: alkylated sites
-
-
?
additional information
?
-
-
no substrate: native DNA
-
-
?
additional information
?
-
enzyme HpXth removes the AP site, 3'-blocking sugar-phosphate, and 3'-terminal phosphate in DNA strand breaks with good efficiency (kcat/KM = 1.240, 0.044, and 0.0054 mM/min, respectively). In the presence of 1 or 5 mM Mg2+ or Mn2+, the purified recombinant His-tagged HpXth protein exerts an efficient AP site cleavage activity by generating fast-migrating 10mer cleavage fragments. 3'-Repair phosphodiesterase, 3'-phosphatase, and nucleotide incision activities of the HpXth protein, overview
-
-
?
additional information
?
-
-
enzyme HpXth removes the AP site, 3'-blocking sugar-phosphate, and 3'-terminal phosphate in DNA strand breaks with good efficiency (kcat/KM = 1.240, 0.044, and 0.0054 mM/min, respectively). In the presence of 1 or 5 mM Mg2+ or Mn2+, the purified recombinant His-tagged HpXth protein exerts an efficient AP site cleavage activity by generating fast-migrating 10mer cleavage fragments. 3'-Repair phosphodiesterase, 3'-phosphatase, and nucleotide incision activities of the HpXth protein, overview
-
-
?
additional information
?
-
enzyme HpXth removes the AP site, 3'-blocking sugar-phosphate, and 3'-terminal phosphate in DNA strand breaks with good efficiency (kcat/KM = 1.240, 0.044, and 0.0054 mM/min, respectively). In the presence of 1 or 5 mM Mg2+ or Mn2+, the purified recombinant His-tagged HpXth protein exerts an efficient AP site cleavage activity by generating fast-migrating 10mer cleavage fragments. 3'-Repair phosphodiesterase, 3'-phosphatase, and nucleotide incision activities of the HpXth protein, overview
-
-
?
additional information
?
-
-
-
-
-
?
additional information
?
-
-
gelonin, pokeweed antiviral protein and ricin belong to the family of ribosome-inactivating proteins with DNA-glycosylase/AP-lyase activities
-
-
?
additional information
?
-
-
unlike other endonucleases endonuclease IV or Exo III, Ape1 does not enhance the rate of product release with a G/A substrate
-
-
?
additional information
?
-
enzyme also has DNA N-glycosylase activity
-
-
?
additional information
?
-
-
enzyme also has DNA N-glycosylase activity
-
-
?
additional information
?
-
-
enzyme has no biologically significant 3'-5'-exonuclease activity, the activity only manifests at enzyme concentrations elevated by 6-7 orders magnitude, activity does not show a preference to mismatched compared to matched DNA structures as well as to nicked or gapped DNA substrates
-
-
?
additional information
?
-
enzyme lacks 3'-endonuclease activity against undamaged DNA
-
-
?
additional information
?
-
-
enzyme lacks 3'-endonuclease activity against undamaged DNA
-
-
?
additional information
?
-
-
enzyme stimulates polymerase beta activity on the 5'-terminal oxidized abasic residue
-
-
?
additional information
?
-
-
corrects apurinic/apyrimidinic sites in the genome
-
-
?
additional information
?
-
-
multifunctional enzyme involved in DNA repair and redox regulation of transcription factors
-
-
?
additional information
?
-
-
key enzyme in repair of oxidatively damaged DNA
-
-
?
additional information
?
-
catalyses the initial step in apruinic/apyrimidinic site repair
-
-
?
additional information
?
-
-
catalyses the initial step in apruinic/apyrimidinic site repair
-
-
?
additional information
?
-
-
enzyme stimulates long patch base excision repair by cleaving the DNA and then facilitating the sequential binding and catalysis by DNA polymerase beta, DNA polymerase delta, FEN1 and DNA ligase I
-
-
?
additional information
?
-
-
AP endonuclease Ape1 is involved in the nucleotide incision repair pathway
-
-
?
additional information
?
-
-
APE1 exonuclease function appears to be modulated by the other BER proteins DNA polymerase beta and poly(ADP-ribose) polymerase 1. Excess APE1 over DNA polymerase beta may allow APE1 to perform both exonuclease function and stimulation of strand-displacement DNA synthesis by DNA polymerase beta
-
-
?
additional information
?
-
-
the enzyme enhances methylpurine-DNA glycosylase-catalyzed excision, complex formation of methylpurine-DNA glycosylase eith proliferating cell nuclear antigen can accomodate binding of APE1
-
-
?
additional information
?
-
-
the function of APE is considered as the rate-limiting step in DNA base excision repair. AP endonuclease suppresses DNA mismatch repair activity leading to microsatellite instability
-
-
?
additional information
?
-
hOgg1 protein catalyzes the excision of 8-oxo-7,8-dihydroguanine and the incision of apurinic and apyrimidinic sites in DNA
-
-
?
additional information
?
-
-
hOgg1 protein catalyzes the excision of 8-oxo-7,8-dihydroguanine and the incision of apurinic and apyrimidinic sites in DNA
-
-
?
additional information
?
-
-
the enzyme remains bound to its incision product when the 5'-incision us in double-stranded DNA. The enzyme dissociates from its single-stranded 5'-incised product
-
-
?
additional information
?
-
-
a DNA base excision repair enzyme with a wide variety of functions, including AP endonuclease (cleaving an AP site 5' to a deoxyribose phosphate moiety), 3' exonuclease, 3' phosphodiesterase, 3' phosphatase, RNaseH, and 5' endonuclease activities
-
-
?
additional information
?
-
-
AP endo acts by a one-step associative phosphoryl transfer mechanism on a THF-containing substrate
-
-
?
additional information
?
-
-
AP endo acts on many types of DNA substrate molecules but demonstrates the most robust activity when acting as a class II AP endonuclease
-
-
?
additional information
?
-
-
APE/Ref-1 is a critical component of the hypoxia-inducible transcriptional complex that interacts with hypoxia-inducible factor-1 and p300
-
-
?
additional information
?
-
-
APE/Ref-1 is a key regulator, it markedly induces and efficiently protects melanocytes from oxidative damage by inducing the antiapoptotic machinery and stimulating cell survival
-
-
?
additional information
?
-
APE1 appears to have endonucleolytic activity as a repair enzyme within the nucleotide incision repair pathway
-
-
?
additional information
?
-
-
APE1 appears to have endonucleolytic activity as a repair enzyme within the nucleotide incision repair pathway
-
-
?
additional information
?
-
-
APE1 can incise DNA at the 5'-position of oxidized pyrimidine bases such as 5,6-dihydro-thymine or 5,6-dihydro-2'-deoxyuracil (DHU), thus initiating a repair process known as nucleotide incision repair (NIR)
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APE1 has been identified as a protein capable of nuclear redox activity, inducing the DNA binding activity of several transcription factors, such as activator protein-1, nuclear factor-kappaB, Myb, polyoma virus enhancer-binding protein-2, HLF, nuclear factor-Y, early growth response protein-1, hypoxia inducible factor-1alpha, ATF/CREB family, p53, and Pax proteins. In each case, this effect is accomplished by maintaining the cysteine residues of the transcription factors in the reduced state.
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APE1 has DNA 3'-phosphatase activity in vitro and 3' to 5' exonuclease activity, which could be physiologically relevant in the removal of mismatched or damaged nucleotides incorporated during the synthesis step of BER
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Ape1 has the ability to incise at AP sites in DNA conformations formed during DNA replication, transcription, and class switch recombination, and that Ape1 can endonucleolytically destroy damaged RNA
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APE1 hydrolytically cleaves the phosphodiester backbone 5' to the AP site, leaving a 3'-hydroxyl and a 5'-abasic deoxyribose phosphate to be processed by the subsequent cascade of BER enzymes
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APE1 hydrolytically cleaves the phosphodiester backbone 5' to the AP site, leaving a 3'-hydroxyl and a 5'-abasic deoxyribose phosphate to be processed by the subsequent cascade of BER enzymes
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APE1 is a fundamental protein in this essential repair pathway and is thought to be responsible for more than 95% of total AP endonuclease activity in human cell culture extracts
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APE1 is a fundamental protein in this essential repair pathway and is thought to be responsible for more than 95% of total AP endonuclease activity in human cell culture extracts
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Ape1 is a multifunctional enzyme of 318 amino acids with redox-dependent regulation of transcription factors, 3' to 5' exonuclease, 3' phosphodiesterase, RNaseH and class II type AP endonuclease activities
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APE1 is also named as redox effector factor-1 because of its redox abilities on different redox-regulated transcription factors
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APE1 is directly responsible for the control of the intracellular ROS levels through its inhibitory effect on Rac1, the regulatory subunit of a membrane nonphagocytic NADPH oxidase system.
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APE1 recognizes AP sites in DNA that arise either spontaneously or as enzymatic products of DNA repair glycosylases that excise substrate base lesions as part of the base excision repair (BER) response. Subsequent to damage recognition, the chemistry central to the function of APE1 is wateractivated by a Mg2+ ion followed by hydrolytic cleavage of the phosphodiester bond immediately 5' to the abasic site
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APE1 utilizes a site located in its N-terminus for redox regulation of important transcription factors such as NF-kappaB, p53, c-Fos, and c-Jun
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APE1 utilizes a site located in its N-terminus for redox regulation of important transcription factors such as NF-kappaB, p53, c-Fos, and c-Jun
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APE1/Ref-1 also has a complex relationship to high-mobility group box 1, a protein secreted by immune cells in response to inflammatory stimuli. APE1/Ref-1 can both promote and suppress inflammatory signaling induced by high-mobility group box 1
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APE1/Ref-1 plays a complex role in the activation of nuclear factor kappa B, a key transcription factor involved in inflammatory and immune signaling
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APE1/Ref-1 plays a role in cardiovascular physiology and pathophysiology. APE1/Ref-1 suppresses myocardial ischemia-reperfusion injury and vascular inflammation, and promotes endothelium-dependent vascular relaxation
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APE1/Ref-1 promotes the effect of angiotensin II on Ca2+-activated K+-channel in human endothelial cells via suppression of NADPH oxidase
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APE1/Ref-1 reduces oxidative stress by regulating the level of reactive oxygen species in the cytoplasm
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APEs have 2 intrinsic activities in DNA repair. They act as an endonuclease in cleaving AP sites to generate 3' OH and 5' phosphodeoxyribose termini. They also act as a 3' phosphodiesterase/exonuclease to remove 3' blocking phosphodeoxyribose or its fragments generated during strand breaks, and by reactive oxygen species or DNA glycosylases that excise oxidized bases in the first step of base excision repair
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enzyme cleaves the AP sites in DNA and allows them to be repaired by other enzymes involved in base excision repair
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enzyme has an essential base excision repair (BER) activity and a redox activity that regulates expression of a number of genes through reduction of their transcription factors, AP-1, NFkappaB, HIF-1alpha, CREB, p53 and others
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enzyme has the ability to reductively activate redoxsensitive transcription factors and negative gene regulation by extracellular calcium
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enzyme stimulates the DNA binding activity of the AP-1 family of transcription factors via a redox-dependent mechanism
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forced cytoplasmic overexpression of APE1 profoundly attenuates the upregulation of high-mobility group box 1-mediated reactive oxygen species generation, cytokine secretion, and cyclooxygenase-2 expression by primary monocytes and macrophage-like THP-1 cell lines
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high-mobility group box 1-induced activation of p38 and c-Jun N-terminal kinase is strongly abrogated by the overexpression of APE1
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hNTH1 and Y-box-binding protein-1 may be part of the same DNA repair pathway in response to cisplatin and UV treatments
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hNTH1 binds directly to Y-box-binding protein-1 in the absence of nucleic acids, it binds to the auto-inhibitory n-terminal tail of NTH1
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human Ape1 is a multifunctional protein with a major role in initiating repair of apurinic/apyrimidinic (AP) sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage
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human apurinic/apyrimidinic endonuclease 1 is a major constituent of the base excision repair (BER) pathway of AP sites of DNA lesions. APE1 specifically binds to abasic sites and cuts the 5'-phosphodiester bond with its endonuclease activity to produce a DNA primer with 3'-hydroxyl end, which is a required step in the BER repair pathway
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human endonuclease III is a relevant target to potentiate cisplatin cytotoxicity in Y-box-binding protein-1 overexpressing tumor cells
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In addition to its primary AP site incision function, APE1 exhibits 3'-5' exonuclease, 3'-phosphodiesterase and RNase H catalysis, and a 3'-phosphatase activity
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In addition to its primary AP site incision function, APE1 exhibits 3'-5' exonuclease, 3'-phosphodiesterase and RNase H catalysis, and a 3'-phosphatase activity
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In addition to the exonuclease function, human APE1 is endowed with another enzymatic activity potentially relevant for the protection against oxidative damage
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In human cells, APE1 excises sugar fragments that block the 3'-ends thus facilitating DNA repair synthesis
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major factor in the maintenance of the integrity of the human genome
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multifunctional protein involved in base excision DNA repair and in transcriptional regulation of gene expression, importance to genomic stability and cell survival
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multifunctional protein involved in reduction-oxidation regulation. It functions as a redox factor that maintains transcription factors in an active reduced state
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multifunctional protein possessing both DNA repair and transcriptional regulatory activities, has a pleiotropic role in controlling cellular response to oxidative stress. APE1 is the main apurinic/apyrimidinic endonuclease in eukaryotic cells, playing a central role in the DNA base excision repair pathway of all DNA lesions (uracil, alkylated and oxidized, and abasic sites), including single-strand breaks, and has also co-transcriptional activity by modulating genes expression directly regulated by either ubiquitous and tissue specific transcription factors. It controls the intracellular redox state by inhibiting the reactive oxygen species production
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overexpression of APE1/Ref-1 suppressed angiotensin II induced production of superoxide and hydrogen peroxide
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small interfering RNA knockdown of endogenous APE1 impairs high-mobility group box 1-mediated cytokine expression and MAPK activation in THP-1 cells. High-mobility group box 1-stimulation induces the translocation of APE1 to the nucleus of the cell
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The BK-Ca current in APE1/Ref-1-overexpressing human umbilical vein endothelial cells is similarly inhibited by angiotensin II, except that inhibition of 43.06% is achieved using only 10 nM angiotensin II
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the DNA-binding ability of NF-kappaB in the Ape1/Ref-1 expressing cells is significantly increased
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the key function is to produce a 3' OH terminus that serves as a primer for repair synthesis.
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ubiquitously expressed protein that functions as both an endonuclease in the repair of oxidatively damaged DNA and an aid in the binding of redox-sensitive transcription factors
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25-mer oligonucleotide 5'-labeled with P32 containing tetrahydrofuran as abasic site analog
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25-mer oligonucleotide 5'-labeled with P32 containing tetrahydrofuran as abasic site analog
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AP endo cleaves the Rp but not the Sp stereoisomer of DNA phosphorothioate oligomers, albeit slowly with respect to a phosphodiester substrate
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The ratio of AP endo reaction product to STM7 49mer hairpin oligomers is varied. Product formation is maximal with an 8:1 ratio of STM7 acceptor to 5' thiophosphate donor DNA and by addition of extra ATP (0.5 mM) and ligase (60 units) midreaction
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Used oligonucleotides are 54mers annealed to a complementary 18mer DNA to form the partial duplex substrates (54F-endbubble or 54F-centerbubble with 18DNA) and two 54mers annealed to create an 18-nt bubble structure (54Fendbubble or 54Fcenterbubble with 54bubble18comp). The abasic site is either centrally located (center bubble DNAs) or located at the ssDNA-dsDNA junction (end bubble DNAs). Ape1 most efficiently incised at an abasic site located centrally in the 18-nt bubble structure (54Fcenterbubble18-54bubblecomp), followed by the centrally located abasic site in the partial duplex DNA (54Fcenterbubble18-18DNA), the abasic site at an ssDNA/dsDNA junction in the bubble conformation (54Fendbubble18-54bubblecomp), and the abasic site at an ssDNA/dsDNA junction in partial duplex DNA (54Fendbubble18-18DNA)
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APE1 at low concentrations does not have any effect on 5'-Cy3-CrUAGGTAGTTATCCrUAG-Black Hole Quencher1-3' (OligoII), under similar conditions, the recombinant APE1 has no effect on fluorescently labeled or 32P-labeled DNAOligoI
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a 2'-OH on the sugar moiety is absolutely required for RNA cleavage by wild-type APE1, consistent with APE1 leaving a 3'-PO4 2? group following cleavage of RNA. the catalytic mechanisms for cleaving RNA, abasic single-stranded RNA, and abasic DNA are not identical
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APE1 adopts a partially unfolded state, which is proposed to be the redox active form of the enzyme
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DNA polymerase beta approaches the Ape1-DNA complex downstream of the incision site, displaces Ape1-DNA binding contacts including residues K227, K228, and K276, and in the process makes minimal interactions with lysine residues in the Ref1 domain, i.e. N-terminal residues 43-93
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wild-type APE1 undergoes at least four conformational transitions during the processing of abasic sites in DNA. Nonspecific interactions of APE1 with undamaged DNA can be described by a two-step kinetic scheme. APE1 molecule undergoes at least four conformational transitions, including nonspecific encounter complex formation, mutual adjustment of the enzyme and DNA substrate structures for catalysis, catalytic incision of the substrate, and release of the enzyme from its complex with the product. The C1'-hydroxyl moiety of the abasic site is required for the most effective recognition and catalysis
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APE1 promotes the removal of a TNR hairpin during BER of a base lesion in the hairpin loop region. This is accomplished by the 3'-5'-exonuclease activity of the enzyme that cleaved the upstream 3'-region exonucleolytically, resolving the double-flap intermediate and preventing TNR expansions. APE1 significantly stimulates the ligation activity of LIG I to specifically facilitate the completion of hairpin removal. This is the first evidence of APE1 preventing TNR expansions by facilitating hairpin removal
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APE1 promotes the removal of a TNR hairpin during BER of a base lesion in the hairpin loop region. This is accomplished by the 3'-5'-exonuclease activity of the enzyme that cleaved the upstream 3'-region exonucleolytically, resolving the double-flap intermediate and preventing TNR expansions. APE1 significantly stimulates the ligation activity of LIG I to specifically facilitate the completion of hairpin removal. This is the first evidence of APE1 preventing TNR expansions by facilitating hairpin removal
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in vivo, APE1 is acetylated (AcAPE1) after binding to the AP sites in chromatin and that AcAPE1 is exclusively present on chromatin throughout the cell cycle. Positive charges of acetylable lysine residues in the N-terminal domain of APE1 are essential for chromatin association. Acetylation-mediated neutralization of the positive charges of the lysine residues in the N-terminal domain of APE1 induces a conformational change; this in turn enhances the AP endonuclease activity of APE1. In the absence of APE1 acetylation, cells accumulate AP sites in the genome and show higher sensitivity to DNA-damaging agents. Positive charges of acetylable Lys residues but not their acetylation are essential for the chromatin binding of APE1
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in vivo, APE1 is acetylated (AcAPE1) after binding to the AP sites in chromatin and that AcAPE1 is exclusively present on chromatin throughout the cell cycle. Positive charges of acetylable lysine residues in the N-terminal domain of APE1 are essential for chromatin association. Acetylation-mediated neutralization of the positive charges of the lysine residues in the N-terminal domain of APE1 induces a conformational change; this in turn enhances the AP endonuclease activity of APE1. In the absence of APE1 acetylation, cells accumulate AP sites in the genome and show higher sensitivity to DNA-damaging agents. Positive charges of acetylable Lys residues but not their acetylation are essential for the chromatin binding of APE1
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The enzyme cleaves an AP site in DNA via Mg2+-dependent hydrolytic mechanism producing a 5'-deoxyribose phosphate and 3'-hydroxyl and, therefore, the interaction with AP sites via the Schiff base formation, which is characteristic of the beta-elimination mechanism, is not required for APE1 catalytic activity
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additional information
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The enzyme cleaves an AP site in DNA via Mg2+-dependent hydrolytic mechanism producing a 5'-deoxyribose phosphate and 3'-hydroxyl and, therefore, the interaction with AP sites via the Schiff base formation, which is characteristic of the beta-elimination mechanism, is not required for APE1 catalytic activity
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the mechanism of catalysis of the APE1 endonuclease reaction includes nucleophilic attack by a hydroxide ion on the phosphorous atom at the 5'-side from AP site. The hydroxide ion is formed from a water molecule activated by the Asp210 residue. The transition complex is stabilized via formation of hydrogen bonds with the Asn174, Asn212, and His309/Asp283 residues. Glu96 participates in binding of one Mg2+, which coordinates the leaving O3'-group, and Asp210 and His309 coordinate a second metal ion participating in formation of a hydroxide ion from a water molecule. A transition state with the phosphorous atom is formed because of the nucleophilic attack, the destabilized P-O3' bond is cleaved, and, as a result, inversion of the phosphate configuration occurs (SN2-mechanism). Slow dissociation of the APE1-DNA complex (product) prevents accumulation of single-strand breaks in DNA. The reaction rate of this step increases with increase in Mg2+ concentration and, as a result, the catalysis itself likely becomes the limiting step. Mechanism of the P-O3' bond cleavage at the 5'-side of an AP site catalyzed by human APE1 derived from the structure of the APE1-DNA complex produced by X-ray at higher resolution, overview
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additional information
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the mechanism of catalysis of the APE1 endonuclease reaction includes nucleophilic attack by a hydroxide ion on the phosphorous atom at the 5'-side from AP site. The hydroxide ion is formed from a water molecule activated by the Asp210 residue. The transition complex is stabilized via formation of hydrogen bonds with the Asn174, Asn212, and His309/Asp283 residues. Glu96 participates in binding of one Mg2+, which coordinates the leaving O3'-group, and Asp210 and His309 coordinate a second metal ion participating in formation of a hydroxide ion from a water molecule. A transition state with the phosphorous atom is formed because of the nucleophilic attack, the destabilized P-O3' bond is cleaved, and, as a result, inversion of the phosphate configuration occurs (SN2-mechanism). Slow dissociation of the APE1-DNA complex (product) prevents accumulation of single-strand breaks in DNA. The reaction rate of this step increases with increase in Mg2+ concentration and, as a result, the catalysis itself likely becomes the limiting step. Mechanism of the P-O3' bond cleavage at the 5'-side of an AP site catalyzed by human APE1 derived from the structure of the APE1-DNA complex produced by X-ray at higher resolution, overview
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a fluorophore-labelled 17-mer oligonucleotide DNA substrate is used
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a fluorophore-labelled 17-mer oligonucleotide DNA substrate is used
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analysis of enzyme activity and kinetics with DNA substrates comprising duplexes of deoxyribonucleotides with one 5'-dangling end that contain a fluorescent 2-aminopurine residue at the 1st, 2nd, 4th, or 6th position from the 3'-end of the short oligonucleotide. The impact of the 3'-end nucleotide, which contains mismatched, undamaged bases or modified bases as well as an abasic site or phosphate group, on the efficiency of 3'-5'-exonuclease activity is determined. The rate-limiting step of 3'-nucleotide removal by APE1 in the 3'-5'-exonuclease process is the release of the detached nucleotide from the enzyme's active site. Exonuclease activity of APE1 is effective toward duplexes containing gaps or 5'-dangling ends. For the kinetic analysis of the 3'-5'-exonuclease reaction, the duplexes of 15 and 28 nucleotides (nt) with a 5'-dangling end served as model DNA substrates
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additional information
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analysis of enzyme activity and kinetics with DNA substrates comprising duplexes of deoxyribonucleotides with one 5'-dangling end that contain a fluorescent 2-aminopurine residue at the 1st, 2nd, 4th, or 6th position from the 3'-end of the short oligonucleotide. The impact of the 3'-end nucleotide, which contains mismatched, undamaged bases or modified bases as well as an abasic site or phosphate group, on the efficiency of 3'-5'-exonuclease activity is determined. The rate-limiting step of 3'-nucleotide removal by APE1 in the 3'-5'-exonuclease process is the release of the detached nucleotide from the enzyme's active site. Exonuclease activity of APE1 is effective toward duplexes containing gaps or 5'-dangling ends. For the kinetic analysis of the 3'-5'-exonuclease reaction, the duplexes of 15 and 28 nucleotides (nt) with a 5'-dangling end served as model DNA substrates
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APE1 cleaved AP sites in the structure of DNA/RNAx02hybrid (DNA strand), singlex02stranded RNA, single-stranded DNA, and double-stranded regions of pseudo-triplex DNA-RNA complexes modeling replication and transcription intermediates. APE1 exhibits endonuclease activity during hydrolysis of an AP site on a single-stranded DNA. The activity on the single-stranded DNA is 20fold lower than on double-stranded DNA. As in the case of double-stranded DNA, endonuclease activity of APE1 depended on the presence of magnesium ions. the cleavage of single-stranded DNA with an AP site does not depend on the presence of DNA glycosylases, and it is not inhibited by the reaction product. Complexes of APE1 with double-stranded DNA containing an tetrahydrofuran residue in the center of a non-cleaved strand are not detected
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APE1 cleaved AP sites in the structure of DNA/RNAx02hybrid (DNA strand), singlex02stranded RNA, single-stranded DNA, and double-stranded regions of pseudo-triplex DNA-RNA complexes modeling replication and transcription intermediates. APE1 exhibits endonuclease activity during hydrolysis of an AP site on a single-stranded DNA. The activity on the single-stranded DNA is 20fold lower than on double-stranded DNA. As in the case of double-stranded DNA, endonuclease activity of APE1 depended on the presence of magnesium ions. the cleavage of single-stranded DNA with an AP site does not depend on the presence of DNA glycosylases, and it is not inhibited by the reaction product. Complexes of APE1 with double-stranded DNA containing an tetrahydrofuran residue in the center of a non-cleaved strand are not detected
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APE1 the base excision DNA repair system catalyzes the hydrolysis of the phosphodiester bond on the 5'-side of an apurinic/apyrimidinic site (AP-site) to give the 5'-phosphate and 3'-hydroxyl group. APE1 exhibits also 3'-5'-exonuclease activity albeit less pronounced compared to its endonuclease activity
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APE1 the base excision DNA repair system catalyzes the hydrolysis of the phosphodiester bond on the 5'-side of an apurinic/apyrimidinic site (AP-site) to give the 5'-phosphate and 3'-hydroxyl group. APE1 exhibits also 3'-5'-exonuclease activity albeit less pronounced compared to its endonuclease activity
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diverse BS-AP DNA duplexes as substrates. Purified recombinant human APE1 is capable of forming the 50 kDa-adducts with efficiency of BS-AP DNAs cross-linking to APE1 being dependent on the mutual orientation of AP sites. Identification of APE1 as a target of cross-linking to BS-AP DNA, and cross-linking of cell extract proteins from HeLa cell cell extract to AP DNA with bistranded AP sites, and AP endonuclease activity of APE1 on BS-AP DNAs, detailed overview
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diverse BS-AP DNA duplexes as substrates. Purified recombinant human APE1 is capable of forming the 50 kDa-adducts with efficiency of BS-AP DNAs cross-linking to APE1 being dependent on the mutual orientation of AP sites. Identification of APE1 as a target of cross-linking to BS-AP DNA, and cross-linking of cell extract proteins from HeLa cell cell extract to AP DNA with bistranded AP sites, and AP endonuclease activity of APE1 on BS-AP DNAs, detailed overview
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electron microscopy imaging of APE1-DNA complexes reveals oligomerization of APE1 along the DNA duplex and APE1-mediated DNA bridging followed by DNA aggregation. APE1 polymerizes on both undamaged and damaged DNA in cooperative mode. Duplex DNA and diverse oligonucleotides with single base lesion are used as substrates, stopped-flow fluorescence measurements
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electron microscopy imaging of APE1-DNA complexes reveals oligomerization of APE1 along the DNA duplex and APE1-mediated DNA bridging followed by DNA aggregation. APE1 polymerizes on both undamaged and damaged DNA in cooperative mode. Duplex DNA and diverse oligonucleotides with single base lesion are used as substrates, stopped-flow fluorescence measurements
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fluorescent-labeled oligodeoxynucleotides substrates are used, overview
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fluorescent-labeled oligodeoxynucleotides substrates are used, overview
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human apurinic/apyrimidinic (AP) endonuclease APE1 catalyses the hydrolysis of phosphodiester bonds on the 5'-side of an AP-site (in the base excision repair pathway) and of some damaged nucleotides (in the nucleotide incision repair pathway). The range of substrate specificity includes structurally unrelated damaged nucleotides. Analysis of the mechanism of broad substrate specificity of APE1, overview. Substrate specificity and substrate binding, molecular dynamics simulations. The damaged nucleotide is everted from the DNA helix and placed into the enzyme's binding pocket, which is formed by Asn174, Asn212, Asn229, Ala230, Phe266, and Trp280. Nevertheless, no damage-specific contacts are detected between these amino acid residues in the active site of the enzyme and model damaged substrates containing 1,N6-ethenoadenosine, alpha-adenosine, 5,6-dihydrouridine, or F-site. The substrate specificity of APE1 is controlled by the ability of a damaged nucleotide to flip out from the DNA duplex in response to an enzyme-induced DNA distortion
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additional information
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human apurinic/apyrimidinic (AP) endonuclease APE1 catalyses the hydrolysis of phosphodiester bonds on the 5'-side of an AP-site (in the base excision repair pathway) and of some damaged nucleotides (in the nucleotide incision repair pathway). The range of substrate specificity includes structurally unrelated damaged nucleotides. Analysis of the mechanism of broad substrate specificity of APE1, overview. Substrate specificity and substrate binding, molecular dynamics simulations. The damaged nucleotide is everted from the DNA helix and placed into the enzyme's binding pocket, which is formed by Asn174, Asn212, Asn229, Ala230, Phe266, and Trp280. Nevertheless, no damage-specific contacts are detected between these amino acid residues in the active site of the enzyme and model damaged substrates containing 1,N6-ethenoadenosine, alpha-adenosine, 5,6-dihydrouridine, or F-site. The substrate specificity of APE1 is controlled by the ability of a damaged nucleotide to flip out from the DNA duplex in response to an enzyme-induced DNA distortion
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substrates are DNA oligonucleotides which contain an 8-oxoguanine (8-oxoG). APE1 fails to directly stimulate FEN1 cleavage on a double-flap intermediate. APE1 promotes the production of the unexpanded repair product by stimulating LIG I
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additional information
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substrates are DNA oligonucleotides which contain an 8-oxoguanine (8-oxoG). APE1 fails to directly stimulate FEN1 cleavage on a double-flap intermediate. APE1 promotes the production of the unexpanded repair product by stimulating LIG I
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usage of a fluorescence-based APE1 endonuclease activity assay and a plasmid DNA nicking assay
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additional information
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usage of a fluorescence-based APE1 endonuclease activity assay and a plasmid DNA nicking assay
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additional information
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catalytic subunit of the HSV-1 DNA polymerase (Pol) (UL30) exhibits apurinic/apyrimidinic (AP) and 5'-deoxyribose phosphate lyase activities which are integral to base excision repair and lead to DNA cleavage on the 3'-side of abasic sites and 5'-deoxyribose-5-phosphate residues that remain after cleavage by 5'-AP endonuclease. DNA lyase activity residues in the Pol domain of UL30.
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enzyme has implications on the role of BER in viral genome maintenance during lytic replication and reactivation from latency
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overexpression of AP endonuclease protects Leishmania major cells against methotrexate induced DNA fragmentation and hydrogen peroxide, key enzyme in mediating repair of abasic sites in these pathogens
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LMAP shares with APE1 the overall 3D structure and most of the catalytic groups in their active sites and can catalyze the removal of damaged nucleotides and phosphate groups from 3'-ends more efficiently than APE1
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additional information
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inositol polyphosphate 5-phosphatase enzymes show high homology to AP endonucleases in regions that correspond to catalytic residues, they also share a similar mechanism of catalysis to the AP endonuclease consistent with other common functional similarities such as an absolute requirement for magnesium
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role in eliminating damaged mitochondrial genomes from the gene pool
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poly(ADP-ribose) polymerase-1 and apurinic/apyrimidinic endonuclease can interact with the same base excision repair intermediate. Competition between theses two proteins may influence their respective base excision repair related functions
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additional information
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the enzyme has two distinct roles in the repair of oxidative DNA damage and in gene regulation. Absolute requirement of the enzyme for cell survival, presumably to protect against spontaneous oxidative DNA damage
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?
additional information
?
-
-
APE/Ref-1 act as tuning molecule in activated B-cells
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-
?
additional information
?
-
-
APE/Ref-1 affect the cell cycle by inducing nucleus-cytoplasm translocation of the cyclin-dependent kinase inhibitor p21
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-
?
additional information
?
-
-
APE1 binds with the highest efficiency to DNA substrate containing 5'-sugar phosphate group in the nick/gap
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-
?
additional information
?
-
-
APE1 exhibits 3'-phosphodiesterase, 3'-phosphatase, and 3'-5'-exonuclease activities
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-
?
additional information
?
-
-
APE1 is one of the candidates for the role of base excision repair (BER) pathway coordinator, which controls the whole process. APE1 participates in stimulation of activity of BER enzymes
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-
?
additional information
?
-
-
APE1 stimulates DNA synthesis catalyzed by DNA polymerase beta, and a human Xray repair cross-complementing group 1 protein stimulates APE1 3'-5'-exonuclease activity on 3'-recessed DNA duplex
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?
additional information
?
-
-
APEX1 is a protein involved both in the base excision repair pathways of DNA lesions and in the regulation of gene expression as a redox coactivator of different transcription factors, such as early growth response protein-1
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-
?
additional information
?
-
-
apurinic/apyrimidinic endonuclease 1 participates in the base excision repair of premutagenic apurinic/apyrimidinic (AP) sites
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-
?
additional information
?
-
-
DNA with the recessed 3'-end (DNArec) is one of the preferential substrates for APE1 3'-5'-exonuclease activity
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-
?
additional information
?
-
-
enzyme cleaves the DNA sugar phosphate backbone at the 5'-position in relation to the AP site, forming a nick with the hydroxyl group at the 3'-end and deoxyribose phosphate at the 5'-end
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?
additional information
?
-
-
enzyme plays a role in controlling CD40-mediated B-cell proliferation, increase in proliferation and decrease in apoptosis of primary mouse B-cells activated by CD40 cross-linking and transfected with functional APE/Ref-1 antisense oligonucleotide.
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?
additional information
?
-
-
high APE1 affinity to dsDNA
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-
?
additional information
?
-
-
regulation of APEX1 expression by S-adenosylmethionine, which may be one of the mechanisms of hepatocellular carconom formation
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?
additional information
?
-
-
When APE1 and DNA polymerase beta are both present, a ternary complex APE1-DNA polymerase beta-DNA is formed with the highest efficiency with DNA product of APE1 endonuclease activity and with DNA containing 5'-flap or mononucleotide-gapped DNA with 5'-p group
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?
additional information
?
-
-
APE1 most efficiently binds to DNA substrate bearing tetrahydrofuran in the middle of one of the strands (AP-dsDNA)
-
-
?
additional information
?
-
-
for APE1 in MEF extract, efficiency of formation of protein-DNA crosslinking changes depending on the nature of 5'-group flanking the nick in DNA structure: DNAFAP-pF (100%), DNAFAP-OH (68.2%), DNAFAP-flap (54.6%), DNAFAP-gap (44.2%), DNAFAP-rec (41.3%), DNAFAP-p (41.1%)
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-
?
additional information
?
-
MtbXthA is a versatile enzyme with AP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
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-
?
additional information
?
-
approximate ninefold augmentation in AP site incision activity at the highest concentration of beta-clamp used. Additionally, marked increase in the generation of shorter oligonucleotide fragments, smaller than 32-mer, is observed due to exonucleolytic excision of nucleotides from the 32 nucleotide oligomer
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-
?
additional information
?
-
nicked DNA and gapped DNA are fair substrates of enzyme MtbXthA, the gap-size does not affect the excision activity, a substrate with a recessed 3'-end is preferred. DNA substrate N1 containing an abasic site analogue tetrahydrofuran (THF), is used for AP site incision activity assays. Substrate N2 that contains propanediol, tetrahydrofuran, ethane or 2' deoxyribose as the abasic residues is used for studying the effect of abasic site structure on the AP site incision activity of MtbXthA. For the preparation of the duplex DNA containing a 2' deoxyribose as abasic residue, first an oligonucleotide containing a 2' deoxyribose is prepared by enzymatic treatment of an oligonucleotide harbouring 2' deoxyuridine with uracil N-glycosylase. DNA elements have no role in the recognition of AP site containing DNA by MtbXthA. Y237 functions as a critical AP site recogniser in MtbXthA. Analysis of the 3' phosphatase and 3' phosphodiesterase activities of MtbXthA with a DNA substrate
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-
?
additional information
?
-
-
nicked DNA and gapped DNA are fair substrates of enzyme MtbXthA, the gap-size does not affect the excision activity, a substrate with a recessed 3'-end is preferred. DNA substrate N1 containing an abasic site analogue tetrahydrofuran (THF), is used for AP site incision activity assays. Substrate N2 that contains propanediol, tetrahydrofuran, ethane or 2' deoxyribose as the abasic residues is used for studying the effect of abasic site structure on the AP site incision activity of MtbXthA. For the preparation of the duplex DNA containing a 2' deoxyribose as abasic residue, first an oligonucleotide containing a 2' deoxyribose is prepared by enzymatic treatment of an oligonucleotide harbouring 2' deoxyuridine with uracil N-glycosylase. DNA elements have no role in the recognition of AP site containing DNA by MtbXthA. Y237 functions as a critical AP site recogniser in MtbXthA. Analysis of the 3' phosphatase and 3' phosphodiesterase activities of MtbXthA with a DNA substrate
-
-
?
additional information
?
-
nicked DNA and gapped DNA are fair substrates of enzyme MtbXthA, the gap-size does not affect the excision activity, a substrate with a recessed 3'-end is preferred. DNA substrate N1 containing an abasic site analogue tetrahydrofuran (THF), is used for AP site incision activity assays. Substrate N2 that contains propanediol, tetrahydrofuran, ethane or 2' deoxyribose as the abasic residues is used for studying the effect of abasic site structure on the AP site incision activity of MtbXthA. For the preparation of the duplex DNA containing a 2' deoxyribose as abasic residue, first an oligonucleotide containing a 2' deoxyribose is prepared by enzymatic treatment of an oligonucleotide harbouring 2' deoxyuridine with uracil N-glycosylase. DNA elements have no role in the recognition of AP site containing DNA by MtbXthA. Y237 functions as a critical AP site recogniser in MtbXthA. Analysis of the 3' phosphatase and 3' phosphodiesterase activities of MtbXthA with a DNA substrate
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-
?
additional information
?
-
MtbXthA is a versatile enzyme with AP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
-
-
?
additional information
?
-
approximate ninefold augmentation in AP site incision activity at the highest concentration of beta-clamp used. Additionally, marked increase in the generation of shorter oligonucleotide fragments, smaller than 32-mer, is observed due to exonucleolytic excision of nucleotides from the 32 nucleotide oligomer
-
-
?
additional information
?
-
nicked DNA and gapped DNA are fair substrates of enzyme MtbXthA, the gap-size does not affect the excision activity, a substrate with a recessed 3'-end is preferred. DNA substrate N1 containing an abasic site analogue tetrahydrofuran (THF), is used for AP site incision activity assays. Substrate N2 that contains propanediol, tetrahydrofuran, ethane or 2' deoxyribose as the abasic residues is used for studying the effect of abasic site structure on the AP site incision activity of MtbXthA. For the preparation of the duplex DNA containing a 2' deoxyribose as abasic residue, first an oligonucleotide containing a 2' deoxyribose is prepared by enzymatic treatment of an oligonucleotide harbouring 2' deoxyuridine with uracil N-glycosylase. DNA elements have no role in the recognition of AP site containing DNA by MtbXthA. Y237 functions as a critical AP site recogniser in MtbXthA. Analysis of the 3' phosphatase and 3' phosphodiesterase activities of MtbXthA with a DNA substrate
-
-
?
additional information
?
-
MtbXthA is a versatile enzyme with AP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
-
-
?
additional information
?
-
approximate ninefold augmentation in AP site incision activity at the highest concentration of beta-clamp used. Additionally, marked increase in the generation of shorter oligonucleotide fragments, smaller than 32-mer, is observed due to exonucleolytic excision of nucleotides from the 32 nucleotide oligomer
-
-
?
additional information
?
-
-
no substrate: native DNA
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?
additional information
?
-
-
no associated exonuclease activity
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?
additional information
?
-
-
no substrate: alkylated sites
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?
additional information
?
-
-
no substrate: native DNA
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?
additional information
?
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-
no substrate: native DNA
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?
additional information
?
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inactive on reduced AP sites
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?
additional information
?
-
-
an increase of APE/Ref-1 mRNA levels in the caudal region of spinal cord strongly correlates with DNA damage after traumatic spinal cord injury
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?
additional information
?
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-
increase in phosphorylation of p53 after a decrease in Ape1 levels in sensory neuronal cultures
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-
?
additional information
?
-
-
multifunctional protein involved in both the repair of oxidative and alkylating DNA damage and the regulation of gene expression
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?
additional information
?
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overexpressing wild-type Ape1 attentuates all the toxic effects of cisplatin in cells containing normal endogenous levels of Ape1 and in cells with reduced Ape1 levels after Ape1siRNA treatment
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?
additional information
?
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-
reducing expression of Ape1 in neuronal cultures using small interfering RNA enhances cisplatin-induced cell killing, apoptosis, ROS generation and cisplatin-induced reduction in iCGRP release
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-
?
additional information
?
-
-
APE1 at low concentrations does not have any effect on 5'-Cy3-CrUAGGTAGTTATCCrUAG-Black Hole Quencher1-3' (OligoII), under similar conditions, the recombinant APE1 has no effect on fluorescently labeled or 32P-labeled DNAOligoI
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-
?
additional information
?
-
-
enzyme also has DNA N-glycosylase activity
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?
additional information
?
-
-
ntg1 possesses N-glycosylase/AP lyase activity that allows recognition and repair of oxidative base damage (primarily of pyrimidines) as well as abasic sites
-
-
?
additional information
?
-
-
ntg2 possesses N-glycosylase/AP lyase activity that allows recognition and repair of oxidative base damage (primarily of pyrimidines) as well as abasic sites
-
-
?
additional information
?
-
the nucleotide incision repair (NIR) recruiting Saccharomyces cerevisiae Apn1 proceeds via multistep rearrangements of the complex of Apn1 with a DHU-containing DNA substrate and results in the incised product of the reaction
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-
?
additional information
?
-
substrate oligodeoxyribonucleotides (ODNs) are synthesized and purified, a fluorescent 2-aminopurine (2-aPu) probe is located either on the 5'- or 3'-side of an abasic site. Cleavage of substrates AP(2-aPu) and F(2-aPu) in several stages (F is tetrahydrofuran) by wild-type and mutant H83A enzymes, overview
-
-
?
additional information
?
-
-
substrate oligodeoxyribonucleotides (ODNs) are synthesized and purified, a fluorescent 2-aminopurine (2-aPu) probe is located either on the 5'- or 3'-side of an abasic site. Cleavage of substrates AP(2-aPu) and F(2-aPu) in several stages (F is tetrahydrofuran) by wild-type and mutant H83A enzymes, overview
-
-
?
additional information
?
-
substrate oligodeoxyribonucleotides (ODNs) are synthesized with a fluorescent 2-aminopurine (2-aPu) probe located either on the 5'- or 3'-side of an abasic site. Cleavage of substrates AP(2-aPu) and F(2-aPu) (F = tetrahydrofuran) in presence of Zn2+ and Mg2+ by wild-type and mutant H83A enzymes, overview. Molecular dynamics simulations elucidates the structural features of complexes of the enzyme with DHU-containing DNAs. The DNA substrate structure affects nucleotide incision repair (NIR) catalysis. Location of the 2-aPu residue near DHU decreases the efficacy of NIR activity of the WT enzyme and of H83A Apn1: nucleotide incision repair (NIR) activity of both enzymes decreases in the following descending order of substrates: DHU, DHU(2-aPu), and (2-aPu)DHU. Apn1 cannot incise the (2-aPu)DHU duplex because of the spatial structure of the (2-aPu)DHU-Apn1 complex, which is probably significantly distorted in the vicinity of the active site because two noncanonical base pairs are placed in close proximity to each other, the access of catalytically active amino acid residues and Zn2+ ions to the 5'-phosphodiester bond to be incised (located between the 2-aPu and DHU residues) might be blocked
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-
?
additional information
?
-
substrate oligodeoxyribonucleotides (ODNs) are synthesized and purified, a fluorescent 2-aminopurine (2-aPu) probe is located either on the 5'- or 3'-side of an abasic site. Cleavage of substrates AP(2-aPu) and F(2-aPu) in several stages (F is tetrahydrofuran) by wild-type and mutant H83A enzymes, overview
-
-
?
additional information
?
-
the nucleotide incision repair (NIR) recruiting Saccharomyces cerevisiae Apn1 proceeds via multistep rearrangements of the complex of Apn1 with a DHU-containing DNA substrate and results in the incised product of the reaction
-
-
?
additional information
?
-
substrate oligodeoxyribonucleotides (ODNs) are synthesized with a fluorescent 2-aminopurine (2-aPu) probe located either on the 5'- or 3'-side of an abasic site. Cleavage of substrates AP(2-aPu) and F(2-aPu) (F = tetrahydrofuran) in presence of Zn2+ and Mg2+ by wild-type and mutant H83A enzymes, overview. Molecular dynamics simulations elucidates the structural features of complexes of the enzyme with DHU-containing DNAs. The DNA substrate structure affects nucleotide incision repair (NIR) catalysis. Location of the 2-aPu residue near DHU decreases the efficacy of NIR activity of the WT enzyme and of H83A Apn1: nucleotide incision repair (NIR) activity of both enzymes decreases in the following descending order of substrates: DHU, DHU(2-aPu), and (2-aPu)DHU. Apn1 cannot incise the (2-aPu)DHU duplex because of the spatial structure of the (2-aPu)DHU-Apn1 complex, which is probably significantly distorted in the vicinity of the active site because two noncanonical base pairs are placed in close proximity to each other, the access of catalytically active amino acid residues and Zn2+ ions to the 5'-phosphodiester bond to be incised (located between the 2-aPu and DHU residues) might be blocked
-
-
?
additional information
?
-
tetrahydrofuran-containing DNA substrates are used
-
-
?
additional information
?
-
tetrahydrofuran-containing DNA substrates are used
-
-
?
additional information
?
-
-
tetrahydrofuran-containing DNA substrates are used
-
-
?
additional information
?
-
Tequatrovirus T4
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-
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-
?
additional information
?
-
Tequatrovirus T4
-
bacteriophage T4 endonuclease V and Escherichia coli endonuclease II catalyze N-glycosylase and 3'-abasic endonuclease reaction, beta-elimination reaction
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?
additional information
?
-
-
enzyme displays AP endonuclease, 3'-repair phosphodiesterase, 3'-phosphatase and 3'-5' exonuclease activities. Enzyme removes 3'-blocking sugar-phosphate and 3'-phosphate groups with good efficiency but possesses a very weak AP endonuclease activity as compared to the human homologue APE1
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?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
AP DNA
fragments of DNA
-
AP sites
-
-
?
DNA containing apurinic/apyrimidinic site
DNA fragments
-
-
-
-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
DNA containing tamdem dihydrouracil
?
-
the human AP endonuclease APE1 can process the 3' termini generated by human endonuclease III (hNTH) and endonuclease VIII. Both human endonuclease III and endonuclease VIII cannot completely remove both dihydrouracil lesions. With the participation of APE1 and polynucleotide kinase, the 3'-lesions remaining in the products of the reaction with human endonuclease III and endonuclease VIII can efficiently removed. The resulting products can be utilized by repair DNA polymerases as primers for repair synthesis
-
-
?
DNA containing tandem dihydrouracil
?
-
the human AP endonuclease APE1 can process the 3' termini generated by human endonuclease III (hNTH) and endonuclease VIII. Both human endonuclease III and endonuclease VIII cannot completely remove both dihydrouracil lesions. With the participation of APE1 and polynucleotide kinase, the 3'-lesions remaining in the products of the reaction with human endonuclease III and endonuclease VIII can efficiently removed. The resulting products can be utilized by repair DNA polymerases as primers for repair synthesis
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-
?
DNA with an abasic site
?
DNA with an abasic site
DNA with 5'-phosphate terminus + DNA with 3'-alpha,beta-unsaturated aldehyde
the enzyme excises an oxidatively-damaged form of guanine. Bifunctional enzyme with both DNA glycosylase and apurinic/apyrimidinic lyase activities
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-
?
additional information
?
-
AP-DNA
fragments of DNA
-
-
-
-
?
AP-DNA
fragments of DNA
-
-
-
-
?
AP-DNA
fragments of DNA
Base excision repair pathway, enzyme cleaves the 5'-phosphodiester bond, generating 3'-OH and 5'-dRP termini
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-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
The latter lesions are processed by AP endonucleases, which are important components of the base excision repair pathway
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-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
170706, 288783, 646938, 648625, 648627, 648629, 648630, 648631, 648637, 648649, 648650, 648651, 648652, 648654, 648655, 648657, 648664, 648665, 648671, 648678, 648679 -
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
648636, 648638, 648657, 648661, 648663, 648664, 648666, 648667, 648672, 648673, 648674, 648676, 648677, 648678, 648682, 648685, 648686, 648687, 694298, 702939, 704731 -
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
base excision repair (BERa) pathway is initiated by lesion-specific glycosylases that excise the damaged base from the sugar-phosphate backbone, resulting in a potentially cytotoxic apurinic/apyrimidinic (AP) site intermediate that becomes the substrate for the major human AP endonuclease
-
-
?
DNA
fragments of DNA
-
bifunctional enzyme is involved in base excision repair, it is a bifunctional DNA glycosylase/apurinic/apyrimidinic lyase which removes hydrated, reduced, or oxidized bases from the DNA backbone as the initial step of base excision repair
-
-
?
DNA
fragments of DNA
-
DNA single-strand breaks containing 3'-blocking groups are generated from attack of the sugar backbone by reactive oxygen species or after base excision by DNA glycosylase/apurinic/apyrimidinic (AP) lyases
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
DNA single-strand breaks containing 3'-blocking groups are generated from attack of the sugar backbone by reactive oxygen species or after base excision by DNA glycosylase, apurinic, apyrimidinic (AP) lyases
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
?
DNA
fragments of DNA
-
enzyme plays an important role in oxidative signalling, transcription factor regulation, and cell cycle control
-
-
ir
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
DNA repair enzyme is involved in base excision repair of apurinic/apyrimidinic sites after oxidative DNA damage
-
-
?
DNA
fragments of DNA
-
multifunctional enzyme involved in DNA base excision repair of oxidative DNA damage and in redox regulation of a number of transcription factors
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
oxidative DNA damage is primarily reversed by the base excision repair pathway, initiated by N-glycosylase apurinic/apyrimidinic lyase proteins
-
-
ir
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
Tequatrovirus T4
-
-
-
-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
-
apurinic/apyrimidinic endonuclease Nfo protects Bacillus subtilis spores from DNA damage accumulated during spore dormancy
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-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
-
C4'-oxidized abasic sites are efficiently excised via intermediate Schiff-base formation. Activity is 100fold less efficient than repair by exonuclease III
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-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
hydrogen bonds to phosphate groups 3' to the cleavage site is essential for the binding of the enzyme to the product DNA, which may be necessary for efficient functioning of the base excision rapair pathway
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-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
inducible enzyme, the enzyme exhibits endonucleolytic activity and is regulated as part of the acid-adaptive response of the organism. Smx is likely the primary, if not the sole, AP endonuclease induced during growth at low pH values, loss of Smx activity renders the mutant strain sensitive to hydrogen peroxide treatment but relatively unaffected by acid-mediated damage or near-UV irradiation
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?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
inducible enzyme, the enzyme exhibits endonucleolytic activity and is regulated as part of the acid-adaptive response of the organism. Smx is likely the primary, if not the sole, AP endonuclease induced during growth at low pH values, loss of Smx activity renders the mutant strain sensitive to hydrogen peroxide treatment but relatively unaffected by acid-mediated damage or near-UV irradiation
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-
?
DNA with an abasic site
?
the enzyme is part of the base excision repair (BER) pathway. It protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine, from single- and double-stranded DNA substrates
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?
DNA with an abasic site
?
the enzyme is part of the base excision repair (BER) pathway. It protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine, from single- and double-stranded DNA substrates
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?
additional information
?
-
major role in plant defence against oxidative DNA damage
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?
additional information
?
-
-
major role in plant defence against oxidative DNA damage
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?
additional information
?
-
-
important role in repair of oxidative DNA damage
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?
additional information
?
-
enzyme plays an important role in repair of DNA damages
-
-
?
additional information
?
-
-
enzyme plays an important role in repair of DNA damages
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?
additional information
?
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-
enzyme has an essential base excision repair (BER) activity and a redox activity that regulates expression of a number of genes through reduction of their transcription factors, AP-1, NFkappaB, HIF-1alpha, CREB, p53 and others
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-
?
additional information
?
-
Escherichia coli endonuclease III is a DNA glycosylase with a broad substrate specificity for oxidized or reduced pyrimidine bases. Endo III possesses two types of activities: N-glycosylase (hydrolysis of the N-glycosidic bond) and AP lyase (elimination of the 3'-phosphate of the AP-site)
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?
additional information
?
-
-
Escherichia coli endonuclease III is a DNA glycosylase with a broad substrate specificity for oxidized or reduced pyrimidine bases. Endo III possesses two types of activities: N-glycosylase (hydrolysis of the N-glycosidic bond) and AP lyase (elimination of the 3'-phosphate of the AP-site)
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?
additional information
?
-
-
enzymatic repair of abasic sites, key intermediate step in base excision repair pathway
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?
additional information
?
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-
enzyme stimulates polymerase beta activity on the 5'-terminal oxidized abasic residue
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?
additional information
?
-
-
corrects apurinic/apyrimidinic sites in the genome
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?
additional information
?
-
-
multifunctional enzyme involved in DNA repair and redox regulation of transcription factors
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?
additional information
?
-
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key enzyme in repair of oxidatively damaged DNA
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?
additional information
?
-
catalyses the initial step in apruinic/apyrimidinic site repair
-
-
?
additional information
?
-
-
catalyses the initial step in apruinic/apyrimidinic site repair
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-
?
additional information
?
-
-
enzyme stimulates long patch base excision repair by cleaving the DNA and then facilitating the sequential binding and catalysis by DNA polymerase beta, DNA polymerase delta, FEN1 and DNA ligase I
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-
?
additional information
?
-
-
AP endonuclease Ape1 is involved in the nucleotide incision repair pathway
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?
additional information
?
-
-
APE1 exonuclease function appears to be modulated by the other BER proteins DNA polymerase beta and poly(ADP-ribose) polymerase 1. Excess APE1 over DNA polymerase beta may allow APE1 to perform both exonuclease function and stimulation of strand-displacement DNA synthesis by DNA polymerase beta
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?
additional information
?
-
-
the enzyme enhances methylpurine-DNA glycosylase-catalyzed excision, complex formation of methylpurine-DNA glycosylase eith proliferating cell nuclear antigen can accomodate binding of APE1
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additional information
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the function of APE is considered as the rate-limiting step in DNA base excision repair. AP endonuclease suppresses DNA mismatch repair activity leading to microsatellite instability
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additional information
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a DNA base excision repair enzyme with a wide variety of functions, including AP endonuclease (cleaving an AP site 5' to a deoxyribose phosphate moiety), 3' exonuclease, 3' phosphodiesterase, 3' phosphatase, RNaseH, and 5' endonuclease activities
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additional information
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AP endo acts by a one-step associative phosphoryl transfer mechanism on a THF-containing substrate
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additional information
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AP endo acts on many types of DNA substrate molecules but demonstrates the most robust activity when acting as a class II AP endonuclease
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additional information
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APE/Ref-1 is a critical component of the hypoxia-inducible transcriptional complex that interacts with hypoxia-inducible factor-1 and p300
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additional information
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APE/Ref-1 is a key regulator, it markedly induces and efficiently protects melanocytes from oxidative damage by inducing the antiapoptotic machinery and stimulating cell survival
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additional information
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APE1 appears to have endonucleolytic activity as a repair enzyme within the nucleotide incision repair pathway
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additional information
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APE1 appears to have endonucleolytic activity as a repair enzyme within the nucleotide incision repair pathway
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additional information
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APE1 can incise DNA at the 5'-position of oxidized pyrimidine bases such as 5,6-dihydro-thymine or 5,6-dihydro-2'-deoxyuracil (DHU), thus initiating a repair process known as nucleotide incision repair (NIR)
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additional information
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APE1 has been identified as a protein capable of nuclear redox activity, inducing the DNA binding activity of several transcription factors, such as activator protein-1, nuclear factor-kappaB, Myb, polyoma virus enhancer-binding protein-2, HLF, nuclear factor-Y, early growth response protein-1, hypoxia inducible factor-1alpha, ATF/CREB family, p53, and Pax proteins. In each case, this effect is accomplished by maintaining the cysteine residues of the transcription factors in the reduced state.
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additional information
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APE1 has DNA 3'-phosphatase activity in vitro and 3' to 5' exonuclease activity, which could be physiologically relevant in the removal of mismatched or damaged nucleotides incorporated during the synthesis step of BER
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?
additional information
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Ape1 has the ability to incise at AP sites in DNA conformations formed during DNA replication, transcription, and class switch recombination, and that Ape1 can endonucleolytically destroy damaged RNA
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?
additional information
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APE1 hydrolytically cleaves the phosphodiester backbone 5' to the AP site, leaving a 3'-hydroxyl and a 5'-abasic deoxyribose phosphate to be processed by the subsequent cascade of BER enzymes
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additional information
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APE1 hydrolytically cleaves the phosphodiester backbone 5' to the AP site, leaving a 3'-hydroxyl and a 5'-abasic deoxyribose phosphate to be processed by the subsequent cascade of BER enzymes
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additional information
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APE1 is a fundamental protein in this essential repair pathway and is thought to be responsible for more than 95% of total AP endonuclease activity in human cell culture extracts
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additional information
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APE1 is a fundamental protein in this essential repair pathway and is thought to be responsible for more than 95% of total AP endonuclease activity in human cell culture extracts
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additional information
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Ape1 is a multifunctional enzyme of 318 amino acids with redox-dependent regulation of transcription factors, 3' to 5' exonuclease, 3' phosphodiesterase, RNaseH and class II type AP endonuclease activities
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additional information
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APE1 is also named as redox effector factor-1 because of its redox abilities on different redox-regulated transcription factors
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additional information
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APE1 is directly responsible for the control of the intracellular ROS levels through its inhibitory effect on Rac1, the regulatory subunit of a membrane nonphagocytic NADPH oxidase system.
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additional information
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APE1 recognizes AP sites in DNA that arise either spontaneously or as enzymatic products of DNA repair glycosylases that excise substrate base lesions as part of the base excision repair (BER) response. Subsequent to damage recognition, the chemistry central to the function of APE1 is wateractivated by a Mg2+ ion followed by hydrolytic cleavage of the phosphodiester bond immediately 5' to the abasic site
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additional information
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APE1 utilizes a site located in its N-terminus for redox regulation of important transcription factors such as NF-kappaB, p53, c-Fos, and c-Jun
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additional information
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APE1 utilizes a site located in its N-terminus for redox regulation of important transcription factors such as NF-kappaB, p53, c-Fos, and c-Jun
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additional information
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APE1/Ref-1 also has a complex relationship to high-mobility group box 1, a protein secreted by immune cells in response to inflammatory stimuli. APE1/Ref-1 can both promote and suppress inflammatory signaling induced by high-mobility group box 1
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additional information
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APE1/Ref-1 plays a complex role in the activation of nuclear factor kappa B, a key transcription factor involved in inflammatory and immune signaling
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additional information
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APE1/Ref-1 plays a role in cardiovascular physiology and pathophysiology. APE1/Ref-1 suppresses myocardial ischemia-reperfusion injury and vascular inflammation, and promotes endothelium-dependent vascular relaxation
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additional information
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APE1/Ref-1 promotes the effect of angiotensin II on Ca2+-activated K+-channel in human endothelial cells via suppression of NADPH oxidase
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?
additional information
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APE1/Ref-1 reduces oxidative stress by regulating the level of reactive oxygen species in the cytoplasm
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?
additional information
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APEs have 2 intrinsic activities in DNA repair. They act as an endonuclease in cleaving AP sites to generate 3' OH and 5' phosphodeoxyribose termini. They also act as a 3' phosphodiesterase/exonuclease to remove 3' blocking phosphodeoxyribose or its fragments generated during strand breaks, and by reactive oxygen species or DNA glycosylases that excise oxidized bases in the first step of base excision repair
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additional information
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enzyme cleaves the AP sites in DNA and allows them to be repaired by other enzymes involved in base excision repair
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additional information
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enzyme has an essential base excision repair (BER) activity and a redox activity that regulates expression of a number of genes through reduction of their transcription factors, AP-1, NFkappaB, HIF-1alpha, CREB, p53 and others
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additional information
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enzyme has the ability to reductively activate redoxsensitive transcription factors and negative gene regulation by extracellular calcium
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additional information
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enzyme stimulates the DNA binding activity of the AP-1 family of transcription factors via a redox-dependent mechanism
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additional information
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forced cytoplasmic overexpression of APE1 profoundly attenuates the upregulation of high-mobility group box 1-mediated reactive oxygen species generation, cytokine secretion, and cyclooxygenase-2 expression by primary monocytes and macrophage-like THP-1 cell lines
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additional information
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high-mobility group box 1-induced activation of p38 and c-Jun N-terminal kinase is strongly abrogated by the overexpression of APE1
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additional information
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hNTH1 and Y-box-binding protein-1 may be part of the same DNA repair pathway in response to cisplatin and UV treatments
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additional information
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hNTH1 binds directly to Y-box-binding protein-1 in the absence of nucleic acids, it binds to the auto-inhibitory n-terminal tail of NTH1
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additional information
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human Ape1 is a multifunctional protein with a major role in initiating repair of apurinic/apyrimidinic (AP) sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage
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additional information
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human apurinic/apyrimidinic endonuclease 1 is a major constituent of the base excision repair (BER) pathway of AP sites of DNA lesions. APE1 specifically binds to abasic sites and cuts the 5'-phosphodiester bond with its endonuclease activity to produce a DNA primer with 3'-hydroxyl end, which is a required step in the BER repair pathway
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additional information
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human endonuclease III is a relevant target to potentiate cisplatin cytotoxicity in Y-box-binding protein-1 overexpressing tumor cells
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additional information
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In addition to its primary AP site incision function, APE1 exhibits 3'-5' exonuclease, 3'-phosphodiesterase and RNase H catalysis, and a 3'-phosphatase activity
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?
additional information
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In addition to its primary AP site incision function, APE1 exhibits 3'-5' exonuclease, 3'-phosphodiesterase and RNase H catalysis, and a 3'-phosphatase activity
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additional information
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In addition to the exonuclease function, human APE1 is endowed with another enzymatic activity potentially relevant for the protection against oxidative damage
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?
additional information
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In human cells, APE1 excises sugar fragments that block the 3'-ends thus facilitating DNA repair synthesis
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additional information
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major factor in the maintenance of the integrity of the human genome
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?
additional information
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multifunctional protein involved in base excision DNA repair and in transcriptional regulation of gene expression, importance to genomic stability and cell survival
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additional information
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multifunctional protein involved in reduction-oxidation regulation. It functions as a redox factor that maintains transcription factors in an active reduced state
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additional information
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multifunctional protein possessing both DNA repair and transcriptional regulatory activities, has a pleiotropic role in controlling cellular response to oxidative stress. APE1 is the main apurinic/apyrimidinic endonuclease in eukaryotic cells, playing a central role in the DNA base excision repair pathway of all DNA lesions (uracil, alkylated and oxidized, and abasic sites), including single-strand breaks, and has also co-transcriptional activity by modulating genes expression directly regulated by either ubiquitous and tissue specific transcription factors. It controls the intracellular redox state by inhibiting the reactive oxygen species production
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?
additional information
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overexpression of APE1/Ref-1 suppressed angiotensin II induced production of superoxide and hydrogen peroxide
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?
additional information
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small interfering RNA knockdown of endogenous APE1 impairs high-mobility group box 1-mediated cytokine expression and MAPK activation in THP-1 cells. High-mobility group box 1-stimulation induces the translocation of APE1 to the nucleus of the cell
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additional information
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The BK-Ca current in APE1/Ref-1-overexpressing human umbilical vein endothelial cells is similarly inhibited by angiotensin II, except that inhibition of 43.06% is achieved using only 10 nM angiotensin II
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?
additional information
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the DNA-binding ability of NF-kappaB in the Ape1/Ref-1 expressing cells is significantly increased
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?
additional information
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the key function is to produce a 3' OH terminus that serves as a primer for repair synthesis.
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?
additional information
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ubiquitously expressed protein that functions as both an endonuclease in the repair of oxidatively damaged DNA and an aid in the binding of redox-sensitive transcription factors
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additional information
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APE1 promotes the removal of a TNR hairpin during BER of a base lesion in the hairpin loop region. This is accomplished by the 3'-5'-exonuclease activity of the enzyme that cleaved the upstream 3'-region exonucleolytically, resolving the double-flap intermediate and preventing TNR expansions. APE1 significantly stimulates the ligation activity of LIG I to specifically facilitate the completion of hairpin removal. This is the first evidence of APE1 preventing TNR expansions by facilitating hairpin removal
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additional information
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APE1 promotes the removal of a TNR hairpin during BER of a base lesion in the hairpin loop region. This is accomplished by the 3'-5'-exonuclease activity of the enzyme that cleaved the upstream 3'-region exonucleolytically, resolving the double-flap intermediate and preventing TNR expansions. APE1 significantly stimulates the ligation activity of LIG I to specifically facilitate the completion of hairpin removal. This is the first evidence of APE1 preventing TNR expansions by facilitating hairpin removal
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?
additional information
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in vivo, APE1 is acetylated (AcAPE1) after binding to the AP sites in chromatin and that AcAPE1 is exclusively present on chromatin throughout the cell cycle. Positive charges of acetylable lysine residues in the N-terminal domain of APE1 are essential for chromatin association. Acetylation-mediated neutralization of the positive charges of the lysine residues in the N-terminal domain of APE1 induces a conformational change; this in turn enhances the AP endonuclease activity of APE1. In the absence of APE1 acetylation, cells accumulate AP sites in the genome and show higher sensitivity to DNA-damaging agents. Positive charges of acetylable Lys residues but not their acetylation are essential for the chromatin binding of APE1
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additional information
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in vivo, APE1 is acetylated (AcAPE1) after binding to the AP sites in chromatin and that AcAPE1 is exclusively present on chromatin throughout the cell cycle. Positive charges of acetylable lysine residues in the N-terminal domain of APE1 are essential for chromatin association. Acetylation-mediated neutralization of the positive charges of the lysine residues in the N-terminal domain of APE1 induces a conformational change; this in turn enhances the AP endonuclease activity of APE1. In the absence of APE1 acetylation, cells accumulate AP sites in the genome and show higher sensitivity to DNA-damaging agents. Positive charges of acetylable Lys residues but not their acetylation are essential for the chromatin binding of APE1
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additional information
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The enzyme cleaves an AP site in DNA via Mg2+-dependent hydrolytic mechanism producing a 5'-deoxyribose phosphate and 3'-hydroxyl and, therefore, the interaction with AP sites via the Schiff base formation, which is characteristic of the beta-elimination mechanism, is not required for APE1 catalytic activity
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additional information
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The enzyme cleaves an AP site in DNA via Mg2+-dependent hydrolytic mechanism producing a 5'-deoxyribose phosphate and 3'-hydroxyl and, therefore, the interaction with AP sites via the Schiff base formation, which is characteristic of the beta-elimination mechanism, is not required for APE1 catalytic activity
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additional information
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the mechanism of catalysis of the APE1 endonuclease reaction includes nucleophilic attack by a hydroxide ion on the phosphorous atom at the 5'-side from AP site. The hydroxide ion is formed from a water molecule activated by the Asp210 residue. The transition complex is stabilized via formation of hydrogen bonds with the Asn174, Asn212, and His309/Asp283 residues. Glu96 participates in binding of one Mg2+, which coordinates the leaving O3'-group, and Asp210 and His309 coordinate a second metal ion participating in formation of a hydroxide ion from a water molecule. A transition state with the phosphorous atom is formed because of the nucleophilic attack, the destabilized P-O3' bond is cleaved, and, as a result, inversion of the phosphate configuration occurs (SN2-mechanism). Slow dissociation of the APE1-DNA complex (product) prevents accumulation of single-strand breaks in DNA. The reaction rate of this step increases with increase in Mg2+ concentration and, as a result, the catalysis itself likely becomes the limiting step. Mechanism of the P-O3' bond cleavage at the 5'-side of an AP site catalyzed by human APE1 derived from the structure of the APE1-DNA complex produced by X-ray at higher resolution, overview
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?
additional information
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the mechanism of catalysis of the APE1 endonuclease reaction includes nucleophilic attack by a hydroxide ion on the phosphorous atom at the 5'-side from AP site. The hydroxide ion is formed from a water molecule activated by the Asp210 residue. The transition complex is stabilized via formation of hydrogen bonds with the Asn174, Asn212, and His309/Asp283 residues. Glu96 participates in binding of one Mg2+, which coordinates the leaving O3'-group, and Asp210 and His309 coordinate a second metal ion participating in formation of a hydroxide ion from a water molecule. A transition state with the phosphorous atom is formed because of the nucleophilic attack, the destabilized P-O3' bond is cleaved, and, as a result, inversion of the phosphate configuration occurs (SN2-mechanism). Slow dissociation of the APE1-DNA complex (product) prevents accumulation of single-strand breaks in DNA. The reaction rate of this step increases with increase in Mg2+ concentration and, as a result, the catalysis itself likely becomes the limiting step. Mechanism of the P-O3' bond cleavage at the 5'-side of an AP site catalyzed by human APE1 derived from the structure of the APE1-DNA complex produced by X-ray at higher resolution, overview
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additional information
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catalytic subunit of the HSV-1 DNA polymerase (Pol) (UL30) exhibits apurinic/apyrimidinic (AP) and 5'-deoxyribose phosphate lyase activities which are integral to base excision repair and lead to DNA cleavage on the 3'-side of abasic sites and 5'-deoxyribose-5-phosphate residues that remain after cleavage by 5'-AP endonuclease. DNA lyase activity residues in the Pol domain of UL30.
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?
additional information
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enzyme has implications on the role of BER in viral genome maintenance during lytic replication and reactivation from latency
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additional information
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overexpression of AP endonuclease protects Leishmania major cells against methotrexate induced DNA fragmentation and hydrogen peroxide, key enzyme in mediating repair of abasic sites in these pathogens
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additional information
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LMAP shares with APE1 the overall 3D structure and most of the catalytic groups in their active sites and can catalyze the removal of damaged nucleotides and phosphate groups from 3'-ends more efficiently than APE1
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additional information
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role in eliminating damaged mitochondrial genomes from the gene pool
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additional information
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poly(ADP-ribose) polymerase-1 and apurinic/apyrimidinic endonuclease can interact with the same base excision repair intermediate. Competition between theses two proteins may influence their respective base excision repair related functions
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additional information
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the enzyme has two distinct roles in the repair of oxidative DNA damage and in gene regulation. Absolute requirement of the enzyme for cell survival, presumably to protect against spontaneous oxidative DNA damage
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additional information
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APE/Ref-1 act as tuning molecule in activated B-cells
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additional information
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APE/Ref-1 affect the cell cycle by inducing nucleus-cytoplasm translocation of the cyclin-dependent kinase inhibitor p21
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?
additional information
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APE1 binds with the highest efficiency to DNA substrate containing 5'-sugar phosphate group in the nick/gap
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additional information
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APE1 exhibits 3'-phosphodiesterase, 3'-phosphatase, and 3'-5'-exonuclease activities
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?
additional information
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APE1 is one of the candidates for the role of base excision repair (BER) pathway coordinator, which controls the whole process. APE1 participates in stimulation of activity of BER enzymes
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additional information
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APE1 stimulates DNA synthesis catalyzed by DNA polymerase beta, and a human Xray repair cross-complementing group 1 protein stimulates APE1 3'-5'-exonuclease activity on 3'-recessed DNA duplex
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additional information
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APEX1 is a protein involved both in the base excision repair pathways of DNA lesions and in the regulation of gene expression as a redox coactivator of different transcription factors, such as early growth response protein-1
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additional information
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apurinic/apyrimidinic endonuclease 1 participates in the base excision repair of premutagenic apurinic/apyrimidinic (AP) sites
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additional information
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DNA with the recessed 3'-end (DNArec) is one of the preferential substrates for APE1 3'-5'-exonuclease activity
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additional information
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enzyme cleaves the DNA sugar phosphate backbone at the 5'-position in relation to the AP site, forming a nick with the hydroxyl group at the 3'-end and deoxyribose phosphate at the 5'-end
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additional information
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enzyme plays a role in controlling CD40-mediated B-cell proliferation, increase in proliferation and decrease in apoptosis of primary mouse B-cells activated by CD40 cross-linking and transfected with functional APE/Ref-1 antisense oligonucleotide.
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additional information
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high APE1 affinity to dsDNA
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additional information
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regulation of APEX1 expression by S-adenosylmethionine, which may be one of the mechanisms of hepatocellular carconom formation
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additional information
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When APE1 and DNA polymerase beta are both present, a ternary complex APE1-DNA polymerase beta-DNA is formed with the highest efficiency with DNA product of APE1 endonuclease activity and with DNA containing 5'-flap or mononucleotide-gapped DNA with 5'-p group
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additional information
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MtbXthA is a versatile enzyme with AP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
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additional information
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MtbXthA is a versatile enzyme with AP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
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additional information
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MtbXthA is a versatile enzyme with AP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
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additional information
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an increase of APE/Ref-1 mRNA levels in the caudal region of spinal cord strongly correlates with DNA damage after traumatic spinal cord injury
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additional information
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increase in phosphorylation of p53 after a decrease in Ape1 levels in sensory neuronal cultures
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additional information
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multifunctional protein involved in both the repair of oxidative and alkylating DNA damage and the regulation of gene expression
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additional information
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overexpressing wild-type Ape1 attentuates all the toxic effects of cisplatin in cells containing normal endogenous levels of Ape1 and in cells with reduced Ape1 levels after Ape1siRNA treatment
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additional information
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reducing expression of Ape1 in neuronal cultures using small interfering RNA enhances cisplatin-induced cell killing, apoptosis, ROS generation and cisplatin-induced reduction in iCGRP release
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additional information
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ntg1 possesses N-glycosylase/AP lyase activity that allows recognition and repair of oxidative base damage (primarily of pyrimidines) as well as abasic sites
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additional information
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ntg2 possesses N-glycosylase/AP lyase activity that allows recognition and repair of oxidative base damage (primarily of pyrimidines) as well as abasic sites
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additional information
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the nucleotide incision repair (NIR) recruiting Saccharomyces cerevisiae Apn1 proceeds via multistep rearrangements of the complex of Apn1 with a DHU-containing DNA substrate and results in the incised product of the reaction
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additional information
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the nucleotide incision repair (NIR) recruiting Saccharomyces cerevisiae Apn1 proceeds via multistep rearrangements of the complex of Apn1 with a DHU-containing DNA substrate and results in the incised product of the reaction
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Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Cu2+
activates at 0.01 mM, inhibits at 0.1 mM
Fe
-
pro-inflammatory activity of iron in the lung injury, at least in part, because of its induction of APE/Ref-1
MgCl2
-
tetrahydrofuran*G incision is efficiently catalyzed at 0.001 mM Mg2+, 5 mM MgCl2 are required for optimal AP endonuclease activity
Na+
-
65 mM included in assay medium
Sm2+
-
the divalent metal ion soaked with the protein crystals is found specifically to associate with the glutamate residue
Ca2+
-
stimulates
Ca2+
presence of 1 or 5 mM Ca2+ causes much less efficient stimulation of HpXth's AP site cleavage activity as compared to Mg2+ or Mn2+
Ca2+
-
optimal concentration at 5-30 mM, only 50% activity at 40 mM
Co2+
-
CoCl2 (500 microM) is essential for AP endonuclease assay. Effects of Co on APE/Ref-1 are concentration dependent
Co2+
-
0.1-1.0 mM, strong stimulation of all DNA repair activities
Fe2+
EndoIV contains two Fe2+ ions and one Zn2+ ion, crystallography data. Fe2+(1) is coordinated by Glu145, Asp179, His214, Glu259, and Fe2+(2) is coordinated by His69, His110 and Glu145
Fe2+
activates at 0.01 mM, inhibits at 0.1 mM
Fe2+
-
Fe2+ is able to support the incision activity of the enzyme at excess protein to DNA ratios of at least 6:1, Mg2+ and Fe2+ compete for the same metal-binding site
Fe2+
-
0.1-1.0 mM, strong stimulation of all DNA repair activities
Iron
-
iron-sulfur protein
Iron
-
native enzyme contains a single [4Fe-4S] cluster in the 2+ oxidation state with a net spin of zero
Iron
-
[4Fe-4S] cluster is not directly involved in catalytic mechanism and therefore has most likely a structural role
Iron
-
iron-sulfur protein
Iron
-
Scr2 but not Scr1 is an iron-sulfur protein
K+
-
both MgCl2 and KCl strongly influence the efficiency of Ape1 as an ssDNA or dsDNA AP endonuclease
K+
-
K+ significantly stimulates recombinant APE1 activity at 20 mM by approximately 1.3fold (compared with the absence of K+)
K+
-
25 mM included in assay medium. DNA structures with a nick and DNArec used for photoaffinity modification are substrates for APE1 3'-5'-exonuclease activity, that is more efficient at decreased salt concentrations.
K+
-
K+ significantly stimulates recombinant APE1 activity at 20 mM by approximately 1.3fold (compared with the absence of K+)
KCl
-
stimulates
KCl
-
optimal concentration: 25-50 mM
KCl
-
optimal concentration: 0.05-0.1 M, activity against apurinic and apyrimidinic sites, 50% inhibition at 0.02 and 0.12 M
KCl
-
optimal concentration: 0.10 M, activity against OsO4-sites, 50% inhibition at 0.05 and 0.15 M
KCl
-
optimal concentration: 125 mM
KCl
-
maximal AP endonuclease activity at 25-200 mM, nucleotide incision repair activity decreases dramatically above 50 mM
KCl
optimum concentration 50-100 mM
KCl
-
optimal concentration: 100 mM
KCl
-
optimal concentration: 50 mM,90% inhibition at 200 mM
KCl
-
enzyme form A: optimal activity in 20 mM NaCl or KCl, enzyme form B: more active without salt
KCl
optimum concentration 50-100 mM
KCl
-
slight stimulation at 10 to 30 mM, inhibition above 100 mM
KCl
-
optimum concentration 20 mM
Mg2+
-
the optimized buffer used for the endonuclease assay contains 5 mM MgCl2
Mg2+
-
optimal concentration: 20 mM
Mg2+
-
or Mn2+, absolutely required
Mg2+
-
Mg2+ or Mn2+ required, Mg2+ better than Mn2+
Mg2+
-
optimal concentration: 10 mM
Mg2+
-
Mg2+ or Mn2+ required
Mg2+
required, activates, best at 5 mM
Mg2+
-
optimal concentration: 3 mM
Mg2+
metal-dependent enzyme
Mg2+
-
repair of 5-OH-C opposite guanine is stimulated 2-fold with increasing concentrations, 5-OH-C paired with adenine is poorly repaired with increasing Mg2+ concentrations, no incision of 5-OH-C opposite adenine above 15 mM Mg2+
Mg2+
-
endonuclease B has an absolute requirement for Mg2+
Mg2+
-
endonuclease A does not require Mg2+ for full activity
Mg2+
-
activity against abasic sites in single-stranded DNA
Mg2+
APE1 binds to AP sites in the absence of Mg2+, a condition in which APE1 does not have endonuclease activity
Mg2+
-
included in assay medium
Mg2+
-
5 mM included in assay medium, required divalent cation
Mg2+
-
APE1 reaches a maximum of 3'-phosphoglycolate excision activity at Mg2+ concentrations around 2.5 mM, APE1 mutant D70A reaches maximum activity at higher metal concentrations. In case of a THF-containing oligonucleotide as substrate, APE1 exhibits the highest AP endonuclease activity at 5 mM of metal while the specific activity of APE1 mutant D70A did not reach a maximum until 40 mM of Mg2+ is added to the reaction.
Mg2+
binds to APE1 and a functional APE1-substrate DNA complex with an overall stoichiometry of one Mg2+ per mole of APE1, the chemistry central to the function of APE1 is water activated by a Mg2+ ion, Mg2+ binding is an absolute requirement for the endonucleolytic activity
Mg2+
-
In presence of Mg2+, ATP has complex effects on Ape1 cleavage activity. Endo- and exonuclease activity of Ape1 is found to be influenced by the MgCl2 concentration, with optimal exonuclease activity at low MgCl2 concentration (0.1-2 mM) and optimal endonuclease activity at high MgCl2 concentration (10-15 mM).
Mg2+
-
Mg2+, with potential binding sites A and B, binds at the B site of wild-type APE1-substrate complex and moves to the A site after cleavage occurs
Mg2+
-
ion concentrations ranging from 0.2 to 2 mM Mg2+ promotes catalysis, APE1 is enhanced approximately 2fold (compared with the absence of Mg2+) in the presence of 2 mM Mg2+
Mg2+
-
required for APE1-catalyzed endonuclease activity
Mg2+
-
both the endoribonuclease and the ssRNA apurinic/apyrimidinic site cleavage activities of wild-type APE1 are present in the absence of Mg2+, while ssDNA apurinic/apyrimidinic site cleavage requires Mg2+, optimally at 0.5-2.0 mM
Mg2+
required. Increasing the Mg2+ concentration alters the ratio of turns to beta-strands, and this change may be associated with the conformational changes required to achieve an active state
Mg2+
activates, Mg2+ or Mn2+ is required for endonuclease and exonuclease activity of APE1. Mg2+ is required for both binding of the protein with DNA and cleavage of phosphodiester bond catalyzed by APE1. Depending on the Mg2+ concentration, the limiting stage of the process can change
Mg2+
activates, required and involved in catalytic mechanism, Mg2+ ions stabilize the protein structure and the enzyme-substrate complex. Analysis of enzyme-substrate complexes with bound Mg2+
Mg2+
-
LMAP mutant A138D reaches a maximum of 3'-PG excision activity at Mg2+ concentrations around 2.5 mM, wild-type enzyme reaches maximum activity at higher metal concentrations. In case of a THF-containing oligonucleotide as substrate, the parasite enzymes LMAP and LMAPA138D, obtains the activity peaks at different magnesium concentrations (10 and 2.5 mM).
Mg2+
-
optimal concentration: 4-5 mM
Mg2+
-
optimal concentration: 1-5 mM
Mg2+
-
2 mM included in assay medium
Mg2+
required. Increasing the Mg2+ concentration alters the ratio of turns to beta-strands, and this change may be associated with the conformational changes required to achieve an active state
Mg2+
required, MtbXthA is inactive in AP site incision assays in the absence of Mg2+, while increasing activity is observed with increasing Mg2+ concentration between 1-10 mM. The protein exhibits maximal incision activity, 60%, when no NaCl is included in the buffer
Mg2+
-
the standard reaction buffer used for the nuclease assay is supplemented with 15 mM MgCl2
Mg2+
maximally stimulated at 10 mM
Mg2+
-
Mg2+ or Mn2+ required
Mg2+
-
optimal concentration: 5-10 mM
Mg2+
-
ion concentrations ranging from 0.2 to 2 mM Mg2+ promotes catalysis, APE1 is enhanced approximately 2fold (compared with the absence of Mg2+) in the presence of 2 mM Mg2+
Mg2+
-
Mg2+ or Mn2+ required
Mg2+
-
optimal concentration: 4 mM for endonuclease D1 and D2
Mg2+
-
optimal concentration: 8 mM, endonuclease D3
Mg2+
-
optimal concentration: 6 mM, endonuclease E
Mg2+
-
optimal concentration: 2 mM (endonuclease D4)
Mg2+
-
optimal concentration: 2.5-30 mM
Mg2+
APN is active in presence and in absence of Mg2+
Mn2+
-
stimulates
Mn2+
-
or Mg2+, absolutely required
Mn2+
-
can only partially replace Mg2+
Mn2+
-
Mn2+ or Mg2+ required
Mn2+
-
Mn2+ or Mg2+ required
Mn2+
-
divalent metal content
Mn2+
-
partial stimulation
Mn2+
-
Glu in amino acid position 96 binds to the divalent cation
Mn2+
activates, Mg2+ or Mn2+ is required for endonuclease and exonuclease activity of APE1
Mn2+
-
In order to cleave phosphodiester bonds in the course of endonuclease and exonuclease reactions catalyzed by APE1, Mg2+ or Mn2+ is needed
Mn2+
maximally stimulated at 10 mM
Mn2+
-
Mn2+ or Mg2+ required
Mn2+
-
Mn2+ or Mg2+ required
Mn2+
-
0.1-1.0 mM, strong stimulation of all DNA repair activities
NaCl
-
50 mM: slight stimulation, 500 mM: complete inhibition
NaCl
-
optimal concentration: 25-50 mM
NaCl
-
optimal concentration: 50 mM
NaCl
-
enzyme form A: optimal activity in 20 mM NaCl or KCl, enzyme form B: more active without salt
NaCl
MtbXthA exhibits an increase in AP site incision activity in a salt-dependent manner. Optimum conditions are 2 mM MgCl2 and 150 mM NaCl with 75% incision activity. Addition of more than 200 mM salt, strongly inhibits the endonuclease activity
NaCl
-
slight stimulation at 10 to 30 mM, inhibition above 100 mM
NaCl
-
150 mM, higher concentrations inhibit
NaCl
-
50 mM, 50% stimulation
Ni2+
activates at 0.01 mM, inhibits at 0.1 mM
Zn2+
-
the optimized buffer used for the exonuclease assay contains 5 mM ZnCl2
Zn2+
-
Divalent metal content, Zn3-site mutations result in major activity loss, whereas Zn1 and Zn2 ligand mutations cause low to severe loss of catalytic efficiency. In the DNA-free wild-type enzyme structure, two metal ions (Zn1 and Zn2) are partially buried from solvent and bind a bridging hydroxide anion. The third metal ion (Zn3) is mostly solvent accessible, is distant from Zn1 and Zn2 and ligates a tightly bound water molecule to complete its coordination shell
Zn2+
EndoIV contains two Fe2+ ions and one Zn2+ ion, crystallography data. The Zn2+ ion is coordinated by His182, Asp227, His229
Zn2+
activates at 0.01 mM, inhibits at 0.1 mM
Zn2+
-
stimulation half as effective as with Mg2+
Zn2+
His83 coordinates one of three Zn2+ ions in Apn1's active site, structure comparisons. Structure of enzyme mutant H83A Apn1-substrate DNA complex with three Zn2+ ions containing Zn2+ ions per molecule of mutant enzyme, overview. Zn2+ ions are involved in catalysis
Zn2+
required for catalysis, molecular dynamics. The active site of H83A Apn1 contains only two Zn2+ ions, with their positions being changed versus a trinuclear Zn2+ cluster of wild-type Apn1
additional information
-
Mn2+ has no effect
additional information
-
equal or higher activity for Zn2+ or Mn2+- containing Endo IV suggests that one site may favor Mn2+ over Zn2+
additional information
in the presence of 1 or 5 mM Mg2+ or Mn2+, the purified recombinant His-tagged HpXth protein exerts an efficient AP site cleavage activity by generating fast-migrating 10mer cleavage fragments. But higher concentrations of Mg2+ or Mn2+ (10-20 mM) result in a strong decrease in the HpXth-catalyzed AP site cleavage
additional information
-
in the presence of 1 or 5 mM Mg2+ or Mn2+, the purified recombinant His-tagged HpXth protein exerts an efficient AP site cleavage activity by generating fast-migrating 10mer cleavage fragments. But higher concentrations of Mg2+ or Mn2+ (10-20 mM) result in a strong decrease in the HpXth-catalyzed AP site cleavage
additional information
effects of monovalent (K+) and divalent (Mg2+, Mn2+, Ca2+, Zn2+, Cu2+, and Ni2+) metal ions on DNA binding and catalytic stages, circular dichroism spectra and calculation of the contact area between APE1 and DNA, overview. The first step of substrate binding (corresponding to formation of a primary enzyme-substrate complex) does not depend on the concentration (0.05-5.0 mM) or the nature of divalent metal ions. In contrast, the initial DNA binding efficiency significantly decreases at a high concentration (5-250 mM) of monovalent K+ ions, indicating the involvement of electrostatic interactions in this stage. The enzymatic activity of APE1 is increased in the ascending order Zn2+, Ni2+, Mn2+, and Mg2+
additional information
-
effects of monovalent (K+) and divalent (Mg2+, Mn2+, Ca2+, Zn2+, Cu2+, and Ni2+) metal ions on DNA binding and catalytic stages, circular dichroism spectra and calculation of the contact area between APE1 and DNA, overview. The first step of substrate binding (corresponding to formation of a primary enzyme-substrate complex) does not depend on the concentration (0.05-5.0 mM) or the nature of divalent metal ions. In contrast, the initial DNA binding efficiency significantly decreases at a high concentration (5-250 mM) of monovalent K+ ions, indicating the involvement of electrostatic interactions in this stage. The enzymatic activity of APE1 is increased in the ascending order Zn2+, Ni2+, Mn2+, and Mg2+
additional information
there is only one bivalent metal ion in the APE1 active site present in the crystal formed at pH 4.6. In the structure produced at pH 7.5, i.e. under conditions optimal for endonuclease activity, two metal ions are located in the active site of the enzyme. MgCl2 concentration in the range 0.5-2.0 mM and low (50 mM or below) concentration of KCl are optimal for cleavage of single-stranded DNA with an AP site, while the endonuclease activity towards the double-stranded AP-DNA is the highest at 10 mM MgCl2 and 50 mM KCl or 2 mM MgCl2 and 200 mM KCl. Co2+ and Ni2+ do not affect APE1 activity
additional information
-
there is only one bivalent metal ion in the APE1 active site present in the crystal formed at pH 4.6. In the structure produced at pH 7.5, i.e. under conditions optimal for endonuclease activity, two metal ions are located in the active site of the enzyme. MgCl2 concentration in the range 0.5-2.0 mM and low (50 mM or below) concentration of KCl are optimal for cleavage of single-stranded DNA with an AP site, while the endonuclease activity towards the double-stranded AP-DNA is the highest at 10 mM MgCl2 and 50 mM KCl or 2 mM MgCl2 and 200 mM KCl. Co2+ and Ni2+ do not affect APE1 activity
additional information
-
cleavage of abasic DNA by UL30 occurs in the presence of EDTA and is independent of Mg2+, UL30 is 10fold less active
additional information
-
presence of divalent cations does not stimulate the activity
additional information
the highly conserved catalytic site in AP endonucleases consists of residues involved in the binding of metal ions. MtbXthA exhibits moderate 3'-5' exonuclease activity at low ionic environment
additional information
-
the highly conserved catalytic site in AP endonucleases consists of residues involved in the binding of metal ions. MtbXthA exhibits moderate 3'-5' exonuclease activity at low ionic environment
additional information
the nucleotide incision repair of the enzyme in presence of Mg2+ is unaltered, Mg2+ does not affect yeast Ape1 activity
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(1E,6E)-1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,6-diene-3,5-dione
-
(2E)-2-(3,4-dihydroxybenzoyl)-3-(3,4-dihydroxyphenyl)prop-2-enenitrile
-
(2E)-2-methyl-3-[3-(methylsulfanyl)-1,4-dioxo-1,4-dihydronaphthalen-2-yl]prop-2-enoic acid
-
(2E)-2-[(3-bromo-1,4-dioxo-1,4-dihydronaphthalen-2-yl)methylidene]-4-methoxybutanoic acid
-
(2E)-2-[(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-yl)methylidene]-4-methoxybutanoic acid
-
(2E)-2-[(4,5-dimethoxy-2-methyl-3,6-dioxocyclohexa-1,4-dien-1-yl)methylidene]-N-methoxydodecanamide
i.e. E3330-amide
(2E)-2-[(4,5-dimethoxy-2-methyl-3,6-dioxocyclohexa-1,4-dien-1-yl)methylidene]dodecanoic acid
i.e. E3330
(2E)-3-(1,4-dioxo-1,4-dihydronaphthalen-2-yl)-2-methylprop-2-enoic acid
-
(2E)-3-(2-chloro-4,5-dimethoxy-3,6-dioxocyclohexa-1,4-dien-1-yl)-2-methylprop-2-enoic acid
-
(2E)-3-(3-bromo-1,4-dioxo-1,4-dihydronaphthalen-2-yl)-2-methylprop-2-enoic acid
-
(2E)-3-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-yl)-2-methylprop-2-enoic acid
-
(2E)-3-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-yl)-N-(2-hydroxyethyl)-2-methylprop-2-enamide
-
(2E)-3-(3-methoxy-1,4-dioxo-1,4-dihydronaphthalen-2-yl)-2-methylprop-2-enoic acid
-
(2E)-3-[3-[dihydroxy(oxido)-lambda5-stibanyl]phenyl]prop-2-enoic acid
-
(2R)-1-(1-benzofuran-2-yl)-2-(1,3-benzothiazol-2-yl)-2-hydroxyethanone
-
(3-chloro-1-benzothiophen-2-yl)[(2Z)-2-[(2-chlorophenyl)imino]-4-methylidene-3-thia-1-azaspiro[4.5]dec-1-yl]methanone
-
(3a'S,6a'R)-5'-(1,3-benzodioxol-5-ylmethyl)-3'-(2-carboxyethyl)-7-chloro-2,4',6'-trioxo-1,2,3',3a',4',5',6',6a'-octahydro-2'H-spiro[indole-3,1'-pyrrolo[3,4-c]pyrrol[2]ium]
-
(5E)-1-(furan-2-ylmethyl)-5-[(2E)-3-(furan-2-yl)prop-2-en-1-ylidene]pyrimidine-2,4,6(1H,3H,5H)-trione
-
(5R)-4-hydroxy-3,5-dimethyl-5-((2S)-3-methylpent-4-en-2-yl)thiophen-2(5H)-one
-
1,1',6,6',7,7'-hexahydroxy-3,3'-dimethyl-5,5'-di(propan-2-yl)-2,2'-binaphthalene-8,8'-dicarbaldehyde
-
1,3-bis(1,3-benzothiazol-2-ylsulfanyl)propan-2-one
-
1,4-dihydroxy-5,8-bis([2-[(2-hydroxyethyl)amino]ethyl]amino)anthracene-9,10-dione
-
1,6,6-trimethyl-6,7,8,9-tetrahydrophenanthro[1,2-b]furan-10,11-dione
-
1-amino-4-[[4-([4-chloro-6-[(4-sulfophenyl)amino]-1,3,5-triazin-2-yl]amino)phenyl]amino]-9,10-dioxo-9,10-dihydroanthracene-2-sulfonic acid
-
1-methyl-4-[(1E)-1-[2-(6-methyl[1,3]dioxolo[4,5-g]quinolin-8-yl)hydrazinylidene]ethyl]-2-phenyl-1,2-dihydro-3H-pyrazol-3-one
1-[3-[(6-chloro-2-methoxyacridin-9-yl)amino]propyl]-3-[3-(2,6-diamino-9H-purin-9-yl)propyl]guanidine
-
1-[4-[(6-chloro-2-methoxyacridin-9-yl)amino]butyl]-3-[4-(2,6-diamino-9H-purin-9-yl)butyl]guanidine
-
1-[[2-(ethylamino)ethyl]amino]-4-(hydroxymethyl)-9H-thioxanthen-9-one
-
1-[[2-(ethylamino)ethyl]amino]-4-methyl-9H-thioxanthen-9-one
-
10,12-dimethyl-2-(propan-2-yl)-6H-[1,3]oxazolo[4,5-g]pyrido[4,3-b]carbazol-10-ium
-
2,2'-(2-oxo-1H-benzimidazole-1,3(2H)-diyl)diacetic acid
-
2,2'-(3,7-dioxo-5,7-dihydro-1H,3H-benzo[1,2-c:4,5-c']difuran-1,5-diyl)diacetic acid
-
2,2'-[(2,5-dimethylfuran-3,4-diyl)bis(carbonylimino)]diacetic acid
-
2,2'-[(6-oxo-6H-benzo[c]chromene-1,3-diyl)bis(oxy)]dipropanoic acid
-
2,2'-[(6-phenylpyrimidine-2,4-diyl)disulfanediyl]diacetic acid
-
2,2'-[butane-1,4-diylbis(1H-benzimidazole-2,1-diyl)]diacetic acid
2,4,9-trimethylbenzo[b][1,8]naphthyridin-5-amine
2,4-di-tert-butylphenyl 3-chloro-1-benzothiophene-2-carboxylate
-
2,5-dihydroxy-DL-tyrosine
-
2-((Z)-2-oxo-3-(4-oxo-2-thioxothiazolidin-5-ylidene)indolin-1-yl)acetic acid
potent inhibitory activity
2-(2,4-dichlorophenyl)-6-nitro-4H-3,1-benzoxazin-4-one
-
2-(4-(2,5-dimethyl-1H-prryol-1-yl)phenoxy) acetic acid
-
i.e. Ape1 repair inhibitor 01, specific inhibitor of AP endonuclease
2-(4-chlorophenyl)-4-(2'-fluorobiphenyl-4-yl)-5-methyl-1,3-thiazole
-
2-(5-((2-(2-carboxyphenyl)-1,3-dioxo)-2,3-dihydro-1H-isoindol-5-yl)carbonyl}-1,3-dioxo-2,3-dihydro-1H-isoindol-2-yl)benzoic acid
potent inhibitory activity
2-(carboxymethyl)-4-([4-[(4-carboxyphenyl)sulfanyl]phenyl]sulfonyl)benzoic acid
-
2-amino-3-(3-[2-amino-1-[2-(6-amino-9H-purin-9-yl)ethyl]triaz-2-en-2-ium-1-yl]propyl)-3-[3-[(6-chloro-2-methoxyacridin-9-yl)amino]propyl]triaz-1-en-2-ium
-
2-aminobenzene-1,3,5-trisulfonamide
-
2-mercaptoethanol
suppresses delta-elimination partially
2-methoxy-3-[(3-methoxybenzyl)carbamoyl]benzoic acid
-
2-[(5R)-3-(naphthalen-2-yl)-5-phenyl-2,5-dihydro-1H-pyrazol-1-yl]-2-oxoethyl 5-nitrothiophene-2-carboxylate
-
2-[(5Z)-5-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]-3-phenylpropanoic acid
-
2-[(Z)-(4-hydroxy-3-methylphenyl)(3-methyl-4-methylidenecyclohexa-2,5-dien-1-ylidene)methyl]benzoic acid
-
2-[5-[1-(carboxymethyl)-2-oxo-2,3-dihydro-1H-indol-3-yl]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]-3-phenylpropanoic acid
-
3,3',4,4',5,5'-hexabromobiphenyl
-
3,3'-(1,3,4-thiadiazole-2,5-diyldisulfanediyl)dipropanoic acid
-
3,3'-(2-thioxo-1H-benzimidazole-1,3(2H)-diyl)dipropanoic acid
-
3,3'-[(3-carboxy-4-oxocyclohexa-2,5-dien-1-ylidene)methanediyl]bis(6-hydroxybenzoic acid)
-
3,5,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-4H-chromen-4-one
-
3,6,7-trimethoxyphenanthrene-2,5-diol
-
3,8,9,10-tetrahydroxypyrano[3,2-c]isochromene-2,6-dione
-
3-((3,4-dimethylphenoxy)methyl)furan-2-carboxylic acid
-
3-((pyridin-2-ylthio)methyl)benzofuran-2-carboxylic acid
-
3-(1-(carboxymethyl)-5-(4-chlorophenyl)-1H-pyrrol-2-yl)propanoic acid
potent inhibitory activity
3-(1-(carboxymethyl)-5-(4-fluorophenyl)-1H-pyrrol-2-yl)propanoic acid
potent inhibitory activity
3-(1-(carboxymethyl)-5-(thiophen-2-yl)-1H-pyrrol-2-yl)propanoic acid
potent inhibitory activity
3-(1-(carboxymethyl)-5-p-tolyl-1H-pyrrol-2-yl)propanoic acid
-
3-(2-carboxyethyl)-4-hydroxyquinoline-6-carboxylic acid
-
3-(5-((E)-(3-(carboxymethyl)-4-oxo-2-sulfanylidene-1,3-thiazolidin-5-ylidene)methyl)furan-2-yl)benzoic acid
potent inhibitory activity
3-[(3,4-dichlorobenzyl)carbamoyl]-2-methoxybenzoic acid
-
3-[(3,4-dimethoxybenzyl)carbamoyl]-2-methoxybenzoic acid
-
3-[(3-chlorobenzyl)carbamoyl]-2-methoxybenzoic acid
-
3-[(4Z)-4-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-5-oxo-2-thioxoimidazolidin-1-yl]propanoic acid
-
3-[(6-amino-9H-purin-8-yl)sulfanyl]propanoic acid
-
3-[1-(carboxymethyl)-5-(4-chlorophenyl)-1H-pyrrol-2-yl]propanoic acid
-
3-[4-[(3aR,9bR)-9-methoxy-1,3a,4,9b-tetrahydrochromeno[3,4-c]pyrrol-2(3H)-yl]butyl]-8-phenylpyrazino[2',3':4,5]thieno[3,2-d]pyrimidine-2,4(1H,3H)-dione
-
3-[5-(2,3-dimethoxy-6-methyl-1,4-benzoquinoyl)]-2-nonyl-2-propionic acid
E3330 specifically blocking the APE1 redox but not DNA activity, an equilibrium constant (KD) of 1.6 nM is obtained for the binding of E3330 to APE1. E3330 is also shown to block the ability of APE1 to reduce NF-kappaB, thus interfering with the redox activity of APE1
3-[[4-(carboxymethyl)benzyl]sulfanyl]-8-methyl-5H-[1,2,4]triazino[5,6-b]indole-5-carboxylic acid
-
4'-(2-chloro-6-nitrophenoxy)biphenyl-4-yl 4-tert-butylbenzenesulfonate
-
4-((2-carboxyphenoxy)methyl)-2,5-dimethylfuran-3-carboxylic acid
potent inhibitory activity
4-(2,6,8-trimethylquinolin-4-ylamino)phenol
-
i.e. Ape1 repair inhibitor 02, specific inhibitor of AP endonuclease
4-(4-(4-carboxyphenoxy)phenylsulfonyl)benzene-1,2-dioic acid
-
4-(4-(4-carboxyphenylsulfonyl)phenyl)sulfanylbenzene-1,2-dioic acid
potent inhibitory activity
4-(4-(4-carboxyphenylthio)phenylsulfonyl)benzene-1,2-dioic acid
potent inhibitory activity
4-([[(3-carboxy-5-methylfuran-2-yl)methyl]sulfanyl]methyl)-5-methylfuran-2-carboxylic acid
-
4-benzyl-1-(3-[[(3-nitrophenyl)sulfonyl]amino]quinoxalin-2-yl)pyridinium
-
4-[(4Z)-4-([5-[4-chloro-3-(ethoxycarbonyl)phenyl]furan-2-yl]methylidene)-3-methyl-5-oxo-4,5-dihydro-1H-pyrazol-1-yl]benzoic acid
-
4-[(4Z)-4-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-5-oxo-2-thioxoimidazolidin-1-yl]butanoic acid
-
4-[dihydroxy(oxido)-lamba5-stibanyl]-2-nitrobenzoic acid
-
4-[methyl(nitroso)amino]benzene-1,2-diol
-
4-[[(2-carboxypropyl)sulfanyl]methyl]-5-methylfuran-2-carboxylic acid
-
5,11-dimethyl-6H-pyrido[4,3-b]carbazol-9-amine
-
5,5'-[ethane-1,2-diylbis(sulfanediylmethanediyl)]bis(2-methylfuran-3-carboxylic acid)
-
5,5'-[methanediylbis(sulfanediylmethanediyl)]bis(2-methylfuran-3-carboxylic acid)
-
5,7-dihydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one
-
5-(((tetrahydrofuran-2-yl)methylthio)methyl)-2-methylfuran-3-carboxylic acid
-
5-(acetylamino)-2-[(E)-2-(4-isothiocyanato-3-sulfophenyl)ethenyl]benzenesulfonic acid (non-preferred name)
-
5-(acetylamino)-2-[2-(4-isothiocyanato-3-sulfophenyl)ethenyl] benzenesulfonic acid
shows no cytotoxicity in MCF10A cells
5-(hydroxymethyl)furan-2-carbaldehyde
-
5-([[(4-carboxy-5-methylfuran-2-yl)methyl]sulfanyl]methyl)-3-methylfuran-2-carboxylic acid
-
5-[(E)-2-(4-hydroxyphenyl)ethenyl]benzene-1,3-diol
-
5-[4-[(6-hydroxy-2,5,7,8-tetramethyl-3,4-dihydro-2H-chromen-2-yl)methoxy]benzyl]-1,3-thiazolidine-2,4-dione
-
6-amino-4-hydroxy-5-[(4-nitro-2-sulfophenyl)azo]-2-naphtalenesulfonic acid
shows no cytotoxicity in MCF10A cells
6-amino-4-hydroxy-5-[(E)-(4-nitro-2-sulfophenyl)diazenyl]naphthalene-2-sulfonic acid
-
6-amino-5-[(4-amino-2-sulfophenyl)azo]-4-hydroxy-2-naphtalenesulfonic acid
shows no cytotoxicity in MCF10A cells
6-amino-5-[(E)-(4-amino-2-sulfophenyl)diazenyl]-4-hydroxynaphthalene-2-sulfonic acid
-
6-hydroxy-DL-DOPA
-
complete inhibition at 0.1 mM
7-chloro-2-(2-fluorophenyl)-4H-3,1-benzoxazin-4-one
-
7-hydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one
-
7-nitro-1H-indole 2-carboxylic acid
-
CRT0044876, binds to the active site of APE/Ref-1 and effectively inhibits its AP endonuclease, 3'-phosphodiesterase and 3'-phosphatase activities at low micromolar concentrations
7-nitro-1H-indole-2-carboxylic acid
8-[(2E)-2-(1,3-benzodioxol-5-ylmethylidene)hydrazinyl]-6-methyl[1,3]dioxolo[4,5-g]quinoline
-
8-[(2E)-2-(3-methoxybenzylidene)hydrazinyl]-6-methyl[1,3]dioxolo[4,5-g]quinoline
inhibitor induces time-dependent increases in the accumulation of abasic sites in cells at levels that correlate with its potency to inhibit APE-1 endonuclease excision. The inhibitor also potentiates by 5fold the toxicity of a DNA methylating agent that creates abasic sites
8-[(2E)-2-[(9-ethyl-9H-carbazol-3-yl)methylidene]hydrazinyl]-6-methyl[1,3]dioxolo[4,5-g]quinoline
8-[3-(2-chloro-10H-phenothiazin-10-yl)propyl]-1-thia-4,8-diazaspiro[4.5]decan-3-one
-
Acridine dimers
-
with a spermidine linker
-
adenine
-
50% inhibition at 0.2 mM
aurintricarboxylic acid
-
potent inhibitor of APE1
beta-mercaptoethanol
-
complete inhibition at 10 mM and higher
biphenyl-4,4'-diyl bis(3,4-dichlorobenzenesulfonate)
-
Cd2+
inhibits the enzyme to a variable degree in the cell extract
Co2+
-
86% inhibition at 10 mM
CRT0044876
weak inhibition
cycloheximide
-
treatment decreases APEX1 protein levels as compared with untreated mouse hepatocytes
d(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))
-
-
d(p(2,3-dihydroxy-5-oxopentyl phosphate))
-
-
dithiothreitol
-
at 1 mM and higher dithiothreitol concentrations AP site incision is strongly inhibited with less than 10% of the activity remaining, the inhibition by dithiothreitol is reverted by H2O2 in a dose-dependent manner, the inhibition by dithiothreitol is not reverted by divalent cations, including Zn2+, Co2+, Ca2+, and Ni+
d[(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))3pT]
-
-
d[(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))5pT]
-
-
d[(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))7pT]
-
-
d[(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))9pT]
-
-
Ethidium bromide
weak inhibition
ethyl 4-[4-[dihydroxy(oxido)-lambda5-stibanyl]phenyl]butanoate
-
granzyme A
-
granzyme A cleaves APE1 at Lys31 and inactivates it
-
human X-ray repair cross-complementing group 1 protein (XRCC1)
-
at high XRCC1 concentrations, inhibition of APE1 exonuclease activity is observed
-
Kainic acid
-
APE/Ref-1 is decreased by kainic acid injury in a time-dependent manner at the level of proteins, not transcripts
lucanthone
-
inhibits repair activity from cellular extracts and enhances cell killing effect of the laboratory alkylating agent methyl methanesulfonate and the clinically relevant agent temozolomide, no inhibition of redox function or exonuclease activity on mismatched nucleotides
MgCl2
-
tetrahydrofuran*G incision activity is inhibited above 2 mM
myricetin
-
above 80% inhibition at 0.1 mM
N-(3,5-dichlorophenyl)-4-(2'-fluorobiphenyl-4-yl)-5-methyl-1,3-thiazol-2-amine
-
N-(3-chlorophenyl)-5,6-dihydro-4H-cyclopenta[d][1,2]oxazole-3-carboxamide
-
N-(3-chlorophenyl)-5,6-dihyro-4H-cyclopenta[d]isoxazole-3-carboxamide
-
i.e. Ape1 repair inhibitor 06, specific inhibitor of AP endonuclease
N-(9,10-dioxo-9,10-dihydroanthracen-1-yl)-2-(1H-1,2,4-triazol-5-ylsulfanyl)acetamide
-
N-benzyl-2-(3-cyanophenyl)-1,3,7-trioxo-2,3,7,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazine-5-carboxamide
-
N-[3-(1,3-benzothiazol-2-yl)-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl]acetamide
-
N-[3-(1,3-benzothiazol-2-yl)-5,6-dihydro-4H-thieno[2,3-c]pyrrol-2-yl]acetamide
-
N-[3-(1,3-benzothiazol-2-yl)-6-(propan-2-yl)-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl]acetamide
-
N-[3-(4-phenyl-1,3-thiazol-2-yl)-6-(propan-2-yl)-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl]acetamide
-
N-[4-[dihydroxy(oxido)-lambda5-stibanyl]phenyl]benzamide
-
Ni2+
activates at 0.01 mM, inhibits at 0.1 mM
NSC-13755
-
complete inhibition at 0.1 mM
nucleotides
dAMP across from the AP site does not cause any distortions in the helix in comparison with the undamaged DNA, while the presence dCMP and dGMP results in changes in the helical structure to a varying degree providing out-of-helix position of the nucleotide and/or AP site
-
oligonucleotide containing 2'-fluorinated 5R- or 5S-thymidine glycol
-
inhibits DNA glycosylase activity, not the AP lyase step, in the Endo III reaction, by stabilizing the glycosidic bond
-
P53
-
after camptothecin treatment, p53 is a negative regulator of APE1 expression, APE1 promoter activity is repressed by wild-type p53, but not by mutant p53
PNRI-299
-
inhibition on AP-1 transcription
polyinosinic-polycytidylic acid
-
transfection of APE1 suppresses the extracellular release of high-mobility group box 1 in response to polyinosinic-polycytidylic acid stimulation
-
proteinBcl2
-
overexpression of Bcl2, a major cellular oncogenic protein, in cells reduces formation of the APE1-XRCC1 complex, Bcl2 not only prolongs cell survival but also suppresses the repair of abasic (AP) sites of DNA lesions. Bcl2 directly interacts with APE1 via its BH domains, and deletion of any of the BH domains from Bcl2 results in loss of the ability of Bcl2 to suppress APE1 endonuclease activity and AP site repair
-
Reactive blue 2
-
above 80% inhibition at 0.1 mM
reactive oxygen species
-
reactive oxygen species not only can inhibit APE/Ref-1 activities by direct oxidation of amino acid residues, but also affects the expression level and subcellular localization of APE/Ref-1
-
resveratrol
-
dock into one of the two drug-treatable pockets located in the redox domain
RPA proteins
RPA proteins are able to suppress the APE1 endonuclease activity in ssDNA of a replicative fork but not in a transcription bubble or in dsDNA
-
tetrahydrofuran-2-ylmethyl 6-(furan-2-yl)-3-methyl-4-oxo-4,5,6,7-tetrahydro-1H-indole-2-carboxylate
-
Triton X-100
-
increases activity of nuclear membrane enzyme, activity of nuclear sap and chromatin non-histone enzyme untouched or decreased
tyrphostin AG 538
-
mild inhibition at 0.1 mM
[(3Z)-3-(3-[[(2-hydroxyphenyl)carbonyl]amino]-4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)-2-oxo-2,3-dihydro-1H-indol-1-yl]acetic acid
-
[(3Z)-3-[3-(4-bromophenyl)-4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene]-2-oxo-2,3-dihydro-1H-indol-1-yl]acetic acid
-
[(5Z)-5-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid
-
[4-(2,5-dimethyl-1H-pyrrol-1-yl)phenoxy]acetic acid
-
1-methyl-4-[(1E)-1-[2-(6-methyl[1,3]dioxolo[4,5-g]quinolin-8-yl)hydrazinylidene]ethyl]-2-phenyl-1,2-dihydro-3H-pyrazol-3-one
inhibitor induces time-dependent increases in the accumulation of abasic sites in cells at levels that correlate with its potency to inhibit APE-1 endonuclease excision. The inhibitor also potentiates by 5fold the toxicity of a DNA methylating agent that creates abasic sites
1-methyl-4-[(1E)-1-[2-(6-methyl[1,3]dioxolo[4,5-g]quinolin-8-yl)hydrazinylidene]ethyl]-2-phenyl-1,2-dihydro-3H-pyrazol-3-one
-
2,2'-[butane-1,4-diylbis(1H-benzimidazole-2,1-diyl)]diacetic acid
-
2,2'-[butane-1,4-diylbis(1H-benzimidazole-2,1-diyl)]diacetic acid
-
2,4,9-trimethylbenzo[b][1,8]naphthyridin-5-amine
-
i.e. Ape1 repair inhibitor 03, specific inhibitor of AP endonuclease
2,4,9-trimethylbenzo[b][1,8]naphthyridin-5-amine
-
2,7-BisNP-NH
-
2,7-BisNP-NH
strong inhibition
2,7-BisNP-O
-
2,7-BisNP-O
strong inhibition
4-chloromercuribenzoate
-
complete inhibition at 1 mM
4-chloromercuribenzoate
-
complete inhibition at 2 mM
4-chloromercuribenzoate
-
complete inhibition at 1 mM
4-chloromercuribenzoate
-
complete inhibition at 1 mM
7-nitro-1H-indole-2-carboxylic acid
-
CRT0044876
7-nitro-1H-indole-2-carboxylic acid
-
7-nitro-1H-indole-2-carboxylic acid
CRT0044876, a direct inhibitor of the DNA repair activity of APE1
8-[(2E)-2-[(9-ethyl-9H-carbazol-3-yl)methylidene]hydrazinyl]-6-methyl[1,3]dioxolo[4,5-g]quinoline
inhibitor induces time-dependent increases in the accumulation of abasic sites in cells at levels that correlate with its potency to inhibit APE-1 endonuclease excision. The inhibitor also potentiates by 5fold the toxicity of a DNA methylating agent that creates abasic sites
8-[(2E)-2-[(9-ethyl-9H-carbazol-3-yl)methylidene]hydrazinyl]-6-methyl[1,3]dioxolo[4,5-g]quinoline
-
AMP
-
-
ATP
-
in presence of 1 mM Mg2+, Ape1 incision activity is inhibited at higher ATP concentrations (2-5 mM). Depending on the relative concentration of Mg2+, ATP can have both inhibitory and stimulatory consequences on Ape1 incision capacity
Ca2+
-
39% inhibition at 10 mM
Ca2+
higher concentrations of Mn2+ (10-20 mM) result in a strong decrease in the HpXth-catalyzed AP site cleavage
Ca2+
50% inhibition at 5-10 mM
Ca2+
Ca2+ cause a complete loss of catalytic activity of APE1 with retention of binding potential
Ca2+
-
complete inhibition at 2 mM
Ca2+
-
50% activity at 40 mM
Ca2+
-
5-10 mM, inhibitory
Cu2+
-
90% inhibition at 10 mM
Cu2+
activates at 0.01 mM, inhibits at 0.1 mM
Cu2+
Cu2+ ions abrogate the DNA binding ability of APE1, possibly, due to a strong interaction with DNA bases and the sugar-phosphate backbone
E3330
-
binds specifically to Ape1/Ref-1 and blocks its redox activity
E3330
-
forms a reversible adduct with DELTA40APE1, an N-terminal truncation of APE1 including residues 40-318. E3330 also increases the extent of disulfide bond formation involving redox critical Cys residues in APE1
E3330
-
APE1 redox-specific inhibitor. E3330 suppresses secretion of inflammatory cytokines including tumor necrosis factor-alpha, interleukin IL-6 and IL-12 and inflammatory mediators nitric oxide as well as prostaglandin E2 from lipopolysaccharide-stimulated RAW264.7 cells and leads to down-regulation of the lipopolysaccharide-dependent expression of inducible nitric oxide synthase and cyclooxygenase-2 genes in the RAW264.7 cells. The effects of E3330 are mediated by the inhibition of transcription factors nuclear factor-kappaB and activator protein 1 in lipopolysaccharide-stimulated macrophages
EDTA
-
96% inhibition at 20 mM
EDTA
-
complete inhibition at 20 mM
EDTA
-
complete inhibition at 5 mM
EDTA
-
complete inhibition at 1 mM
EDTA
incision activity is completely abolished when 10 mM EDTA is added to the reaction
EDTA
-
complete inhibition at 2 mM
EDTA
-
90% inhibition at 0.1 mM
Fe2+
activates at 0.01 mM, inhibits at 0.1 mM
Fe2+
-
inhibitory effects on APE/Ref-1 activity
Fe2+
inhibits the enzyme to a variable degree in the cell extract
Harmane
-
i.e. 1-methyl-9H-pyrido-[3,4-b]indole, inhibits Escherichia coli endonuclease III and its associated dihydroxythymidine-DNA glycosylase activity, 50% inhibition at 0.4 mM, 80% inhibition at 1 mM
Harmane
-
i.e. 1-methyl-9H-pyrido-[3,4-b]indole, only slight inhibition of AP endocunlease I and II
Harmane
Tequatrovirus T4
-
i.e. 1-methyl-9H-pyrido-[3,4-b]indole, inhibits Escherichia coli endonuclease III and its associated dihydroxythymidine-DNA glycosylase activity, 50% inhibition at 0.4 mM, 80% inhibition at 1 mM
isoflavones
-
soy isoflavones decrease apurinic/apyrimidinic endonuclease 1/redox factor-1 expression
isoflavones
-
soy isoflavones decrease apurinic/apyrimidinic endonuclease 1/redox factor-1 expression
K+
-
K+ is inhibitory to the native APE1 at 0.2-10 mM with approximately 5fold inhibition
K+
initial DNA binding efficiency significantly decreases at a high concentration (5-250 mM) of monovalent K+ ions
K+
-
K+ is inhibitory to the native APE1 at 0.2-10 mM with approximately 5fold inhibition
KCl
-
50 mM: 70% inhibition
KCl
-
maximal AP endonuclease activity at 25-200 mM, nucleotide incision repair activity decreases dramatically above 50 mM
KCl
-
varying concentrations of KCl show an initial decrease followed by a significant increase in KD value for the APE/AP DNA binding
KCl
-
inhibition above 100 mM, 5fold inhibition at 500 mM
methoxyamine
methoxyamine (CH3ONH2) specifically inhibits virtually all AP endonucleases, irrespective of their action modes
methoxyamine
MX, an indirect inhibitor. MX increases the cytotoxicity of chemotherapeutic drugs such as temozolomide, carmustine, pemetrexed, and 5-iodo-2'-deoxyuridine in preclinical models
methoxyamine
treatment completely abrogates APE1 acetylation in a dose- and time-dependent manner. Methoxyamine (MX) covalently binds to AP sites to form methoxyamine-bound AP (MX-AP) sites and competitively inhibits the binding of APE1 to AP sites. These MX-AP sites are resistant to recognition and repair by APE1
Mg2+
-
MgCl2 above 20 mM
Mg2+
-
selectively inhibits endonuclease III activity when apurinic/apyrimidinic DNA is used as substrate, but has no effect when DNA containing either urea or thymine glycol is used as substrate
Mg2+
-
57% inhibition at 10 mM
Mg2+
higher concentrations of Mg2+ (10-20 mM) result in a strong decrease in the HpXth-catalyzed AP site cleavage
Mg2+
50% inhibition at 5-10 mM
Mg2+
-
AP-endonuclease activity of the C99S mutant as well as of the double mutants C138S/C99S and C65S/C99S is strongly inhibits in the presence of 10 mM Mg2+. Increasing Mg2+ concentration to 10 mM inhibited product formation by 5.4-fold. At 20 mM Mg2+, the product formation with wild-type APE1 is inhibited 4.2-fold and with the C99S mutant 14-fold relative to the activity of the wild-type protein in 5 mM Mg2+
Mg2+
-
In case of APE 1, the excision being severely inhibited (below 25%) at 10 mM and higher ion concentrations. APE1 mutant D70A is more refractory to Mg2+ inhibition, thus still retaining about 50% of activity at 20 mM Mg2+. In case of a THF-containing oligonucleotide as substrate, inhibition is not evidenced until 80mM is reached.
Mg2+
-
10-20 mM Mg2+ is inhibitory to the RNA-cleaving activity of APE1
Mg2+
-
In case of LMAP mutant A138D, the excision being severely inhibited (below 25%) at 10 mM and higher ion concentrations. Wild-type enzyme is more refractory to Mg2+ inhibition, thus still retaining about 50% of activity at 20 mM Mg2+
Mg2+
-
10-20 mM Mg2+ is inhibitory to the RNA-cleaving activity of APE1
Mg2+
-
5-10 mM, inhibitory
Mn2+
-
above 20 mM
Mn2+
-
37% inhibition at 10 mM
Mn2+
higher concentrations of Mn2+ (10-20 mM) result in a strong decrease in the HpXth-catalyzed AP site cleavage
Mn2+
50% inhibition at 5-10 mM
N-ethylmaleimide
-
-
N-ethylmaleimide
-
treatment of fully denatured full-length APE1 and DELTA40APE1, an N-terminal truncation of APE1 including residues 40-318, results in modification of 7 and 2 resiudes, respectively
NaCl
catalytic activity is inhibited in buffer more than 100 mM NaCl
NaCl
-
complete inhibition at 1 M, 40% inhibition at 0.5 M
NaCl
-
above 50 mM: slight stimulation, 500 mM: complete inhibition
NaCl
-
1 mM: complete inhibition
NaCl
-
50 mM: 70% inhibition
NaCl
-
above 10 mM; complete inhibition at 500 mM
NaCl
-
50% inhibition by 50 mM
NaCl
-
inhibition above 50 mM
NaCl
-
inhibition above 100 mM, 5fold inhibition at 500 mM
NaCl
-
inhibition above 150 mM
Pb2+
-
inhibitory effects on APE/Ref-1 activity
Pb2+
inhibits the enzyme to a variable degree in the cell extract
Zn2+
-
86% inhibition at 10 mM
Zn2+
activates at 0.01 mM, inhibits at 0.1 mM
additional information
-
no inhibition by N-ethylmaleimide
-
additional information
-
-
-
additional information
-
5-OH-C paired with adenine was poorly repaired with increasing Mg2+ concentrations, no incision of 5-OH-C opposite adenine above 15 mM Mg2+
-
additional information
-
enzyme is inhibited by the product of its DNA N-glycosylase activity directed against Tg:G, the AP:G site, but not inhibited by the AP:A site arising from release of Tg from Tg:A
-
additional information
-
in contrast to activity against abasic sites in souble-stranded DNA the enzyme does not display product inhibition when acting on absic sites in single-stranded DNA
-
additional information
-
the enzyme activity of apurinic/apyrimidinic endonuclease is blocked by APE-specific siRNAs
-
additional information
-
the enzyme activity of apurinic/apyrimidinic endonuclease is blocked by APE-specific siRNAs
-
additional information
-
APE1 silencing via siRNA transfection inhibits both the nuclear and cytoplasmic expression of APE1
-
additional information
-
methoxyamine binds to and occludes abasic sites in DNA and thereby inhibits Ape1/Ref-1-mediated DNA repair
-
additional information
-
hiolactomycin and methyl 3,4-dephostatin have no effect on total AP site cleavage activity
-
additional information
-
the presence within the G quadruplex DNA structure of an abasic site decreases the efficiency of human AP endonuclease activity. This effect is mostly the result of a decreased enzymatic activity and not of decreased binding of the enzyme to the damaged site
-
additional information
the cleavage of single-stranded DNA with an AP site does not depend on the presence of DNA glycosylases, and it is not inhibited by the reaction product. Replacement of tetrahydrofuran with a positively charged analogue pyrrolidine decreases endonuclease activity of the APE1 21fold and the DNA binding activity by 4fold. Endonuclease activity on DNA with an tetrahydrofuran residue decreases 7300fold in 4 mM EDTA in comparison with the activity in the presence of 10 mM Mg2+, and the activity decreases only 20-30fold on DNA containing ethane and propanediol in the center of the strand instead of an AP site
-
additional information
-
the cleavage of single-stranded DNA with an AP site does not depend on the presence of DNA glycosylases, and it is not inhibited by the reaction product. Replacement of tetrahydrofuran with a positively charged analogue pyrrolidine decreases endonuclease activity of the APE1 21fold and the DNA binding activity by 4fold. Endonuclease activity on DNA with an tetrahydrofuran residue decreases 7300fold in 4 mM EDTA in comparison with the activity in the presence of 10 mM Mg2+, and the activity decreases only 20-30fold on DNA containing ethane and propanediol in the center of the strand instead of an AP site
-
additional information
identification of small molecule inhibitors against APE1/Ref-1 activities, structures and activities of APE1/Ref-1 inhibitors, that target both DNA repair and redox activities, molecular docking, overview
-
additional information
identification of small molecule inhibitors against APE1/Ref-1 activities, structures and activities of APE1/Ref-1 inhibitors, that target both DNA repair and redox activities, molecular docking, overview
-
additional information
-
identification of small molecule inhibitors against APE1/Ref-1 activities, structures and activities of APE1/Ref-1 inhibitors, that target both DNA repair and redox activities, molecular docking, overview
-
additional information
the enzyme is a promising target for the development of small-molecule inhibitors to be used in combination with anticancer agents, structure-based virtual library screening study based on compounds molecular docking analysis, overview. Compounds 5-(acetylamino)-2-[2-(4-isothiocyanato-3-sulfophenyl)ethenyl] benzenesulfonic acid, 6-amino-4-hydroxy-5-[(4-nitro-2-sulfophenyl)azo]-2-naphtalenesulfonic acid, and 6-amino-5-[(4-amino-2-sulfophenyl)azo]-4-hydroxy-2-naphtalenesulfonic acid appear to be important scaffolds for the design of novel APE1 inhibitors. Docking study uses the APE1 enzyme crystal structure, PDB ID 1BIX. All assayed molecules fit well within the APE1-binding site, occupying the pocket defined by the amino acids Asp70, Glu96, Arg177, His309, Asp210, Asn212, Trp280, Phe266, and Leu282. Evaluation of the cytotoxicity of potential APE1 inhibitors in MCF10A cells
-
additional information
-
the enzyme is a promising target for the development of small-molecule inhibitors to be used in combination with anticancer agents, structure-based virtual library screening study based on compounds molecular docking analysis, overview. Compounds 5-(acetylamino)-2-[2-(4-isothiocyanato-3-sulfophenyl)ethenyl] benzenesulfonic acid, 6-amino-4-hydroxy-5-[(4-nitro-2-sulfophenyl)azo]-2-naphtalenesulfonic acid, and 6-amino-5-[(4-amino-2-sulfophenyl)azo]-4-hydroxy-2-naphtalenesulfonic acid appear to be important scaffolds for the design of novel APE1 inhibitors. Docking study uses the APE1 enzyme crystal structure, PDB ID 1BIX. All assayed molecules fit well within the APE1-binding site, occupying the pocket defined by the amino acids Asp70, Glu96, Arg177, His309, Asp210, Asn212, Trp280, Phe266, and Leu282. Evaluation of the cytotoxicity of potential APE1 inhibitors in MCF10A cells
-
additional information
bis-naphthalene macrocycles, which bind with high affinity and selectivity to abasic sites in DNA, efficiently inhibit their cleavage by APE1 (IC50 value is 55-60 nM in the kinetic assay with a model THF substrate). Substrate masking by non-covalent abasic-site ligands is an efficient strategy for inhibition of APE1. Inhibition of abasic site-specific endonuclease activity of nuclear extracts and gel-based assays for APE1 inhibition
-
additional information
-
bis-naphthalene macrocycles, which bind with high affinity and selectivity to abasic sites in DNA, efficiently inhibit their cleavage by APE1 (IC50 value is 55-60 nM in the kinetic assay with a model THF substrate). Substrate masking by non-covalent abasic-site ligands is an efficient strategy for inhibition of APE1. Inhibition of abasic site-specific endonuclease activity of nuclear extracts and gel-based assays for APE1 inhibition
-
additional information
association of APE1 with undamaged DNA reduces effective concentration of the enzyme and subsequently decreases APE1-catalyzed cleavage rates on long DNA substrates
-
additional information
-
association of APE1 with undamaged DNA reduces effective concentration of the enzyme and subsequently decreases APE1-catalyzed cleavage rates on long DNA substrates
-
additional information
preparation of modified oligonucleotide derivatives as unreactive substrate analogues of human apurinic/apyrimidinic endonuclease APE1 for rational design of enzyme inhibitors or as potential APE1 inhibitors themselves. The 3'-terminal internucleotide phosphate group is chemically modified by the replacement of its oxygen atom by either a sulphur or a Tmg group to make the phosphate resistant to the exonuclease activity of the enzyme. Instead of the natural AP-site, the oligonucleotides incorporate its chemically stable analogue (2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran (F-site). It is known that such a substitution scarcely affects the activity of APE1. Structure of the F-site and chemical modifications of the phosphate group on its 5'-side that are resistant to APE1 hydrolysis, overview. The endonuclease activity of APE1 is considerably retarded for DNA duplexes containing phosphate modifications on the 5'-side of the F-site. But analysis of the products of chain scission of those duplexes reveals that some 3'-5'-exonuclease reaction, that removes the 3'-terminal nucleotide, also occurs. To suppress the removal of the 3'-terminal nucleotide from the model oligonucleotides, their 3'-terminal internucleotide phosphate group is modified. The tetramethyl phosphoryl guanidine group (Tmg) is employed as a nuclease-resistant phosphate group isostere. It is observed that such a modification blocks 3'-5'-exonuclease activity of APE1 for more than 12 h
-
additional information
-
preparation of modified oligonucleotide derivatives as unreactive substrate analogues of human apurinic/apyrimidinic endonuclease APE1 for rational design of enzyme inhibitors or as potential APE1 inhibitors themselves. The 3'-terminal internucleotide phosphate group is chemically modified by the replacement of its oxygen atom by either a sulphur or a Tmg group to make the phosphate resistant to the exonuclease activity of the enzyme. Instead of the natural AP-site, the oligonucleotides incorporate its chemically stable analogue (2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran (F-site). It is known that such a substitution scarcely affects the activity of APE1. Structure of the F-site and chemical modifications of the phosphate group on its 5'-side that are resistant to APE1 hydrolysis, overview. The endonuclease activity of APE1 is considerably retarded for DNA duplexes containing phosphate modifications on the 5'-side of the F-site. But analysis of the products of chain scission of those duplexes reveals that some 3'-5'-exonuclease reaction, that removes the 3'-terminal nucleotide, also occurs. To suppress the removal of the 3'-terminal nucleotide from the model oligonucleotides, their 3'-terminal internucleotide phosphate group is modified. The tetramethyl phosphoryl guanidine group (Tmg) is employed as a nuclease-resistant phosphate group isostere. It is observed that such a modification blocks 3'-5'-exonuclease activity of APE1 for more than 12 h
-
additional information
analysis of enzyme activity and kinetics with DNA substrates comprising duplexes of deoxyribonucleotides with one 5'-dangling end that contain a fluorescent 2-aminopurine residue at the 1st, 2nd, 4th, or 6th position from the 3'-end of the short oligonucleotide. The impact of the 3'-end nucleotide, which contains mismatched, undamaged bases or modified bases as well as an abasic site or phosphate group, on the efficiency of 3'-5'-exonuclease activity is determined
-
additional information
-
analysis of enzyme activity and kinetics with DNA substrates comprising duplexes of deoxyribonucleotides with one 5'-dangling end that contain a fluorescent 2-aminopurine residue at the 1st, 2nd, 4th, or 6th position from the 3'-end of the short oligonucleotide. The impact of the 3'-end nucleotide, which contains mismatched, undamaged bases or modified bases as well as an abasic site or phosphate group, on the efficiency of 3'-5'-exonuclease activity is determined
-
additional information
while a clamp-specific inhibitor can disrupt the beta-clamp-XthA complex, a proliferating cell nuclear antigen (PCNA)-specific inhibitor is not able to do so
-
additional information
-
inhibition at high ionic strength, factor 5 at 500 mM
-
additional information
-
exposing neuronal cultures to Api1 small interfering RNA significantly reduces the expression of Api1
-
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0.004
(dA)230*(dT,dU)230
-
ratio dT:dU is 15, partially depyrimidinated by uracil-DNA glycosylase, pH 8
-
0.065
1-amino-4-(4-{(E)-[(4E)-6-chloro-4-[(3-sulfophenyl)imino]-3,4-dihydro-1,3,5-triazin-2(1H)-ylidene]amino}-3-sulfoanilino)-9,10-dioxo-9,10-dihydroanthracene-2-sulfonic acid
-
-
0.000093 - 0.00022
12-mer oligodeoxyribonucleotide containing a natural AP site
-
0.000098
12-mer oligodeoxyribonucleotide containing a tetrahydrofuran analogue at the natural AP site
-
wild-type, pH 7.5, 25°C
-
0.000048 - 0.000081
18-mer containing P33-labeled tetrahydrofuran
-
0.0000262
26-bp-oligonucleotide
pH 7.5, 37°C
-
0.000015
30mer THF-T duplex
pH 8.0, 37°C, recombinant His-tagged enzyme
-
0.0000091 - 0.14
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite A
-
0.0000036 - 0.000133
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite G
-
0.0000097 - 0.004
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite A
-
0.0000059 - 0.00192
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite G
-
0.000011 - 0.0000218
37mer with AP/A
-
0.000037 - 0.000046
37mer with AP/C
-
0.0000064 - 0.000025
37mer with AP/G
-
0.0000067 - 0.0000094
37mer with AP/T
-
0.00016 - 0.000227
37mer with dihydrouridine
-
0.0000034 - 0.0000278
43-mer oligonucleotide containing apurinic/apyrimidinic sites
-
0.0000368 - 0.0000536
43-mer oligonucleotide containing the AP-site analog THF at nt 31
-
0.0000035 - 0.0014
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
0.00058 - 0.0013
5'-CTCTCCCTTC-8-oxo-7,8-dihydroguanine-CTCCTTTCCTCT-3'
0.0000642 - 0.000424
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
-
0.0000023 - 0.00024
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
0.0000023 - 0.00021
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
0.00082 - 0.00091
5'-TCGAGGATCCTGAGCTCGAGTCGACGXTCGCGAATTCTGCGGATCCAAGC-3'
-
0.00003
alkylated-depurinated DNA
-
pH 8
-
0.000088 - 0.011
AP-DNA
-
0.0000238
AP-DNA-DNA
-
1 mM Mg2+
-
0.0000057
AP-DNA-RNA
-
1 mM Mg2+
-
0.0061
CAAXACCTTCATCCTTTCC
-
ssDNA, X: AP site, pH 7.5, 37°C
0.0075
CAXAACCTTCATCCTTTCC
-
ssDNA, X: AP site, pH 7.5, 37°C
0.013
CTAGTCAXCACTGTCTGTGGATAC
-
ssDNA, X: AP site, pH 7.5, 37°C
0.0091
CXAAACCTTCATCCTTTCC
-
ssDNA, X = AP site, pH 7.5, 37°C
0.00028
cytosine-labeled DNA
-
-
-
0.00005
DNA containing 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine/C
-
pH 7.5, 37°C
-
0.000023 - 0.000038
DNA containing 5,6-dihydrothymidine/A
-
0.000026 - 0.000316
DNA containing 5-hydroxy-2'-deoxyuridine/G
-
0.00000007 - 0.0000035
DNA containing 5-OH-C/A
-
0.000000048 - 0.0000012
DNA containing 5-OH-C/G
-
100 - 413
DNA containing an abasic site
0.0000027 - 0.00062
DNA containing apurinic site
-
0.00000052 - 0.008
DNA containing apurinic sites
-
0.0000213
DNA containing apurinic/apyrimidinic site
-
pH 7.6, room temperature
-
0.000000083 - 0.000028
DNA containing apurinic/apyrimidinic sites
-
0.000069 - 0.00017
DNA containing dihydrouracil
-
0.000103
DNA containing dihydrouridine/G
-
pH 7.5, 37°C
-
0.00000167
DNA containing O-benzylhydroxylamine
-
pH 7.5
-
0.00000284
DNA containing O-methylhydroxylamine
-
pH 7.5
-
0.0000009 - 0.0000013
DNA containing tetrahydrofuranyl/G
-
0.0000002 - 0.0000015
DNA containing thymine glycol
-
0.00000056
DNA containing urea
-
pH 7.5, 30°C
-
0.00025
DNA with 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine/C
-
pH 7.5, 37°C
0.000098
DNA with 2-deoxyribonolactone
-
pH 7.6, room temperature
-
0.000024
double-stranded DNA with abasic sites
-
-
-
0.0000084
duplex oligonucleotide containing a 5,6-dihydro-2'-deoxyuridine*G pair
-
pH 6.8, 37°C, nucleotide incison repair activity
-
0.0000072
duplex oligonucleotide containing a alpha-2'-deoxyadenosine*T pair
-
pH 6.8, 37°C, nucleotide incison repair activity
-
0.0000027
duplex oligonucleotide containing a tetrahydrofuran*G pair
-
pH 6.8, 37°C, nucleotide incison repair activity
-
0.0163
GTACGTAXCCACAGACAGTGATGA
-
ssDNA, X: AP site, pH 7.5, 37°C
0.00005 - 0.0013
oligomer with G/U pair
-
0.000428
single-stranded DNA with abasic sites
-
-
-
0.000136 - 0.0002
THF-containing oligonucleotide
-
0.000015
thymidine-labeled DNA
-
-
-
additional information
AP-DNA
-
0.000093
12-mer oligodeoxyribonucleotide containing a natural AP site
-
wild-type, pH 7.5, 25°C
-
0.00022
12-mer oligodeoxyribonucleotide containing a natural AP site
-
mutant Y171F/P173L/N174K, pH 7.5, 25°C
-
0.000048
18-mer containing P33-labeled tetrahydrofuran
-
enzyme dephosphorylated by lambda phosphatase, pH 7.5, 22°C
-
0.000081
18-mer containing P33-labeled tetrahydrofuran
-
enzyme phosphorylated by casein kinase II, pH 7.5, 22°C
-
0.0000091
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite A
-
pH 7.6, 37°C, wild-type enzyme
-
0.14
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite A
-
pH 7.6, 37°C, mutant enzyme R184A
-
0.0000036
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite G
-
pH 7.6, 37°C, wild-type enzyme
-
0.000133
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite G
-
pH 7.6, 37°C, mutant enzyme R184A
-
0.0000097
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite A
-
pH 7.6, 37°C, wild-type enzyme
-
0.004
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite A
-
pH 7.6, 37°C, mutant enzyme R184A
-
0.0000059
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite G
-
pH 7.6, 37°C, wild-type enzyme
-
0.00192
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite G
-
pH 7.6, 37°C, mutant enzyme R184A
-
0.000011
37mer with AP/A
-
pH 6.8, 37°C, Ntg1p
-
0.0000218
37mer with AP/A
-
pH 6.8, 37°C, Ntg2p
-
0.000037
37mer with AP/C
-
pH 6.8, 37°C, Ntg1p
-
0.000046
37mer with AP/C
-
pH 6.8, 37°C, Ntg2p
-
0.0000064
37mer with AP/G
-
pH 6.8, 37°C, Ntg2p
-
0.000025
37mer with AP/G
-
pH 6.8, 37°C, Ntg1p
-
0.0000067
37mer with AP/T
-
pH 6.8, 37°C, Ntg1p
-
0.0000094
37mer with AP/T
-
pH 6.8, 37°C, Ntg2p
-
0.00016
37mer with dihydrouridine
-
pH 6.8, 37°C, Scr2
-
0.000227
37mer with dihydrouridine
-
pH 6.8, 37°C, Scr1
-
0.0000034
43-mer oligonucleotide containing apurinic/apyrimidinic sites
37°C, wild-type enzyme
-
0.0000136
43-mer oligonucleotide containing apurinic/apyrimidinic sites
37°C, mutant enzyme N226A
-
0.0000184
43-mer oligonucleotide containing apurinic/apyrimidinic sites
37°C, mutant enzyme N229A
-
0.0000278
43-mer oligonucleotide containing apurinic/apyrimidinic sites
37°C, mutant enzyme N226A/N229A
-
0.0000368
43-mer oligonucleotide containing the AP-site analog THF at nt 31
-
wild-type, presence of 2 mM Mg2+
-
0.0000536
43-mer oligonucleotide containing the AP-site analog THF at nt 31
-
mutant C99S, presence of 2 mM Mg2+
-
0.0000035
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite T
0.0000066
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite C
0.0000085
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite G
0.000038
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant QLY/AAA, Nei placed opposite A
0.000042
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant QLY/AAA, Nei placed opposite G
0.000054
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant deltaQLY, Nei placed opposite G
0.000077
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant Q261A, Nei placed opposite G
0.00014
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant QLY/AAA, Nei placed opposite C
0.00016
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant QLY/AAA, Nei placed opposite T
0.00016
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite A
0.00026
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant Q261A, Nei placed opposite A
0.00027
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant Q261A, Nei placed opposite C
0.0014
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant Q261A, Nei placed opposite T
0.00058
5'-CTCTCCCTTC-8-oxo-7,8-dihydroguanine-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite G
0.00061
5'-CTCTCCCTTC-8-oxo-7,8-dihydroguanine-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite A
0.00068
5'-CTCTCCCTTC-8-oxo-7,8-dihydroguanine-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite C
0.0013
5'-CTCTCCCTTC-8-oxo-7,8-dihydroguanine-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite T
0.0000642
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
-
native enzyme
-
0.000424
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
-
recombinant enzyme
-
0.0000023
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite G
0.0000032
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite A
0.0000044
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite C
0.0000044
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite T
0.000049
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
mutant QLY/AAA, Nei placed opposite G
0.000066
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
mutant deltaQLY, Nei placed opposite A
0.00019
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
mutant QLY/AAA, Nei placed opposite T
0.00024
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
mutant Q261A, Nei placed opposite G
0.0000023
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite G
0.0000046
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite T
0.0000047
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite C
0.000016
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite A
0.00021
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
mutant Q261A, Nei placed opposite G
0.00082
5'-TCGAGGATCCTGAGCTCGAGTCGACGXTCGCGAATTCTGCGGATCCAAGC-3'
pH 7.5, 37°C
-
0.00091
5'-TCGAGGATCCTGAGCTCGAGTCGACGXTCGCGAATTCTGCGGATCCAAGC-3'
pH 7.5, 37°C
-
0.000088
AP-DNA
-
wild-type in rAP-containing oligonucleotide cleavage assay
-
0.00012
AP-DNA
-
mutant Y72F in rAP-containing oligonucleotide cleavage assay
-
0.0075
AP-DNA
-
mutant Y72A in rAP-containing oligonucleotide cleavage assay
-
0.011
AP-DNA
-
mutant R37A in rAP-containing oligonucleotide cleavage assay
-
0.000884
DNA
-
LMAP mutant A138D, 3'-phosphodiesterase activity
0.001365
DNA
-
LMAP, 3'-phosphodiesterase activity
0.001587
DNA
-
APE1 mutant D70A, 3'-phosphodiesterase activity
0.001689
DNA
-
APE1, 3'-phosphodiesterase activity
0.000023
DNA containing 5,6-dihydrothymidine/A
-
pH 7.5, 37°C
-
0.000038
DNA containing 5,6-dihydrothymidine/A
-
pH 7.5, 37°C
-
0.000026
DNA containing 5-hydroxy-2'-deoxyuridine/G
-
pH 7.5, 37°C
-
0.000316
DNA containing 5-hydroxy-2'-deoxyuridine/G
-
pH 7.5, 37°C
-
0.00000007
DNA containing 5-OH-C/A
-
wild-type, pH 7.5, 37°C, presence of EDTA
-
0.00000014
DNA containing 5-OH-C/A
-
P211R mutant, pH 7.5, 37°C, presence of Mg2+
-
0.0000002
DNA containing 5-OH-C/A
-
P211R mutant, pH 7.5, 37°C, presence of EDTA
-
0.0000002
DNA containing 5-OH-C/A
-
wild-type, pH 7.5, 37°C, presence of Mg2+
-
0.0000017
DNA containing 5-OH-C/A
-
G212 mutant, pH 7.5, 37°C, presence of Mg2+
-
0.0000035
DNA containing 5-OH-C/A
-
G212 mutant, pH 7.5, 37°C, presence of EDTA
-
0.000000048
DNA containing 5-OH-C/G
-
P211R mutant, pH 7.5, 37°C, presence of Mg2+
-
0.00000005
DNA containing 5-OH-C/G
-
wild-type, pH 7.5, 37°C, presence of Mg2+ or EDTA
-
0.00000009
DNA containing 5-OH-C/G
-
P211R mutant, pH 7.5, 37°C, presence of EDTA
-
0.000001
DNA containing 5-OH-C/G
-
G212 mutant, pH 7.5, 37°C, presence of EDTA
-
0.0000012
DNA containing 5-OH-C/G
-
G212 mutant, pH 7.5, 37°C, presence of Mg2+
-
100
DNA containing an abasic site
-
pH 7.5, wild-type enzyme, low salt concentration (82 mM NaCl)
108
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y128A, high salt concentration (150 mM NaCl)
110
DNA containing an abasic site
-
pH 7.5, wild-type enzyme, high salt concentration (150 mM NaCl)
140
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y128A, low salt concentration (82 mM NaCl)
165
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y269A, low salt concentration (82 mM NaCl)
255
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y171F, low salt concentration (82 mM NaCl)
310
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y171A, high salt concentration (150 mM NaCl)
360
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y171A, low salt concentration (82 mM NaCl)
413
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y269A, high salt concentration (150 mM NaCl)
0.0000027
DNA containing apurinic site
-
37°C, pH 8
-
0.000075 - 0.00062
DNA containing apurinic site
-
dsDNA, pH 7.5, 37°C
-
0.00000052
DNA containing apurinic sites
-
pH 7.5, 30°C
-
0.008
DNA containing apurinic sites
-
-
-
0.000000083
DNA containing apurinic/apyrimidinic sites
wild-type, Nei placed opposite A
-
0.00000011
DNA containing apurinic/apyrimidinic sites
wild-type, Nei placed opposite G
-
0.000022
DNA containing apurinic/apyrimidinic sites
mutant QLY/AAA, Nei placed opposite G
-
0.000028
DNA containing apurinic/apyrimidinic sites
mutant QLY/AAA, Nei placed opposite A
-
0.000069
DNA containing dihydrouracil
wild-type, pH 8, 37°C
-
0.00017
DNA containing dihydrouracil
K212R mutant, pH 8, 37°C
-
0.0000009
DNA containing tetrahydrofuranyl/G
-
pH 7.5, 37°C
-
0.0000013
DNA containing tetrahydrofuranyl/G
-
pH 7.5, 37°C
-
0.0000002
DNA containing thymine glycol
-
pH 7.5, 30°C
-
0.0000015
DNA containing thymine glycol
-
pH 7.5
-
0.00005
oligomer with G/U pair
-
D308A mutant, pH 7.5
-
0.0001
oligomer with G/U pair
-
wild-type, pH 7.5
-
0.00012
oligomer with G/U pair
-
D283A mutant, pH 7.5
-
0.00024
oligomer with G/U pair
-
D283/D308A mutant, pH 7.5
-
0.0013
oligomer with G/U pair
-
H309N mutant, pH 7.5
-
0.000136
THF-containing oligonucleotide
-
APE1 mutant D70A, AP endonuclease activity
-
0.000154
THF-containing oligonucleotide
-
Ape1, AP endonuclease activity
-
0.000184
THF-containing oligonucleotide
-
LMAP mutant A138D, AP endonuclease activity
-
0.0002
THF-containing oligonucleotide
-
LMAP, AP endonuclease activity
-
additional information
AP-DNA
-
not detected in mutant E261Q in rAP-containing oligonucleotide cleavage assay
-
additional information
additional information
-
-
-
additional information
additional information
-
-
-
additional information
additional information
steady-state kinetic analysis
-
additional information
additional information
-
steady-state kinetic analysis
-
additional information
additional information
-
Km for AP cleavage is similar to that for 5'-deoxyribose-5-phosphate removal, it explains the relative difference in apurinic/apyrimidinic cleavage observed with the plasmid and apurinic/apyrimidinic duplex oligonucleotide with the former containing a 100fold higher concentration of apurinic/apyrimidinic sites (100 uracil residues per plasmid molecule) than the oligonucleotides-based substrate.
-
additional information
additional information
-
Steady-state kinetic analysis of Ape1 AP endonuclease activity at 10 mM Mg2+ with and without 5 mM ATP indicates a less than 2fold difference in KM-value but an 19fold enhancement in kcat in the presence of ATP, suggesting an enhancement of the catalytic reaction specifically
-
additional information
additional information
kinetic analysis of human 8-oxoguanine-DNA glycosylase activation through APE1, overview
-
additional information
additional information
-
kinetic analysis of human 8-oxoguanine-DNA glycosylase activation through APE1, overview
-
additional information
additional information
kinetic mechanism of 3'-end nucleotide removal in the 3'-5'-exonuclease process catalyzed by APE1 under pre-steady-state conditions, interaction of enzyme APE1 with DNA containing an abasic site, overview
-
additional information
additional information
-
kinetic mechanism of 3'-end nucleotide removal in the 3'-5'-exonuclease process catalyzed by APE1 under pre-steady-state conditions, interaction of enzyme APE1 with DNA containing an abasic site, overview
-
additional information
additional information
measurement of conformational dynamics of DNA at pre-steady-state conditions, stopped-flow measurements. Rate and equilibrium constants for wild-type enzyme and mutant H83A Apn1 interactions with DNA substrates F(2-aPu) and AP(2-aPu), F is tetrahydrofuran
-
additional information
additional information
-
measurement of conformational dynamics of DNA at pre-steady-state conditions, stopped-flow measurements. Rate and equilibrium constants for wild-type enzyme and mutant H83A Apn1 interactions with DNA substrates F(2-aPu) and AP(2-aPu), F is tetrahydrofuran
-
additional information
additional information
Michaelis-Menten kinetic study, overview
-
additional information
additional information
-
Michaelis-Menten kinetic study, overview
-
additional information
additional information
pKa calculations
-
additional information
additional information
pre-steady-state kinetic analysis of structural rearrangements of the DNA substrates and uncleavable ligands during their interaction with Endo III
-
additional information
additional information
-
pre-steady-state kinetic analysis of structural rearrangements of the DNA substrates and uncleavable ligands during their interaction with Endo III
-
additional information
additional information
pre-steady-state kinetic analysis, kinetic analysis of DNA binding, stopped flow measurements, overview
-
additional information
additional information
-
pre-steady-state kinetic analysis, kinetic analysis of DNA binding, stopped flow measurements, overview
-
additional information
additional information
rate constants of DNA substrate cleavage by APE1 and dissociation constants of APE1/DNA substrate complexes. Analysis of efficacy of APE1 binding to modified DNA duplexes and kinetics of enzyme-substrate complex formation by stopped flow measurements, kinetics, overview
-
additional information
additional information
-
rate constants of DNA substrate cleavage by APE1 and dissociation constants of APE1/DNA substrate complexes. Analysis of efficacy of APE1 binding to modified DNA duplexes and kinetics of enzyme-substrate complex formation by stopped flow measurements, kinetics, overview
-
additional information
additional information
stopped-flow fluorescence measurements, kinetic analysis of nucleotide incision repair (NIR) pathway compared to base excision DNA repair (BER) pathway. Rate constants of wild-type Apn1 interaction with substrate DHU(2-aPu), overview. Proposed kinetic mechanisms, containing two or three binding steps, for the interaction of wild-type Apn1 with substrate DHU(2-aPu)
-
additional information
additional information
stopped-flow fluorescence techniques to conduct a comparative kinetic analysis of the conformational transitions in human apurinic/apyrimidinic endonuclease 1 (APE1) and in DNA containing an abasic site in the course of their interaction. Influence of different concentrations of Mg2+ and other metal ions on stopped-flow kinetics, overview
-
additional information
additional information
-
stopped-flow fluorescence techniques to conduct a comparative kinetic analysis of the conformational transitions in human apurinic/apyrimidinic endonuclease 1 (APE1) and in DNA containing an abasic site in the course of their interaction. Influence of different concentrations of Mg2+ and other metal ions on stopped-flow kinetics, overview
-
additional information
additional information
steady-state Michaelis-Menten kinetic analysis
-
additional information
additional information
-
steady-state Michaelis-Menten kinetic analysis
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
0.000153 - 2.8
12-mer oligodeoxyribonucleotide containing a natural AP site
-
1
12-mer oligodeoxyribonucleotide containing a tetrahydrofuran analogue at the natural AP site
-
wild-type, pH 7.5, 25°C
-
0.58 - 5.7
18-mer containing P33-labeled tetrahydrofuran
-
0.0005
3'-fluorescein-labeled 5'-AACTTCGTGCAGGCATGGTAG(dU)TTGTCTACT-3'
pH 8, 37°C
-
0.308
30mer THF-T duplex
pH 8.0, 37°C, recombinant His-tagged enzyme
-
0.03 - 1.37
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite A
-
0.043 - 0.17
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite G
-
0.098
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite A
-
0.075 - 1.6
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite G
-
0.0007 - 0.00512
37mer with AP/A
-
0.015 - 0.0225
37mer with AP/C
-
0.00108 - 0.00323
37mer with AP/G
-
0.007 - 0.0233
37mer with AP/T
-
0.00833 - 0.0717
37mer with dihydrouridine
-
0.00417 - 0.00567
4-hydroxy-5-N-methylformamidopyrimidine/C
-
2.91 - 3.36
43-mer oligonucleotide containing the AP-site analog THF at nt 31
-
0.0000048 - 0.07167
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
0.00783 - 0.023
5'-CTCTCCCTTC-8-oxo-7,8-dihydroguanine-CTCCTTTCCTCT-3'
0.0272 - 0.168
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
-
0.0025 - 0.0483
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
0.00567 - 0.0567
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
3.2 - 4.2
5'-TCGAGGATCCTGAGCTCGAGTCGACGXTCGCGAATTCTGCGGATCCAAGC-3'
-
0.0117 - 0.0158
DNA containing 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine/C
-
0.00333
DNA containing 5,6-dihydrothymidine/A
-
pH 7.5, 37°C
-
0.0267
DNA containing 5-hydroxy-2'-deoxyuridine/G
-
pH 7.5, 37°C
-
0.000035 - 0.0005
DNA containing 5-OH-C/A
-
0.000233 - 0.00117
DNA containing 5-OH-C/G
-
0.0007 - 10
DNA containing an abasic site
2.4
DNA containing apurinic/apyrimidinic site
-
pH 7.6, room temperature
-
0.0015 - 10
DNA containing apurinic/apyrimidinic sites
-
0.0000567 - 0.002
DNA containing dihydrouracil
-
0.01 - 0.0283
DNA containing tetrahydrofuranyl/G
-
2.3
DNA with 2-deoxyribonolactone
-
pH 7.6, room temperature
-
4.1
double-stranded DNA with abasic sites
-
-
-
0.0027
duplex oligonucleotide containing a 5,6-dihydro-2'-deoxyuridine*G pair
-
pH 6.8, 37°C, necleotide incison repair activity
-
0.002
duplex oligonucleotide containing a alpha-2'-deoxyadenosine*T pair
-
pH 6.8, 37°C,nucleotide incison repair activity
-
0.002
duplex oligonucleotide containing a tetrahydrofuran*G pair
-
pH 6.8, 37°C, nucleotide incison repair activity
-
0.0003 - 10
oligomer with G/U pair
-
4.2
single-stranded DNA with abasic sites
-
-
-
1020 - 19260
THF-containing oligonucleotide
-
additional information
AP-DNA
-
0.000153
12-mer oligodeoxyribonucleotide containing a natural AP site
-
mutant Y171F/P173L/N174K, pH 7.5, 25°C
-
2.8
12-mer oligodeoxyribonucleotide containing a natural AP site
-
wild-type, pH 7.5, 25°C
-
0.58
18-mer containing P33-labeled tetrahydrofuran
-
enzyme phosphorylated by casein kinase II, pH 7.5, 22°C
-
5.7
18-mer containing P33-labeled tetrahydrofuran
-
enzyme dephosphorylated by lambda phosphatase, pH 7.5, 22°C
-
0.03
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite A
-
pH 7.6, 37°C, wild-type enzyme
-
1.37
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite A
-
pH 7.6, 37°C, mutant enzyme R184A
-
0.043
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite G
-
pH 7.6, 37°C, wild-type enzyme
-
0.17
35 base pair oligonucleotide containing 5,6-dihydrouracil opposite G
-
pH 7.6, 37°C, mutant enzyme R184A
-
0.098
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite A
-
pH 7.6, 37°C, wild-type enzyme
-
0.098
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite A
-
pH 7.6, 37°C, mutant enzyme R184A
-
0.075
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite G
-
pH 7.6, 37°C, wild-type enzyme
-
1.6
35 base pair oligonucleotide containing 5,6-dihydroxy-5,6-dihydrothymine opposite G
-
pH 7.6, 37°C, mutant enzyme R184A
-
0.0007
37mer with AP/A
-
pH 6.8, 37°C, Ntg1p
-
0.00512
37mer with AP/A
-
pH 6.8, 37°C, Ntg2p
-
0.015
37mer with AP/C
-
pH 6.8, 37°C, Ntg2p
-
0.0225
37mer with AP/C
-
pH 6.8, 37°C, Ntg1p
-
0.00108
37mer with AP/G
-
pH 6.8, 37°C, Ntg1p
-
0.00323
37mer with AP/G
-
pH 6.8, 37°C, Ntg2p
-
0.007
37mer with AP/T
-
pH 6.8, 37°C, Ntg1p
-
0.0233
37mer with AP/T
-
pH 6.8, 37°C, Ntg2p
-
0.00833
37mer with dihydrouridine
-
pH 6.8, 37°C, Scr2
-
0.0717
37mer with dihydrouridine
-
pH 6.8, 37°C, Scr1
-
0.00417
4-hydroxy-5-N-methylformamidopyrimidine/C
-
pH 7.5, 37°C
-
0.00567
4-hydroxy-5-N-methylformamidopyrimidine/C
-
pH 7.5, 37°C
-
2.91
43-mer oligonucleotide containing the AP-site analog THF at nt 31
-
mutant C99S, presence of 2 mM Mg2+
-
3.36
43-mer oligonucleotide containing the AP-site analog THF at nt 31
-
wild-type, presence of 2 mM Mg2+
-
0.0000048
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant deltaQLY, Nei placed opposite G
0.000013
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant Q261A, Nei placed opposite C
0.000015
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant Q261A, Nei placed opposite G
0.000023
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant Q261A, Nei placed opposite A
0.000065
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant QLY/AAA, Nei placed opposite G
0.000067
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant Q261A, Nei placed opposite T
0.00007167
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant QLY/AAA, Nei placed opposite A
0.000583
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite A
0.003167
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite T
0.008167
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite C
0.01167
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant QLY/AAA, Nei placed opposite T
0.013
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
mutant QLY/AAA, Nei placed opposite C
0.07167
5'-CTCTCCCTTC-5,6-dihydrouracil-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite G
0.00783
5'-CTCTCCCTTC-8-oxo-7,8-dihydroguanine-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite A
0.01317
5'-CTCTCCCTTC-8-oxo-7,8-dihydroguanine-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite G
0.01583
5'-CTCTCCCTTC-8-oxo-7,8-dihydroguanine-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite C
0.023
5'-CTCTCCCTTC-8-oxo-7,8-dihydroguanine-CTCCTTTCCTCT-3'
wild-type, Nei placed opposite T
0.0272
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
-
recombinant enzyme
-
0.168
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
-
native enzyme
-
0.0025
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
mutant deltaQLY, Nei placed opposite A
0.00583
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
mutant Q261A, Nei placed opposite G
0.016
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
mutant QLY/AAA, Nei placed opposite G
0.02167
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
mutant QLY/AAA, Nei placed opposite T
0.03
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite G
0.035
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite A
0.04167
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite C
0.0483
5'-GACAAGCGCAG-(5R,6S)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite T
0.00567
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
mutant Q261A, Nei placed opposite G
0.0112
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite T
0.0115
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite C
0.023
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite A
0.0567
5'-GACAAGCGCAG-(5S,6R)-2'-deoxy-5,6-dihydroxyuridine-CAGCCGAACAC-3'
wild-type, Nei placed opposite G
3.2
5'-TCGAGGATCCTGAGCTCGAGTCGACGXTCGCGAATTCTGCGGATCCAAGC-3'
pH 7.5, 37°C
-
4.2
5'-TCGAGGATCCTGAGCTCGAGTCGACGXTCGCGAATTCTGCGGATCCAAGC-3'
pH 7.5, 37°C
-
72
AP-DNA
-
mutant Y72A
-
354
AP-DNA
-
mutant Y72F
-
7680
AP-DNA
-
mutant R37A
-
1140
DNA
-
LMAP mutant A138D, 3'-phosphodiesterase activity
2340
DNA
-
Ape1, 3'-phosphodiesterase activity
10440
DNA
-
LMAP, 3'-phosphodiesterase activity
16440
DNA
-
Ape mutant D70A, 3'-phosphodiesterase activity
0.0117
DNA containing 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine/C
-
pH 7.5, 37°C
-
0.0158
DNA containing 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine/C
-
pH 7.5, 37°C
-
0.000035
DNA containing 5-OH-C/A
-
+ G 212 mutant, pH 7.5, 37°C, presence of Mg2+
-
0.0000667
DNA containing 5-OH-C/A
-
+ G 212 mutant, pH 7.5, 37°C, presence of EDTA
-
0.0001
DNA containing 5-OH-C/A
-
P211R mutant, pH 7.5, 37°C, presence of Mg2+
-
0.000333
DNA containing 5-OH-C/A
-
wild-type, pH 7.5, 37°C, presence of Mg2+
-
0.0005
DNA containing 5-OH-C/A
-
P211R mutant, pH 7.5, 37°C, presence of EDTA
-
0.0005
DNA containing 5-OH-C/A
-
wild-type, pH 7.5, 37°C, presence of EDTA
-
0.000233
DNA containing 5-OH-C/G
-
+ G 212 mutant, pH 7.5, 37°C, presence of Mg2+
-
0.0005
DNA containing 5-OH-C/G
-
P211R mutant, pH 7.5, 37°C, presence of Mg2+
-
0.000583
DNA containing 5-OH-C/G
-
P211R mutant, pH 7.5, 37°C, presence of EDTA
-
0.000667
DNA containing 5-OH-C/G
-
wild-type, pH 7.5, 37°C, presence of EDTA
-
0.000833
DNA containing 5-OH-C/G
-
wild-type, pH 7.5, 37°C, presence of Mg2+
-
0.00117
DNA containing 5-OH-C/G
-
+ G 212 mutant, pH 7.5, 37°C, presence of EDTA
-
0.0007
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y171A, high salt concentration (150 mM NaCl)
0.0008
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y171A, low salt concentration (82 mM NaCl)
0.0009
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y171F, low salt concentration (82 mM NaCl)
0.2
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y128A, high salt concentration (150 mM NaCl)
0.3
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y269A, high salt concentration (150 mM NaCl)
0.5
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y128A, low salt concentration (82 mM NaCl)
1.3
DNA containing an abasic site
-
pH 7.5, mutant enzyme Y269A, low salt concentration (82 mM NaCl)
1.6
DNA containing an abasic site
-
pH 7.5, wild-type enzyme, high salt concentration (150 mM NaCl)
10
DNA containing an abasic site
-
pH 7.5, wild-type enzyme, low salt concentration (82 mM NaCl)
0.0015
DNA containing apurinic/apyrimidinic sites
mutant QLY/AAA, Nei placed opposite A
-
0.00183
DNA containing apurinic/apyrimidinic sites
mutant QLY/AAA, Nei placed opposite G
-
0.00883
DNA containing apurinic/apyrimidinic sites
wild-type, Nei placed opposite G
-
0.01067
DNA containing apurinic/apyrimidinic sites
wild-type, Nei placed opposite A
-
10
DNA containing apurinic/apyrimidinic sites
-
5' cleavage of a reduced AP site
-
0.0000567
DNA containing dihydrouracil
K212R mutant, pH 8, 37°C
-
0.002
DNA containing dihydrouracil
wild-type, pH 8, 37°C
-
0.01
DNA containing tetrahydrofuranyl/G
-
pH 7.5, 37°C
-
0.0283
DNA containing tetrahydrofuranyl/G
-
pH 7.5, 37°C
-
0.0003
oligomer with G/U pair
-
H309N mutant, pH 7.5
-
0.02
oligomer with G/U pair
-
D283/D308A mutant, pH 7.5
-
0.3
oligomer with G/U pair
-
D283A mutant, pH 7.5
-
1.2
oligomer with G/U pair
-
D308A mutant, pH 7.5
-
10
oligomer with G/U pair
-
wild-type, pH 7.5
-
1020
THF-containing oligonucleotide
-
APE1 mutant D70A, AP endonuclease activity
-
6300
THF-containing oligonucleotide
-
LMAP mutant A138D, AP endonuclease activity
-
12120
THF-containing oligonucleotide
-
APE1, AP endonuclease activity
-
19260
THF-containing oligonucleotide
-
LMAP, AP endonuclease activity
-
additional information
AP-DNA
-
not detected in mutant E261Q
-
additional information
additional information
-
wild-type APE1 cleaves AP sites more efficiently than D70A mutant with a kcat value for the incision of an AP site aproximately 10fold higher
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
0.00028
(2E)-2-(3,4-dihydroxybenzoyl)-3-(3,4-dihydroxyphenyl)prop-2-enenitrile
Homo sapiens
pH and temperature not specified in the publication
0.001
(2E)-2-methyl-3-[3-(methylsulfanyl)-1,4-dioxo-1,4-dihydronaphthalen-2-yl]prop-2-enoic acid
Homo sapiens
pH and temperature not specified in the publication
0.001
(2E)-2-[(3-bromo-1,4-dioxo-1,4-dihydronaphthalen-2-yl)methylidene]-4-methoxybutanoic acid
Homo sapiens
pH and temperature not specified in the publication
0.003
(2E)-2-[(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-yl)methylidene]-4-methoxybutanoic acid
Homo sapiens
pH and temperature not specified in the publication
0.0085
(2E)-2-[(4,5-dimethoxy-2-methyl-3,6-dioxocyclohexa-1,4-dien-1-yl)methylidene]-N-methoxydodecanamide
Homo sapiens
pH and temperature not specified in the publication
0.01
(2E)-2-[(4,5-dimethoxy-2-methyl-3,6-dioxocyclohexa-1,4-dien-1-yl)methylidene]dodecanoic acid
Homo sapiens
pH and temperature not specified in the publication
0.003
(2E)-3-(1,4-dioxo-1,4-dihydronaphthalen-2-yl)-2-methylprop-2-enoic acid
Homo sapiens
pH and temperature not specified in the publication
0.003
(2E)-3-(2-chloro-4,5-dimethoxy-3,6-dioxocyclohexa-1,4-dien-1-yl)-2-methylprop-2-enoic acid
Homo sapiens
pH and temperature not specified in the publication
0.002
(2E)-3-(3-bromo-1,4-dioxo-1,4-dihydronaphthalen-2-yl)-2-methylprop-2-enoic acid
Homo sapiens
pH and temperature not specified in the publication
0.001
(2E)-3-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-yl)-2-methylprop-2-enoic acid
Homo sapiens
pH and temperature not specified in the publication
0.001
(2E)-3-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-yl)-N-(2-hydroxyethyl)-2-methylprop-2-enamide
Homo sapiens
pH and temperature not specified in the publication
0.001
(2E)-3-(3-methoxy-1,4-dioxo-1,4-dihydronaphthalen-2-yl)-2-methylprop-2-enoic acid
Homo sapiens
pH and temperature not specified in the publication
0.0002
(2E)-3-[3-[dihydroxy(oxido)-lambda5-stibanyl]phenyl]prop-2-enoic acid
Homo sapiens
pH and temperature not specified in the publication
0.002
(2R)-1-(1-benzofuran-2-yl)-2-(1,3-benzothiazol-2-yl)-2-hydroxyethanone
Homo sapiens
pH and temperature not specified in the publication
0.0014
(3-chloro-1-benzothiophen-2-yl)[(2Z)-2-[(2-chlorophenyl)imino]-4-methylidene-3-thia-1-azaspiro[4.5]dec-1-yl]methanone
Homo sapiens
pH and temperature not specified in the publication
0.0018
(3a'S,6a'R)-5'-(1,3-benzodioxol-5-ylmethyl)-3'-(2-carboxyethyl)-7-chloro-2,4',6'-trioxo-1,2,3',3a',4',5',6',6a'-octahydro-2'H-spiro[indole-3,1'-pyrrolo[3,4-c]pyrrol[2]ium]
Homo sapiens
pH and temperature not specified in the publication
0.0028
(5E)-1-(furan-2-ylmethyl)-5-[(2E)-3-(furan-2-yl)prop-2-en-1-ylidene]pyrimidine-2,4,6(1H,3H,5H)-trione
Homo sapiens
pH and temperature not specified in the publication
0.001
(5R)-4-hydroxy-3,5-dimethyl-5-((2S)-3-methylpent-4-en-2-yl)thiophen-2(5H)-one
Homo sapiens
pH and temperature not specified in the publication
0.003
1,3-bis(1,3-benzothiazol-2-ylsulfanyl)propan-2-one
Homo sapiens
pH and temperature not specified in the publication
0.002
1,4-dihydroxy-5,8-bis([2-[(2-hydroxyethyl)amino]ethyl]amino)anthracene-9,10-dione
Homo sapiens
pH and temperature not specified in the publication
0.00025
1-amino-4-[[4-([4-chloro-6-[(4-sulfophenyl)amino]-1,3,5-triazin-2-yl]amino)phenyl]amino]-9,10-dioxo-9,10-dihydroanthracene-2-sulfonic acid
Homo sapiens
pH and temperature not specified in the publication
0.0044
1-methyl-4-[(1E)-1-[2-(6-methyl[1,3]dioxolo[4,5-g]quinolin-8-yl)hydrazinylidene]ethyl]-2-phenyl-1,2-dihydro-3H-pyrazol-3-one
Homo sapiens
pH and temperature not specified in the publication
0.00008
1-[[2-(ethylamino)ethyl]amino]-4-(hydroxymethyl)-9H-thioxanthen-9-one
Homo sapiens
pH and temperature not specified in the publication
0.005
1-[[2-(ethylamino)ethyl]amino]-4-methyl-9H-thioxanthen-9-one
Homo sapiens
pH and temperature not specified in the publication
0.016
2,2'-(2-oxo-1H-benzimidazole-1,3(2H)-diyl)diacetic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.011
2,2'-(3,7-dioxo-5,7-dihydro-1H,3H-benzo[1,2-c:4,5-c']difuran-1,5-diyl)diacetic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50 mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.008
2,2'-[(6-oxo-6H-benzo[c]chromene-1,3-diyl)bis(oxy)]dipropanoic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.019
2,2'-[(6-phenylpyrimidine-2,4-diyl)disulfanediyl]diacetic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.004
2,2'-[butane-1,4-diylbis(1H-benzimidazole-2,1-diyl)]diacetic acid
0.0021
2,4,9-trimethylbenzo[b][1,8]naphthyridin-5-amine
Homo sapiens
pH and temperature not specified in the publication
0.0021
2,4,9-trimethylpyridino[2,3-b]quinoline-5-ylamine
Homo sapiens
-
-
0.0008
2,4-di-tert-butylphenyl 3-chloro-1-benzothiophene-2-carboxylate
Homo sapiens
pH and temperature not specified in the publication
0.00011
2,5-dihydroxy-DL-tyrosine
Homo sapiens
pH and temperature not specified in the publication
0.009
2-((Z)-2-oxo-3-(4-oxo-2-thioxothiazolidin-5-ylidene)indolin-1-yl)acetic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.002
2-(2,4-dichlorophenyl)-6-nitro-4H-3,1-benzoxazin-4-one
Homo sapiens
pH and temperature not specified in the publication
0.0013
2-(4-chlorophenyl)-4-(2'-fluorobiphenyl-4-yl)-5-methyl-1,3-thiazole
Homo sapiens
pH and temperature not specified in the publication
0.008
2-(5-(2-(2-carboxyphenyl)-1,3-dioxo-2,3-dihydro-1H-isoindol-5-yl)carbonyl-1,3-dioxo-2,3-dihydro-1H-isoindol-2-yl)benzoic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.004
2-(carboxymethyl)-4-([4-[(4-carboxyphenyl)sulfanyl]phenyl]sulfonyl)benzoic acid
Homo sapiens
pH and temperature not specified in the publication
0.0014
2-aminobenzene-1,3,5-trisulfonamide
Homo sapiens
pH and temperature not specified in the publication
0.019
2-methoxy-3-[(3-methoxybenzyl)carbamoyl]benzoic acid
Homo sapiens
pH and temperature not specified in the publication
0.003
2-[(5R)-3-(naphthalen-2-yl)-5-phenyl-2,5-dihydro-1H-pyrazol-1-yl]-2-oxoethyl 5-nitrothiophene-2-carboxylate
Homo sapiens
pH and temperature not specified in the publication
0.003
2-[(5Z)-5-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]-3-phenylpropanoic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.0017
2-[(Z)-(4-hydroxy-3-methylphenyl)(3-methyl-4-methylidenecyclohexa-2,5-dien-1-ylidene)methyl]benzoic acid
Homo sapiens
pH and temperature not specified in the publication
0.003
2-[5-[1-(carboxymethyl)-2-oxo-2,3-dihydro-1H-indol-3-yl]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]-3-phenylpropanoic acid
Homo sapiens
pH and temperature not specified in the publication
0.0002
3,3',4,4',5,5'-hexabromobiphenyl
Homo sapiens
pH and temperature not specified in the publication
0.017
3,3'-(1,3,4-thiadiazole-2,5-diyldisulfanediyl)dipropanoic acid
Homo sapiens
small-molecule inhibitor containing 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.015
3,3'-(2-thioxo-1H-benzimidazole-1,3(2H)-diyl)dipropanoic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.000055
3,3'-[(3-carboxy-4-oxocyclohexa-2,5-dien-1-ylidene)methanediyl]bis(6-hydroxybenzoic acid)
Homo sapiens
pH and temperature not specified in the publication
0.00032
3,5,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-4H-chromen-4-one
Homo sapiens
pH and temperature not specified in the publication
0.0004
3,6,7-trimethoxyphenanthrene-2,5-diol
Homo sapiens
pH and temperature not specified in the publication
0.0004
3,8,9,10-tetrahydroxypyrano[3,2-c]isochromene-2,6-dione
Homo sapiens
pH and temperature not specified in the publication
0.011
3-((3,4-dimethylphenoxy)methyl)furan-2-carboxylic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.027
3-((pyridin-2-ylthio)methyl)benzofuran-2-carboxylic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.004
3-(1-(carboxymethyl)-5-(4-chlorophenyl)-1H-pyrrol-2-yl)propanoic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.009
3-(1-(carboxymethyl)-5-(4-fluorophenyl)-1H-pyrrol-2-yl)propanoic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.009
3-(1-(carboxymethyl)-5-(thiophen-2-yl)-1H-pyrrol-2-yl)propanoic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.012
3-(1-(carboxymethyl)-5-p-tolyl-1H-pyrrol-2-yl)propanoic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.02
3-(2-carboxyethyl)-4-hydroxyquinoline-6-carboxylic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.006
3-(5-((E)-(3-(carboxymethyl)-4-oxo-2-sulfanylidene-1,3-thiazolidin-5-ylidene)methyl)furan-2-yl)benzoic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.018
3-[(3,4-dichlorobenzyl)carbamoyl]-2-methoxybenzoic acid
Homo sapiens
pH and temperature not specified in the publication
0.018
3-[(3,4-dimethoxybenzyl)carbamoyl]-2-methoxybenzoic acid
Homo sapiens
pH and temperature not specified in the publication
0.016
3-[(3-chlorobenzyl)carbamoyl]-2-methoxybenzoic acid
Homo sapiens
pH and temperature not specified in the publication
0.006
3-[(4Z)-4-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-5-oxo-2-thioxoimidazolidin-1-yl]propanoic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.02
3-[(6-amino-9H-purin-8-yl)sulfanyl]propanoic acid
Homo sapiens
small-molecule inhibitor containing 3 H-bond acceptors and 1 negative ionizable feature, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.004
3-[1-(carboxymethyl)-5-(4-chlorophenyl)-1H-pyrrol-2-yl]propanoic acid
Homo sapiens
pH and temperature not specified in the publication
0.015
3-[[4-(carboxymethyl)benzyl]sulfanyl]-8-methyl-5H-[1,2,4]triazino[5,6-b]indole-5-carboxylic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.0017
4'-(2-chloro-6-nitrophenoxy)biphenyl-4-yl 4-tert-butylbenzenesulfonate
Homo sapiens
pH and temperature not specified in the publication
0.0064
4-((2,6,8-trimethylquinolin-4-yl)amino)phenol
Homo sapiens
-
-
0.006
4-((2-carboxyphenoxy)methyl)-2,5-dimethylfuran-3-carboxylic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.01
4-(4-(4-carboxyphenoxy)phenylsulfonyl)benzene-1,2-dioic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.006
4-(4-(4-carboxyphenylsulfonyl)phenyl)sulfanylbenzene-1,2-dioic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. Then, 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.004
4-(4-(4-carboxyphenylthio)phenylsulfonyl)benzene-1,2-dioic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.02
4-([[(3-carboxy-5-methylfuran-2-yl)methyl]sulfanyl]methyl)-5-methylfuran-2-carboxylic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.0068
4-benzyl-1-(3-[[(3-nitrophenyl)sulfonyl]amino]quinoxalin-2-yl)pyridinium
Homo sapiens
pH and temperature not specified in the publication
0.0068
4-[(4Z)-4-([5-[4-chloro-3-(ethoxycarbonyl)phenyl]furan-2-yl]methylidene)-3-methyl-5-oxo-4,5-dihydro-1H-pyrazol-1-yl]benzoic acid
Homo sapiens
pH and temperature not specified in the publication
0.012
4-[(4Z)-4-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-5-oxo-2-thioxoimidazolidin-1-yl]butanoic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.000004
4-[dihydroxy(oxido)-lamba5-stibanyl]-2-nitrobenzoic acid
Homo sapiens
pH and temperature not specified in the publication
0.0005
4-[methyl(nitroso)amino]benzene-1,2-diol
Homo sapiens
pH and temperature not specified in the publication
0.022
4-[[(2-carboxypropyl)sulfanyl]methyl]-5-methylfuran-2-carboxylic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.005
5,5'-[ethane-1,2-diylbis(sulfanediylmethanediyl)]bis(2-methylfuran-3-carboxylic acid)
Homo sapiens
pH and temperature not specified in the publication
0.005
5,5'-[methanediylbis(sulfanediylmethanediyl)]bis(2-methylfuran-3-carboxylic acid)
Homo sapiens
small-molecule inhibitor containing 4 H-bond acceptors and 3 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.016
5-(((tetrahydrofuran-2-yl)methylthio)methyl)-2-methylfuran-3-carboxylic acid
Homo sapiens
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.00025
5-(acetylamino)-2-[(E)-2-(4-isothiocyanato-3-sulfophenyl)ethenyl]benzenesulfonic acid (non-preferred name)
Homo sapiens
pH and temperature not specified in the publication
0.00025
5-(acetylamino)-2-[2-(4-isothiocyanato-3-sulfophenyl)ethenyl] benzenesulfonic acid
Homo sapiens
pH 8.0, 37°C, recombinant enzyme
0.006
5-([[(4-carboxy-5-methylfuran-2-yl)methyl]sulfanyl]methyl)-3-methylfuran-2-carboxylic acid
Homo sapiens
small-molecule inhibitor containing 4 H-bond acceptors and 3 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.00776
6-amino-4-hydroxy-5-[(4-nitro-2-sulfophenyl)azo]-2-naphtalenesulfonic acid
Homo sapiens
pH 8.0, 37°C, recombinant enzyme
0.00776
6-amino-4-hydroxy-5-[(E)-(4-nitro-2-sulfophenyl)diazenyl]naphthalene-2-sulfonic acid
Homo sapiens
pH and temperature not specified in the publication
0.00885
6-amino-5-[(4-amino-2-sulfophenyl)azo]-4-hydroxy-2-naphtalenesulfonic acid
Homo sapiens
pH 8.0, 37°C, recombinant enzyme
0.00885
6-amino-5-[(E)-(4-amino-2-sulfophenyl)diazenyl]-4-hydroxynaphthalene-2-sulfonic acid
Homo sapiens
pH and temperature not specified in the publication
0.0005
6-hydroxy-DL-DOPA
Homo sapiens
-
IC50 less than 0.0005 mM
0.0016
7-chloro-2-(2-fluorophenyl)-4H-3,1-benzoxazin-4-one
Homo sapiens
pH and temperature not specified in the publication
0.0031
7-nitro-1H-indole-2-carboxylic acid
Homo sapiens
pH and temperature not specified in the publication
0.0029
8-[(2E)-2-(1,3-benzodioxol-5-ylmethylidene)hydrazinyl]-6-methyl[1,3]dioxolo[4,5-g]quinoline
Homo sapiens
pH and temperature not specified in the publication
0.0041
8-[(2E)-2-[(9-ethyl-9H-carbazol-3-yl)methylidene]hydrazinyl]-6-methyl[1,3]dioxolo[4,5-g]quinoline
Homo sapiens
pH and temperature not specified in the publication
0.0018
biphenyl-4,4'-diyl bis(3,4-dichlorobenzenesulfonate)
Homo sapiens
pH and temperature not specified in the publication
0.05
ceftriaxone sodium
Homo sapiens
-
IC50 above 0.05 mM
0.05
cephapirin sodium
Homo sapiens
-
IC50 above 0.05 mM
0.000017
ethyl 4-[4-[dihydroxy(oxido)-lambda5-stibanyl]phenyl]butanoate
Homo sapiens
pH and temperature not specified in the publication
0.0005
mitoxanthrone
Homo sapiens
-
IC50 less than 0.0005 mM
0.0005
myricetin
Homo sapiens
-
IC50 less than 0.0005 mM
0.0009
N-(3,5-dichlorophenyl)-4-(2'-fluorobiphenyl-4-yl)-5-methyl-1,3-thiazol-2-amine
Homo sapiens
pH and temperature not specified in the publication
0.0016
N-(3-chlorophenyl)-5,6-dihydro-4H-cyclopenta[d]isoxazole-3-carboxamide
Homo sapiens
-
-
0.0016
N-(3-chlorophenyl)-5,6-dihydro-4H-cyclopenta[d][1,2]oxazole-3-carboxamide
Homo sapiens
pH and temperature not specified in the publication
0.004
N-(9,10-dioxo-9,10-dihydroanthracen-1-yl)-2-(1H-1,2,4-triazol-5-ylsulfanyl)acetamide
Homo sapiens
pH and temperature not specified in the publication
0.0029
N-[3-(1,3-benzothiazol-2-yl)-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl]acetamide
Homo sapiens
pH and temperature not specified in the publication
0.0033
N-[3-(1,3-benzothiazol-2-yl)-5,6-dihydro-4H-thieno[2,3-c]pyrrol-2-yl]acetamide
Homo sapiens
pH and temperature not specified in the publication
0.002
N-[3-(1,3-benzothiazol-2-yl)-6-(propan-2-yl)-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl]acetamide
Homo sapiens
pH and temperature not specified in the publication
0.0029
N-[3-(4-phenyl-1,3-thiazol-2-yl)-6-(propan-2-yl)-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl]acetamide
Homo sapiens
pH and temperature not specified in the publication
0.0003
N-[4-[dihydroxy(oxido)-lambda5-stibanyl]phenyl]benzamide
Homo sapiens
pH and temperature not specified in the publication
0.0005
Reactive blue 2
Homo sapiens
-
IC50 less than 0.0005 mM
0.0071
tetrahydrofuran-2-ylmethyl 6-(furan-2-yl)-3-methyl-4-oxo-4,5,6,7-tetrahydro-1H-indole-2-carboxylate
Homo sapiens
pH and temperature not specified in the publication
0.011
[(3Z)-3-(3-[[(2-hydroxyphenyl)carbonyl]amino]-4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)-2-oxo-2,3-dihydro-1H-indol-1-yl]acetic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.006
[(3Z)-3-[3-(4-bromophenyl)-4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene]-2-oxo-2,3-dihydro-1H-indol-1-yl]acetic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.013
[(5Z)-5-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid
Homo sapiens
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.0017
[4-(2,5-dimethyl-1H-pyrrol-1-yl)phenoxy]acetic acid
additional information
additional information
-
0.004
2,2'-[butane-1,4-diylbis(1H-benzimidazole-2,1-diyl)]diacetic acid
Homo sapiens
small-molecule inhibitor containing 4 H-bond acceptors and 3 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30°C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.004
2,2'-[butane-1,4-diylbis(1H-benzimidazole-2,1-diyl)]diacetic acid
Homo sapiens
pH and temperature not specified in the publication
0.0017
[4-(2,5-dimethyl-1H-pyrrol-1-yl)phenoxy]acetic acid
Homo sapiens
-
-
0.0017
[4-(2,5-dimethyl-1H-pyrrol-1-yl)phenoxy]acetic acid
Homo sapiens
pH and temperature not specified in the publication
additional information
additional information
Homo sapiens
The APE1 inhibitory profile of some of the most potent compounds indicates that along with two terminal fingerprint negatively ionizable features or bioisostere groups of negatively ionizable features, an optimum sized central hydrophobic core with or without a favorably substituted H-bond acceptor-donor functional group is essential for a compound being recognized by APE1 and inhibit its catalytic activity
-
additional information
additional information
Homo sapiens
-
The APE1 inhibitory profile of some of the most potent compounds indicates that along with two terminal fingerprint negatively ionizable features or bioisostere groups of negatively ionizable features, an optimum sized central hydrophobic core with or without a favorably substituted H-bond acceptor-donor functional group is essential for a compound being recognized by APE1 and inhibit its catalytic activity
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evolution
basic human AP endonuclease is a multifunctional protein. AP endonucleases fall into two families depending on the similarity of their amino acid sequence with exonuclease III (ExoIII or Xth) or endonuclease IV (EndoIV or Nfo) from Escherichia coli. APE1 belongs to the large nuclease family related to ExoIII from Escherichia coli. Enzymes of the ExoIII family including APE1 exhibit several enzymatic activities manifested more or less effectively: AP endonuclease, 3'-phosphodiesterase, 3'-phosphatase, and 3'-5'-exonuclease
evolution
endonuclease III belongs to the DNA glycosylases of the helix-hairpin-helix-GPD structural superfamily
evolution
AP endonucleases have been classified into XthA and Nfo families based on sequence homology and structural conservation studies involving Escherichia coli exonuclease III (ExoIII) or endonuclease IV (EndoIV) respectively. The catalytic site in AP endonucleases is highly conserved from bacteria to humans and consists of residues involved in the binding of metal ions
evolution
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AP endonucleases have been classified into XthA and Nfo families based on sequence homology and structural conservation studies involving Escherichia coli exonuclease III (ExoIII) or endonuclease IV (EndoIV) respectively. The catalytic site in AP endonucleases is highly conserved from bacteria to humans and consists of residues involved in the binding of metal ions
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evolution
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AP endonucleases have been classified into XthA and Nfo families based on sequence homology and structural conservation studies involving Escherichia coli exonuclease III (ExoIII) or endonuclease IV (EndoIV) respectively. The catalytic site in AP endonucleases is highly conserved from bacteria to humans and consists of residues involved in the binding of metal ions
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malfunction
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APE1 knockdown abrogates neuroprotection against cerebral ischemia
malfunction
-
knockdown of ZAP1 levels does not alter base excision repair in early embryogenesis
malfunction
-
knocking down Ape1/Ref-1 expression enhances estrogen responsiveness of the progesterone receptor and pS2 genes but does not alter the expression of the constitutively active 36B4 gene
malfunction
-
short hairpin RNA-mediated stable suppression of APE-1 results in increased apoptosis in gastric epithelial cells after Helicobacter pylori infection
malfunction
-
siRNA knockdown of endogenous APE1 impairs high-mobility group box 1-mediated cytokine expression and MAPK activation in THP-1 cells
malfunction
APE1 lacking the first 34 amino acids at the Nterminus, unlike wild-type enzyme, is unable to form cross-links with BS-AP DNAs that testifies to the involvement of disordered N-terminal extension, which is enriched in lysine residues, in the interaction with AP sites.
malfunction
disruption of the disulfide bond connecting beta8 and beta9 sheets only has a slight effect on the AP endonuclease activity
malfunction
inactivation of the APE1 gene causes early embryonic lethality in mice
malfunction
mutation of active site residue D144 in HpXth predicted to be essential for catalysis results in a complete loss of enzyme activities
malfunction
protein acetylation is an important protein modification in living cells and has an impact on pathological conditions. A profound deregulation of APE1/Ref-1 acetylation (on Lys35) status in triple negative breast cancer is revealed
malfunction
the expression of transforming growth factor beta (TGFbeta) is significantly reduced in APE1-deficient osteosarcoma cells. Transforming growth factor beta promotes cancer metastasis through various mechanisms including immunosuppression, angiogenesis, and invasion. APE1, TGFbeta, and microvessel density (MVD) have a pairwise correlation in osteosarcoma tissue samples, whereas TGFbeta, tumor size, and MVD are inversely related to the prognosis of the cohort. High expression of APE1, TGFbeta, and microvessel density (MVD) correlate with poor prognosis of osteosarcoma patients. Apurinic/apyrimidinic endonuclease 1-siRNA-mediated downregulation in osteosarcoma cells inhibits expression of TGFbeta1. Apurinic/apyrimidinic endonuclease 1-siRNA inhibits the capability to enhance HUVEC migration and tube formation of tumor cells through the TGFbeta/Smad3 signaling pathway. Tumor angiogenesis and growth in xenografts are suppressed by APE1-siRNA
malfunction
the redox-deficient truncated APE1 protein lacking the first N-terminal 61 amino acid residues (APE1-N?61) cannot stimulate DNA glycosylase activities of OGG1, MBD4, and ANPG on duplex DNA substrates
malfunction
-
disruption of the disulfide bond connecting beta8 and beta9 sheets only has a slight effect on the AP endonuclease activity
-
malfunction
-
mutation of active site residue D144 in HpXth predicted to be essential for catalysis results in a complete loss of enzyme activities
-
metabolism
mechanisms of AP site cleavage by enzymes from the base excision repair system (BER), overview. Enzyme Polbeta in combination with APE1 is able to perform synthesis with strand displacement and simultaneously correction of Polbeta errors with catalysis by 3'-5'-exonuclease activity of the APE1. A Schiff base is formed as an intermediate in the reactions catalyzed by AP lyases and 5'-dRP lyases. One of the repair proteins interacting with the AP sites via formation of a Schiff base is poly(ADP-ribose)polymerase 1 (PARP1). PARP1 is known as a sensor of single-stranded breaks and as a protein regulator of BER. If exogenous APE1 is added prior to irradiation, the efficiency of the PARP1 and FEN1 labeling decreases (but not of the Polbeta), these proteins compete for binding to this DNA substrate. Interaction between various enzymes and proteins participating in BER, overview
metabolism
a nucleophilic residue of ALKBH1 reacts with the electrophilic C3' of the alpha,beta-unsaturated aldehyde of the 5'-product. The addition of a competing nucleophile, specifically 2-mercaptoethanol, reduces the extent of adduct formation
physiological function
AP endonuclease and proliferating cell nuclear antigen form a functional complex to generate a gap of several nucleotides for efficient DNA repair synthesis
physiological function
-
AP endonuclease pE296R is essential for virus growth in swine macrophages. DNA repair functions of pE296R are AP endonucleolytic, 3'-5' exonuclease, 3-diesterase and nucleotide incision repair activities
physiological function
-
APE1 functions as a critical rate-limiting enzyme in DNA base excision repair and accounts for nearly all of the AP site incision activities in cell extracts, APE1 also exerts unique redox activity to regulate the DNA-binding affinity of certain transcriptional factors by controlling the redox status of their DNA-binding domain
physiological function
-
APE1 has a central role in the coordination of base excision repair
physiological function
-
APE1 is a dual regulator of inflammatory signaling to high-mobility group box 1 by human monocytes/macrophages. Forced cytoplasmic overexpression of APE1 profoundly attenuates the upregulation of high-mobility group box 1-mediated reactive oxygen species generation, cytokine secretion, and cyclooxygenase-2 expression by primary monocytes and macrophage-like THP-1 cell lines, the extracellular release of high-mobility group box 1 by activated macrophages is inhibited by APE1 transfection
physiological function
-
APE1 is a key multifunctional protein involved in DNA base excision repair
physiological function
-
APE1 is a key upstream regulator in TLR2-dependent keratinocyte inflammatory responses
physiological function
-
APE1 is a multifunctional enzyme that plays a central role in base excision repair of DNA and is also involved in the alternative nucleotide incision repair pathway
physiological function
-
APE1 is required for pituitary adenylate cyclase-activating polypeptide-induced neuroprotection against global cerebral ischemia
physiological function
-
APE1 is the major nuclease for excising abasic sites and particular 3'-obstructive termini from DNA, and is an integral participant in the base excision repair pathway
physiological function
-
APE1 regulates c-myc mRNA level possibly via its endoribonuclease activity
physiological function
-
APE1 regulates c-myc mRNA level possibly via its endoribonuclease activity
physiological function
-
APE1 stimulates the multiple-turnover excision of hypoxanthine by alkyladenine DNA glycosylase but has no effect on single-turnover excision
physiological function
-
Ape1/Ref-1 enhances the interaction of estrogen receptor alpha with estrogen-response elements in DNA, Ape1/Ref-1 alters expression of the endogenous, estrogen-responsive progesterone receptor and pS2 genes in MCF-7 cells and associates with estrogen-response elements-containing regions of these genes in native chromatin
physiological function
-
both DNA repair and acetylation functions of APE-1 modulate programmed cell death, the DNA repair activity of APE-1 inhibits the mitochondrial pathway, whereas the acetylation function inhibits the extrinsic pathway during Helicobacter pylori infection
physiological function
-
in addition to the apurinic/apyrimidinic DNA endonuclease activity, APE1 has 3'-5' DNA exonuclease, 3' phosphodiesterase, and RNase H activities
physiological function
-
in addition to the apurinic/apyrimidinic DNA endonuclease activity, APE1 has 3'-5' DNA exonuclease, 3'-phosphodiesterase, and RNase H activities
physiological function
-
nuclear factor -kappaB is activated by cytoplasmic, but not nuclear, Ape1 to cause Cox-2 expression. Ape1 can enhance lung tumor malignancy through nuckear factor-kappaB activation
physiological function
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overexpression of Nfo about 50fold in spores increases the wet heat resistance of exoA nfo Bacillus subtilis spores that lack most alpha/beta-type small, acid-soluble spore proteins, but has no effect on these spores' UV-C resistance. Nfo overexpression also increases these spores' dry heat resistance, and to levels slightly greater than that of wild type spores
physiological function
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mice deficient for the base excision repair enzyme, apurinic/apyrimidinic endonuclease APE2 protein develop relatively normally, but they display defects in lymphopoiesis. Mice nullizygous for APE2 show an inhibition of the pro-B to pre-B cell transition. APE2 is not required for V(D)J recombination and the turnover rate of APE2-deficient progenitor B cells is nearly normal. The production rate of pro- and pre-B cells is reduced due to a p53-dependent DNA damage response. Progenitors from APE2-deficient mice differentiate normally in response to IL-7 in in vitro stromal cell cocultures, but pro-B cells show defective expansion. APE2-deficient mice show a delay in recovery of B lymphocyte progenitors following bone marrow depletion by 5-fluorouracil, with the pro-B and pre-B cell pools still markedly decreased 2 weeks after a single treatment
physiological function
over-expression of APN in Toxoplasma gondii confers protection from DNA damage, and viable knockouts of APN are not obtainable. An inducible APN knockdown mutant demonstrates that APN is critical for Toxoplasma to recover from DNA damage
physiological function
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overexpression of APE/Ref-1 using adenovirus and restoration of APE small peptides significantly reduces kainic acid-induced hippocampal cell death. Both silencing of APE/Ref-1 by siRNA and inhibition of endonuclease by an antibody significantly increase caspase-3 activity and apoptotic cell death triggered from the early time after exposure to kainic acid. Findings suggest that cell death is initiated by reducing APE/Ref-1 protein and inhibiting its repair function in spite of enough protein amounts
physiological function
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spores lacking both AP endonucleases Nfo and ExoA and major alpha/beta-type small acid-soluble spore proteins are significantly more sensitive to 254-nm UVC, environmental UV >280 nm, X-ray exposure, and high-energy charged particle bombardment and have elevated mutation frequencies compared to those of wild-type spores and spores lacking only one or both AP endonucleases or major alpha/beta-type small acid-soluble spore proteins
physiological function
the enzyme is part of the base excision repair (BER) pathway. It protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine, from single- and double-stranded DNA substrates. Bifunctional enzyme that catalyzes the excision of 8-oxoguanine by cleaving the N-glycosylic bond between the base and the deoxyribose moiety (glycosylase activity) and subsequently cleave the DNA backbone (lyase activity, EC 4.2.99.18)
physiological function
isoform Ape1 is an essential factor stabilizing telomeric DNA, and its deficiency is associated with telomere dysfunction and segregation defects in immortalized cells maintaining telomeres by either the alternative lengthening of telomeres pathway or telomerase expression or in normal human fibroblasts
physiological function
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isoform APE1-deficient cell lines derived from bloodstream stage trypanosomes, confirm that the AP endonuclease is not essential for viability in this cell type under in vitro culture conditions. An inverse correlation exists between the level of AP endonuclease in the cell and the number of endogenously generated abasic sites in its genomic DNA. Depletion of APE1 renders cells hypersensitive to AP site and strand break-inducing agents such as methotrexate and phleomycin, respectively, but not to alkylating agents. The increased susceptibility of APE1-depleted cells to nitric oxide suggests an essential role in protection against the immune defenses of the mammalian host
physiological function
overexpression of isoform AP1 increases epimastigotes viability when they are exposed to acute ROS/RNS attack. This protective effect is more evident when parasites are submitted to persistent reactive oxygen species/reactive nitrogen species exposition
physiological function
AP endonuclease 1 (APE1) is a multifunctional protein abundant in human cells that is essential in maintaining multiple cellular functions. AP endonuclease 1 (APE1) takes part in the base excision repair (BER). It prevents trinucleotide repeat (TNR) expansions via its 3'-5'-exonuclease activity and stimulatory effect on DNA ligation during BER in a hairpin loop. Coordinating with flap endonuclease 1, the APE1 3'-5'-exonuclease activity cleaves the annealed upstream 3'-flap of a double-flap intermediate resulting from 5'-incision of an abasic site in the hairpin loop. Furthermore, APE1 stimulates DNA ligase I to resolve a long double-flap intermediate, thereby promoting hairpin removal and preventing TNR expansions
physiological function
APE1 is one of the key enzymes taking part in the repair of damage to DNA. The primary role of APE1 is the initiation of the repair of AP-sites by catalyzing the hydrolytic incision of the phosphodiester bond immediately 5' to the damage. In addition to the AP-endonuclease activity, APE1 possesses 3'-5'-exonuclease activity, which presumably is responsible for cleaning up nonconventional 3'-ends that were generated as a result of DNA damage or as transition intermediates in DNA repair pathways
physiological function
APE1 is unable to cleave apurinic/apyrimidinic (AP) sites in spite of formation of the Schiff-base-dependent intermediate, which is prerequisite for the beta-elimination mechanism. Clustered AP sites are more cytotoxic than isolated AP lesions because double strand breaks (DSB) can be formed during repair of closely positioned bistranded AP sites. Formation of DSB due to simultaneous cleavage of bistranded AP sites may be regulated by proteins specifically interacting with this complex lesion
physiological function
apurinic/apyrimidinic (AP) endonucleases play critical roles in the repair of abasic sites and strand breaks in DNA. Helicobacter pylori contains one single AP endonuclease. The DNA substrate specificity of Helicobacter pylori AP endonuclease HpXth counteracts the genotoxic effects of DNA damage generated by endogenous and host-imposed factors. The presence of Helicobacter pylori Xth protein in AP endonuclease-deficient Escherichia coli xth nfo strain significantly reduces the sensitivity to an alkylating agent and H2O2
physiological function
Apurinic/apyrimidinic (AP) sites, the most frequently formed DNA lesions in the genome, inhibit transcription and block replication. The primary enzyme that repairs AP sites in mammalian cells is the AP endonuclease (APE1), which functions through the base excision repair (BER) pathway. Human DNA repair enzyme APE1 is a ubiquitous and multifunctional protein. It plays a central role in the repair of spontaneously generated AP sites and oxidative and alkylated DNA damage in the genome via the BER pathwayMammalian cells, unlike Saccharomyces cerevisiae or Escherichia coli cells, require acetylation of APE1 for the efficient repair of AP sites and base damage in the genome. APE1 acetylation is an integral part of the BER pathway for maintaining genomic integrity. Apart from its DNA repair function, APE1 functions as a redox activator of many transcription factors, as well as a direct transcriptional coregulator of many genes. APE1 is essential for embryonic development and for cell viability and/or proliferation in cultures. Human APE1 is unique in that it has an N-terminal disordered 42 amino acids and has both DNA repair and transcriptional regulatory activities. AcAPE1 is exclusively associated with chromatin throughout the cell cycle. Acetylation of APE1 enhances its AP catalytic efficiency, and APE1 acetylation enhances its interaction with downstream BER proteins and stability on chromatin. APE1 acetylation plays a role in cell survival and/or proliferation in response to genotoxic stress
physiological function
apurinic/apyrimidinic endonuclease 1 (Ape1) is an important enzyme in the base excision repair mechanism, responsible for the backbone cleavage of abasic DNA through a phosphate hydrolysis reaction
physiological function
apurinic/apyrimidinic endonuclease 1 is a multifunctional protein playing crucial roles in DNA base excision repair and redox regulation of gene expression, activities that are functionally and structurally independent of each other. The APE1 redox activity stimulates numerous transcriptional factors, including activator protein-1 (AP-1), nuclear factor-kappaB (NF-happaB), and HIF-1. These factors are involved in mediating VEGF gene expression; HIF-1 and NF-kappaB, in particular, increased VEGF expression in response to hypoxia. Apurinic/apyrimidinic endonuclease 1 (APE1) is a dually functional protein possessing both base excision repair and redox activities, it is involved in tumor angiogenesis. APE1, TGFbeta, and microvessel density (MVD) have a pairwise correlation in osteosarcoma tissue samples, whereas TGFbeta, tumor size, and MVD are inversely related to the prognosis of the cohort. High expression of APE1, TGFbeta, and microvessel density (MVD) correlate with poor prognosis of osteosarcoma patients. APE1 may indirectly regulate angiogenesis through a TGFbeta-dependent pathway
physiological function
apurinic/apyrimidinic endonuclease Apn1 of Saccharomyces cerevisiae is known as a key player of the base excision DNA repair (BER) pathway in yeast. BER is initiated by DNA glycosylases, whereas Apn1 can start DNA repair individually in the nucleotide incision repair (NIR) pathway. More delicate regulation of Apn1's NIR activity is necessary due to the more complicated kinetic mechanism, as compared to BER
physiological function
apurinic/apyrimidinic sites (AP sites) are among the most abundant DNA damages. They can emerge because of spontaneous hydrolysis of the N-glycoside bond and during removal of the damaged DNA bases by DNA glycosylases. In mammalian cells up to 10000 AP sites emerge daily primarily due to apurinization of DNA. The number of such damages increases dramatically during intensive oxidative stress, X-ray and UV irradiation, and other actions. The deoxyribose residues in the AP sites exist in different forms that are in equilibrium. The acyclic aldehyde form of an AP site can form a Schiff base with amino groups in proteins, most often with the epsilon-NH2 group of lysine residues. AP endonucleases are the most important enzymes involved in the DNA repair that initiates the repair of AP sites. APE1 exhibits 3'-phosphodiesterase, 3'-5'-exonuclease, and 3'-phosphatase activities. Role of APE1 in the DNA repair process and in other metabolic processes, overview. APE1 stimulates the activity of the mouse adeninex02DNA glycosylase (Myh) and enhances affinity of this enzyme to adenine/8-oxoguanine pairs in comparison with adenine/guanine pairs
physiological function
apurinic/apyrimidinic sites (AP sites) are among the most abundant DNA damages. They can emerge because of spontaneous hydrolysis of the N-glycoside bond and during removal of the damaged DNA bases by DNA glycosylases. In mammalian cells up to 10000 AP sites emerge daily primarily due to apurinization of DNA. The number of such damages increases dramatically during intensive oxidative stress, X-ray and UV irradiation, and other actions. The deoxyribose residues in the AP sites exist in different forms that are in equilibrium. The acyclic aldehyde form of an AP site can form a Schiff base with amino groups in proteins, most often with the epsilon-NH2 group of lysine residues. AP endonucleases are the most important enzymes involved in the DNA repair that initiates the repair of AP sites. Human apurinic/apyrimidinic endonuclease 1 (APE1) is one of the key participants in the DNA base excision repair system. The major contribution to AP site cleavage in mammalian cells is provided by APE1 (over 95% of damages). APE1 hydrolyzes DNA adjacent to the 5'-end of an AP site to produce a nick with a 3'-hydroxyl group and a 5'-deoxyribose phosphate moiety. APE1 exhibits 3'-phosphodiesterase, 3'-5'-exonuclease, and 3'-phosphatase activities. APE1 is also identified as a redox factor (Ref-1). Role of APE1 in the DNA repair process and in other metabolic processes, overview. The APE1 protein is required for viability of human cell culture. APE1 is required not only for hydrolysis of AP sites generated by monofunctional DNA glycosylases, but also for processing of the products of bifunctional DNA glycosylases catalyzing beta-elimination. The enzyme is obviously involved in the cell response system to the action of some genotoxic agents. Participation of APE1 in stimulation of the DNA glycosylase, lyase, polymerase, flap endonuclease, and DNA ligase activities of BER enzymes likely reflects the role of this enzyme in coordination of different stages of DNA repair to achieve its optimal efficiency
physiological function
Endonuclease III (Endo III) is a bifunctional DNA glycosylase possessing N-glycosylase and AP lyase activities. Endonuclease III is responsible for base excision repair of oxidized or reduced pyrimidine bases
physiological function
human apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/Ref-1) is a multifunctional protein which is essential in the base excision repair (BER) pathway of DNA lesions caused by oxidation and alkylation. This protein hydrolyzes DNA adjacent to the 5'-end of an apurinic/apyrimidinic (AP) site to produce a nick with a 3'-hydroxyl group and a 5'-deoxyribose phosphate moiety or activates the DNA binding activity of certain transcription factors through its redox function. Role for APE1/Ref-1 in the pathogenesis of cancer and in resistance to DNA-interactive drugs. APE1/Ref-1 plays a vital role in mammalian cells with implication in human pathologies. DNA damage and chronic oxidative stress are involved in various neurodegenerative disorders, including Alzheimer's, Parkinson's, Huntington's diseases, and amyotrophic lateral sclerosis. APE1/Ref-1 signaling pathway in hepatocellular carcinoma stimulates cellular proliferation, enhances anti-apoptosis, and facilitates metastasis
physiological function
human apurinic/apyrimidinic endonuclease APE1 is one of the key enzymes of the base excision DNA repair system. The main biological function of APE1 is the hydrolysis of the phosphodiester bond on the 5'-side of an apurinic/apyrimidinic site (AP-site) to give the 5'-phosphate and 3'-hydroxyl group. The level of enzymatic activity of human AP-endonuclease APE1 has a considerable influence on the process of the removal of DNA lesions. APE1 is an extremely active enzyme which is able to process many synthetic analogues of the AP-site such as tetrahydrofuran (F-site) or alpha,omega-alkane diols
physiological function
human enzyme APE2 performs most of the essential functional residues of the exonuclease III-like proteins. APE2 has 518 amino acids. Unlike APE1/Ref-1, APE2 shows only weak capacity to exhibit AP site repair activity. APE2 has no the N-terminal tail that is present in APE1/Ref-1 and as such does not possess redox activity
physiological function
most of the biological importance of APE1 in the DNA repair pathways is associated with the high affinity for the abasic nucleotide and nicking of DNA hydrolytically 5' to the AP-site. APE1 has the ability to incise the DNA sugar-phosphate backbone 5' to structurally unrelated lesions such as alpha-anomeric 2'-deoxynucleosides, various red/ox-modified pyrimidines and etheno-adducts
physiological function
the apurinic/apyrimidinic (AP) endonuclease Apn1 from Saccharomyces cerevisiae is a key enzyme involved in the base excision repair (BER) at the cleavage stage of abasic sites (AP sites) in DNA
physiological function
the base excision repair (BER) pathway consists of sequential action of DNA glycosylase and apurinic/apyrimidinic (AP) endonuclease necessary to remove a damaged base and generate a single-strand break in duplex DNA. Human multifunctional AP endonuclease 1 (APE1) plays essential roles in BER by acting downstream of DNA glycosylases to incise a DNA duplex at AP sites and remove 3'-blocking sugar moieties at DNA strand breaks. Human apurinic/apyrimidinic (AP) endonuclease, APE1, stimulates DNA glycosylases, e.g. human 8-oxoguanine-DNA glycosylase (OGG1), by increasing their turnover rate on duplex DNA substrates, overview. The redox domain of APE1 is necessary for the active mode of stimulation of DNA glycosylases (e.g. of uracil-DNA glycosylase activity of MBD4). Consequently, APE1 shows DNA length dependence with preferential repair of short DNA duplexes. APE1-catalyzed oligomerization along DNA induces helix distortions, which in turn enable conformational selection and stimulation of DNA glycosylases
physiological function
MtbXthA is a versatile enzyme with AP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. the sliding DNA beta-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239QLRFPKK245 motif in the DNA-binding domain of XthA is found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of beta-clamp located on different domains interact with XthA. The beta-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. Addition of beta-clamp binding peptides disrupts the MtbXthA-clamp complex and inhibits clamp-dependent stimulation of MtbXthA, overview. In the AP incision activities, the control experiments involving a random peptide had no effect on activity stimulation, while addition of peptides derived from alpha subunit, delta subunit, and MtbXthA, respectively, result in 2.0-2.5fold decreased stimulation of MtbXthA activity. The beta-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the beta-clamp onto DNA is required for activity stimulation. In the absence of DNA, the PBG located on the second domain of the beta-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence. The C-terminal domain of beta-clamp predominantly mediates interactions with XthA in the presence of DNA
physiological function
Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair. The enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as AP-endonuclease at high ionic environments, while the 3'-5' exonuclease activity is predominant at low ionic environments
physiological function
the 6-methyl adenine demethylase activity is very low. The demethylase activity is less than half that of the apurinic/apyrimidinic lyase activity when ALKBH1 samples are assayed using identical buffer conditions. The two enzymatic activities are located in distinct but partially overlapping active sites for the two reactions
physiological function
-
the enzyme is part of the base excision repair (BER) pathway. It protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine, from single- and double-stranded DNA substrates. Bifunctional enzyme that catalyzes the excision of 8-oxoguanine by cleaving the N-glycosylic bond between the base and the deoxyribose moiety (glycosylase activity) and subsequently cleave the DNA backbone (lyase activity, EC 4.2.99.18)
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physiological function
-
the apurinic/apyrimidinic (AP) endonuclease Apn1 from Saccharomyces cerevisiae is a key enzyme involved in the base excision repair (BER) at the cleavage stage of abasic sites (AP sites) in DNA
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physiological function
-
apurinic/apyrimidinic endonuclease Apn1 of Saccharomyces cerevisiae is known as a key player of the base excision DNA repair (BER) pathway in yeast. BER is initiated by DNA glycosylases, whereas Apn1 can start DNA repair individually in the nucleotide incision repair (NIR) pathway. More delicate regulation of Apn1's NIR activity is necessary due to the more complicated kinetic mechanism, as compared to BER
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physiological function
-
overexpression of isoform AP1 increases epimastigotes viability when they are exposed to acute ROS/RNS attack. This protective effect is more evident when parasites are submitted to persistent reactive oxygen species/reactive nitrogen species exposition
-
physiological function
-
overexpression of Nfo about 50fold in spores increases the wet heat resistance of exoA nfo Bacillus subtilis spores that lack most alpha/beta-type small, acid-soluble spore proteins, but has no effect on these spores' UV-C resistance. Nfo overexpression also increases these spores' dry heat resistance, and to levels slightly greater than that of wild type spores
-
physiological function
-
Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair. The enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as AP-endonuclease at high ionic environments, while the 3'-5' exonuclease activity is predominant at low ionic environments
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physiological function
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MtbXthA is a versatile enzyme with AP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. the sliding DNA beta-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239QLRFPKK245 motif in the DNA-binding domain of XthA is found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of beta-clamp located on different domains interact with XthA. The beta-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. Addition of beta-clamp binding peptides disrupts the MtbXthA-clamp complex and inhibits clamp-dependent stimulation of MtbXthA, overview. In the AP incision activities, the control experiments involving a random peptide had no effect on activity stimulation, while addition of peptides derived from alpha subunit, delta subunit, and MtbXthA, respectively, result in 2.0-2.5fold decreased stimulation of MtbXthA activity. The beta-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the beta-clamp onto DNA is required for activity stimulation. In the absence of DNA, the PBG located on the second domain of the beta-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence. The C-terminal domain of beta-clamp predominantly mediates interactions with XthA in the presence of DNA
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physiological function
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Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair. The enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as AP-endonuclease at high ionic environments, while the 3'-5' exonuclease activity is predominant at low ionic environments
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physiological function
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MtbXthA is a versatile enzyme with AP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. the sliding DNA beta-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239QLRFPKK245 motif in the DNA-binding domain of XthA is found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of beta-clamp located on different domains interact with XthA. The beta-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. Addition of beta-clamp binding peptides disrupts the MtbXthA-clamp complex and inhibits clamp-dependent stimulation of MtbXthA, overview. In the AP incision activities, the control experiments involving a random peptide had no effect on activity stimulation, while addition of peptides derived from alpha subunit, delta subunit, and MtbXthA, respectively, result in 2.0-2.5fold decreased stimulation of MtbXthA activity. The beta-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the beta-clamp onto DNA is required for activity stimulation. In the absence of DNA, the PBG located on the second domain of the beta-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence. The C-terminal domain of beta-clamp predominantly mediates interactions with XthA in the presence of DNA
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physiological function
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isoform APE1-deficient cell lines derived from bloodstream stage trypanosomes, confirm that the AP endonuclease is not essential for viability in this cell type under in vitro culture conditions. An inverse correlation exists between the level of AP endonuclease in the cell and the number of endogenously generated abasic sites in its genomic DNA. Depletion of APE1 renders cells hypersensitive to AP site and strand break-inducing agents such as methotrexate and phleomycin, respectively, but not to alkylating agents. The increased susceptibility of APE1-depleted cells to nitric oxide suggests an essential role in protection against the immune defenses of the mammalian host
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physiological function
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apurinic/apyrimidinic (AP) endonucleases play critical roles in the repair of abasic sites and strand breaks in DNA. Helicobacter pylori contains one single AP endonuclease. The DNA substrate specificity of Helicobacter pylori AP endonuclease HpXth counteracts the genotoxic effects of DNA damage generated by endogenous and host-imposed factors. The presence of Helicobacter pylori Xth protein in AP endonuclease-deficient Escherichia coli xth nfo strain significantly reduces the sensitivity to an alkylating agent and H2O2
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additional information
a set of AP DNA duplexes containing AP sites in both strands in different mutual orientation (BS-AP DNAs) is used for search in the extracts of human cells proteins specifically recognizing clustered AP sites
additional information
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a set of AP DNA duplexes containing AP sites in both strands in different mutual orientation (BS-AP DNAs) is used for search in the extracts of human cells proteins specifically recognizing clustered AP sites
additional information
association of APE1 with undamaged DNA reduces effective concentration of the enzyme and subsequently decreases APE1-catalyzed cleavage rates on long DNA substrates. APE1 oligomers on DNA induce helix distortions thereby enhancing molecular recognition of DNA lesions by DNA glycosylases via a conformational proofreading/selection mechanism. Thus, APE1-mediated structural deformations of the DNA helix stabilize the enzyme-substrate complex and promote dissociation of human DNA glycosylases from the AP site with a subsequent increase in their turnover rate. APE1 shows DNA length dependence with preferential repair of short DNA duplexes. Electron microscopic analysis of DNA complexes with the APE1 protein
additional information
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association of APE1 with undamaged DNA reduces effective concentration of the enzyme and subsequently decreases APE1-catalyzed cleavage rates on long DNA substrates. APE1 oligomers on DNA induce helix distortions thereby enhancing molecular recognition of DNA lesions by DNA glycosylases via a conformational proofreading/selection mechanism. Thus, APE1-mediated structural deformations of the DNA helix stabilize the enzyme-substrate complex and promote dissociation of human DNA glycosylases from the AP site with a subsequent increase in their turnover rate. APE1 shows DNA length dependence with preferential repair of short DNA duplexes. Electron microscopic analysis of DNA complexes with the APE1 protein
additional information
endonuclease III uses a multistep mechanism of damage recognition, which likely involves Gln41 and Leu81 as lesion sensors. The principal amino acids involved in the catalysis are Lys120 and Asp138. The former is the nucleophile that attacks the C1' atom of deoxyribose, resulting in the cleavage of the N-glycosydic bond and subsequent formation of a Schiff base covalent intermediate. The following beta-elimination reaction leads to the departure of the 3'-phosphate. The subsequent Schiff base hydrolysis releases the enzyme and leads to formation of a single-strand break in DNA duplex with an alpha/beta-unsaturated aldehyde at the 3'-end and a phosphate at the 5'-end
additional information
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endonuclease III uses a multistep mechanism of damage recognition, which likely involves Gln41 and Leu81 as lesion sensors. The principal amino acids involved in the catalysis are Lys120 and Asp138. The former is the nucleophile that attacks the C1' atom of deoxyribose, resulting in the cleavage of the N-glycosydic bond and subsequent formation of a Schiff base covalent intermediate. The following beta-elimination reaction leads to the departure of the 3'-phosphate. The subsequent Schiff base hydrolysis releases the enzyme and leads to formation of a single-strand break in DNA duplex with an alpha/beta-unsaturated aldehyde at the 3'-end and a phosphate at the 5'-end
additional information
enzyme HpXth homology modeling
additional information
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enzyme HpXth homology modeling
additional information
molecular dynamics simulations elucidates the structural features of complexes of the enzyme with DHU-containing DNAs. Enzyme three-dimensional structure homology modeling using the structure of Endo IV (PDB ID 1QTW) as template
additional information
molecular dynamics simulations of Ape1 complexed to its substrate DNA performed for models containing 1 or 2 Mg21-ions as cofactor located at different positions show a complex with 1 metal ion bound on the leaving group site of the scissile phosphate to be the most likely reaction-competent conformation. Active-site residue His309 is found to be protonated based on pKa calculations and the higher conformational stability of the Ape1-DNA substrate complex compared to scenarios with neutral His309. Simulations of the D210N mutant further support the prevalence of protonated His309 and strongly suggest Asp210 as the general base for proton acceptance by a nucleophilic water molecule. Enzyme modelling based on the crystal structure of the phosphorothioate substrate complex with Mn2+ as metal cofactor (PDB ID 5DG0). Residue His309 is essential for substrate binding and the phosphate hydrolysis step. In terms of substrate binding, Tyr171 has the possibility to form a hydrogen bond with the non-bridging oxygen atom of the AP-site
additional information
residue His83 properly coordinates the active site Zn2+ ion playing a crucial role in catalytic incision stage. Substrate binding structure analysis using DNA duplex crystal structure (PDB ID 2NQJ) for molecular dynamics simulations
additional information
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residue His83 properly coordinates the active site Zn2+ ion playing a crucial role in catalytic incision stage. Substrate binding structure analysis using DNA duplex crystal structure (PDB ID 2NQJ) for molecular dynamics simulations
additional information
stopped-flow fluorescence techniques are used to conduct a comparative kinetic analysis of the conformational transitions in human apurinic/apyrimidinic endonuclease 1 (APE1) and in DNA containing an abasic site in the course of their interaction. Analysis of enzyme-substrate complexes with bound Mg2+
additional information
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stopped-flow fluorescence techniques are used to conduct a comparative kinetic analysis of the conformational transitions in human apurinic/apyrimidinic endonuclease 1 (APE1) and in DNA containing an abasic site in the course of their interaction. Analysis of enzyme-substrate complexes with bound Mg2+
additional information
substrate specificity and substrate binding, molecular dynamics simulations. Molecular modelling of the APE1 complex with 13 ntDNA duplexes containing 1,N6-ethenoadenosine, alpha-adenosine, 5,6-dihydrouridine or F-site. Model structures of APE1-DNA complexes show that the pocket of the active site is formed by amino acid residues Asn174, Asn212, Asn229, Ala230, Phe266 and Trp280
additional information
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substrate specificity and substrate binding, molecular dynamics simulations. Molecular modelling of the APE1 complex with 13 ntDNA duplexes containing 1,N6-ethenoadenosine, alpha-adenosine, 5,6-dihydrouridine or F-site. Model structures of APE1-DNA complexes show that the pocket of the active site is formed by amino acid residues Asn174, Asn212, Asn229, Ala230, Phe266 and Trp280
additional information
the N-terminal domain (about 6 kDa, 60 amino acids) is responsible for the redox function of APE1, which is independent of the repair functions of this enzyme, and it contains the nuclear export signal. The second human AP endonuclease (APE2) also belongs to the ExoIII family, but the level of its endonuclease activity is significantly lower than of APE1. Amino acids such as Asp219, Asp90, and Asp308 are functionally important, D219 in APE1 plays a key function in repair. Tyr171 does not interact directly with the AP site, but participates in the catalysis of the APE1 endonuclease reaction in the form of a phenolate ion, i.e. it attacks phosphate at the 5'-side of the AP site
additional information
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the N-terminal domain (about 6 kDa, 60 amino acids) is responsible for the redox function of APE1, which is independent of the repair functions of this enzyme, and it contains the nuclear export signal. The second human AP endonuclease (APE2) also belongs to the ExoIII family, but the level of its endonuclease activity is significantly lower than of APE1. Amino acids such as Asp219, Asp90, and Asp308 are functionally important, D219 in APE1 plays a key function in repair. Tyr171 does not interact directly with the AP site, but participates in the catalysis of the APE1 endonuclease reaction in the form of a phenolate ion, i.e. it attacks phosphate at the 5'-side of the AP site
additional information
enzyme residues E57 and D251 are critical for catalysis, molecular modelling and mutational analysis. Determinants of abasic-site recognition, overview. Determinants of abasic-site recognition: the first three determinants, i.e. the base opposite the abasic site, the abasic ribose ring itself, and local distortions in the AP-site, do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, conserved residues located near the active site, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision. MtbXthA binds with high affinity to abasic sites in DNA e.g. to a 5'-FAM labelled duplex DNA substrate N1 that has an abasic site analogue, tetrahydrofuran (THF), incorporated into it. Homology modeling of MtbXthA using the structure of the Neisseria meningitidis protein (PDB ID 2JC4) as a template
additional information
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enzyme residues E57 and D251 are critical for catalysis, molecular modelling and mutational analysis. Determinants of abasic-site recognition, overview. Determinants of abasic-site recognition: the first three determinants, i.e. the base opposite the abasic site, the abasic ribose ring itself, and local distortions in the AP-site, do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, conserved residues located near the active site, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision. MtbXthA binds with high affinity to abasic sites in DNA e.g. to a 5'-FAM labelled duplex DNA substrate N1 that has an abasic site analogue, tetrahydrofuran (THF), incorporated into it. Homology modeling of MtbXthA using the structure of the Neisseria meningitidis protein (PDB ID 2JC4) as a template
additional information
the PIP motif mediates critical interactions between AP endonuclease and proliferating cell nuclear antigen (PCNA), both in vitro and in vivo. The PIP motif in PCNA-interacting proteins is a defined consensus sequence (QxxLxxFF), while the consensus sequence corresponding to the beta-clamp interacting motif in prokaryotes is relatively less conserved. Structure comparison of homodimeric mycobacterial beta-clamp and homotrimeric human PCNA, overview
additional information
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residue His83 properly coordinates the active site Zn2+ ion playing a crucial role in catalytic incision stage. Substrate binding structure analysis using DNA duplex crystal structure (PDB ID 2NQJ) for molecular dynamics simulations
-
additional information
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molecular dynamics simulations elucidates the structural features of complexes of the enzyme with DHU-containing DNAs. Enzyme three-dimensional structure homology modeling using the structure of Endo IV (PDB ID 1QTW) as template
-
additional information
-
enzyme residues E57 and D251 are critical for catalysis, molecular modelling and mutational analysis. Determinants of abasic-site recognition, overview. Determinants of abasic-site recognition: the first three determinants, i.e. the base opposite the abasic site, the abasic ribose ring itself, and local distortions in the AP-site, do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, conserved residues located near the active site, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision. MtbXthA binds with high affinity to abasic sites in DNA e.g. to a 5'-FAM labelled duplex DNA substrate N1 that has an abasic site analogue, tetrahydrofuran (THF), incorporated into it. Homology modeling of MtbXthA using the structure of the Neisseria meningitidis protein (PDB ID 2JC4) as a template
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additional information
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the PIP motif mediates critical interactions between AP endonuclease and proliferating cell nuclear antigen (PCNA), both in vitro and in vivo. The PIP motif in PCNA-interacting proteins is a defined consensus sequence (QxxLxxFF), while the consensus sequence corresponding to the beta-clamp interacting motif in prokaryotes is relatively less conserved. Structure comparison of homodimeric mycobacterial beta-clamp and homotrimeric human PCNA, overview
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additional information
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enzyme residues E57 and D251 are critical for catalysis, molecular modelling and mutational analysis. Determinants of abasic-site recognition, overview. Determinants of abasic-site recognition: the first three determinants, i.e. the base opposite the abasic site, the abasic ribose ring itself, and local distortions in the AP-site, do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, conserved residues located near the active site, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision. MtbXthA binds with high affinity to abasic sites in DNA e.g. to a 5'-FAM labelled duplex DNA substrate N1 that has an abasic site analogue, tetrahydrofuran (THF), incorporated into it. Homology modeling of MtbXthA using the structure of the Neisseria meningitidis protein (PDB ID 2JC4) as a template
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additional information
-
the PIP motif mediates critical interactions between AP endonuclease and proliferating cell nuclear antigen (PCNA), both in vitro and in vivo. The PIP motif in PCNA-interacting proteins is a defined consensus sequence (QxxLxxFF), while the consensus sequence corresponding to the beta-clamp interacting motif in prokaryotes is relatively less conserved. Structure comparison of homodimeric mycobacterial beta-clamp and homotrimeric human PCNA, overview
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additional information
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enzyme HpXth homology modeling
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F200S
site-directed mutagenesis, by expanding the size of the binding pocket the unspecific endonucleolytic activity is increased
F200S/W215S
site-directed mutagenesis, by expanding the size of the binding pocket the unspecific endonucleolytic activity is increased
V217G
site-directed mutagenesis, by expanding the size of the binding pocket the unspecific endonucleolytic activity is increased
W215S
site-directed mutagenesis, by expanding the size of the binding pocket the unspecific endonucleolytic activity is increased
D292A
decrease in activity
H308N
decrease in activity
R282A
loss of DNA binding
D190A
-
mutant enzyme is completely devoid of DNA repair activity and fails to rescue the genetic instability of Saccharomyces cerevisiae strain YW778
E68A
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mutant retains both AP endonuclease and 3'-diesterase repair activity, lacks ability to protect Saccharomyces cerevisiae strain YW778 from spontaneous and drug-induced DNA lesions
H279A
-
mutant enzyme is completely devoid of DNA repair activity and fails to rescue the genetic instability of Saccharomyces cerevisiae strain YW778
T58C
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Mutant enzyme is redox active. Site-directed mutagenesis is performed on the full-length zebrafish Ape pET15b vector using Stratagene Quikchange kit and verified by DNA sequencing. The T58C zApe vector is then transformed into Rosetta Escherichia coli (DE3). Stable ovarian cancer Skov-3X cells with the NFkappaB-Luc gene are cotransfected with plasmid pcDNA-mutant and a Renilla luciferase control reporter vector pRL-CMV using lipofectamine.
D179N
-
mild (10fold reduction) activity
D229N
-
reduction in activity
D44V
-
mutant retains glycosylase activity against oxidized pyrimidines, but the apparent rate constant for the lyase activity is significantly lower than the wild-type value
deltaQLY69-71
deletion of the entire loop, interferes with eversion of the damaged base from the helix, deficient in processing damaged DNA
E145Q
-
complete loss of catalytic activity
E261Q
-
catalytically inactive mutant, Glu261 is essential to catalysis
H109N
-
mild (10fold reduction) activity
H182N
-
reduction in activity
H216N
-
reduction in activity
H231N
-
reduction in activity
H69N
-
reduction in activity
Q261A
perturbs the conserved zinc finger, deficient in processing damaged DNA, can be reductively cross-linked to damaged base-containing DNA, deficient in regenerating free enzyme from the Nei-DNA covalent complex formed during the reaction
QLY69-71AAA
all amino acids in the QLY loop substituted with alanines, interferes with eversion of the damaged base from the helix, deficient in processing damaged DNA
R171A
perturbs the conserved zinc finger, deficient in processing damaged DNA
R184A
-
mutant enzyme maintains lyase activity but exhibits glycosylase specificity different from wild-type enzyme
R37A
-
strong positive effect on catalytic activity
R37A/E261Q
-
shows a three-fold decrease in AP-DNA binding affinity (Kd 340 nM)
S39L
-
mutant does not have significant glycosylase activity for oxidized pyrimidines, alhough it maintains AP lysae activity
Y72A
-
Tyr72 is important for the stability of the enzyme-substrate complex
Y72A/E261Q
-
double mutant shows a dissociation constant of Kd 97 nM
Y72F
-
Tyr72 is important for the stability of the enzyme-substrate complex
D179N
-
mild (10fold reduction) activity
-
E261Q
-
catalytically inactive mutant, Glu261 is essential to catalysis
-
H231N
-
reduction in activity
-
Y72A
-
Tyr72 is important for the stability of the enzyme-substrate complex
-
Y72F
-
Tyr72 is important for the stability of the enzyme-substrate complex
-
K267A
compared with wild-type, the affinity for the substrate analogue, 21 bp double-stranded DNA containing an apurinic/apyrimidinic-site analogue, is drastically decreased. The dissociation constant of the mutant is 0.38 microM
C118A
m6A demethylase activity similar to wild-type, about 25% decrease in apurinic/apyrimidinic lyase activity
C118A/C129A
about 50% decrease in m6A demethylase activity, about 20% decrease in apurinic/apyrimidinic lyase activity
C129A
about 90% decrease in m6A demethylase activity, about 30% decrease in apurinic/apyrimidinic lyase activity
C138A
-
stable Skov-3X cells with the NFB-Luc gene are cotransfected with plasmid pcDNA-mutant, mutant is redox active
C138S
-
repair activity is not affected
C138S/C99S
-
double mutants
C208A
-
stable Skov-3X cells with the NFB-Luc gene are cotransfected with plasmid pcDNA-mutant, mutant is redox active
C208S
-
repair activity is not affected
C296A
-
stable Skov-3X cells with the NFB-Luc gene are cotransfected with plasmid pcDNA-mutant, mutant is redox active
C296S
-
repair activity is not affected
C310A
-
stable Skov-3X cells with the NFB-Luc gene are cotransfected with plasmid pcDNA-mutant, mutant is redox active
C310S
-
repair activity is not affected
C65A/C93A
-
mutant form of TAT-APE1 is generated by insertion of full-length of APE1 C65A/C93A into pTAT-2.1
C65S/C99S
-
double mutants
C93A
-
stable Skov-3X cells with the NFB-Luc gene are cotransfected with plasmid pcDNA-mutant, mutant is redox active
C93S
-
repair activity is not affected
C99A
-
stable Skov-3X cells with the NFB-Luc gene are cotransfected with plasmid pcDNA-mutant, mutant is redox active
C99S
-
the mutant loses affinity for DNA and its activity is inhibited by 10 mM Mg2+, involvement of Cys99 in APE1's substrate binding and catalysis provides an example of involvement of a residue far from the active site
D210A
-
reduced single-turnover rate
D219A
replacement of Asp219 with alanine decreases both the DNA binding and the AP endonuclease activity of the enzyme compared to wild-type
D233A
no residual m6A demethylase activity, about 30% decrease in apurinic/apyrimidinic lyase activity
D283A
-
altered kinetic values
D283A/D308A
-
altered kinetic values compared to wild-type enzyme
D70R
-
binding affinity nearly identical with wild-type enzyme, reduced specific endonuclease activity, at Mg2+ concentrations below 1 mM the activity of the mutant sharply decreases
D90A
replacement of Asp90 with alanine results in decrease in endonuclease activity, but the DNA binding activity is preserved compared to wild-type
DELTA1-20
-
nuclear localization is significantly decreased
DELTA1-29
-
mutant enzyme retains activity against abasic sites in single-stranded DNA
DELTA1-36
-
mutant enzyme retains activity against abasic sites in single-stranded DNA
DELTA1-7
-
mutant shows nearly normal nuclear localization
DELTA1-7/E12A/D13A
-
nuclear localization is significantly decreased
DELTAP211
-
truncated hairpin, mutant protein is inactive
E12A/D13A
-
mutant shows nearly normal nuclear localization
E96Q/D210N
mutation (APE1 ED or simply ED) is created by site-specific mutagenesis of the pETApe1 plasmid, mutant cannot bind Mg2+ in the active site
F266A
-
30fold reduction in abasic dsDNA incision, complete loss of endoribonuclease activity against c-myc CRD
F319A
DNA glycosylase activity is reduced 52.6fold, activity towards abasic sites is reduced 1.5fold
H113A/C118A/C129A/H134A
no residual m6A demethylase activity, about 55% decrease in apurinic/apyrimidinic lyase activity
H231A
no residual m6A demethylase activity, about 20% decrease in apurinic/apyrimidinic lyase activity
H270A
DNA glycosylase activity is reduced 50fold, activity towards abasic sites is reduced 2.3fold
H270L
DNA glycosylase activity is reduced 71.4fold, activity towards abasic sites is reduced 3.7fold
H270R
DNA glycosylase activity is reduced 3.9fold, activity towards abasic sites is nearly identical to wild-type activity
H287A
no residual m6A demethylase activity, about 25% decrease in apurinic/apyrimidinic lyase activity
H309S
-
loss of abasic dsDNA incision
InsG212
-
extended hairpin, diminished recognition and binding to 5-hydroxycytosine-containing DNA
K133A
about 50% decrease in m6A demethylase activity, about 45% decrease in apurinic/apyrimidinic lyase activity
K212R
lower catalytic specificity than wild-type enzyme
K212S
-
mutant protein is inactive
K27Q
site-directed mutagenesis, chromatin-binding defective K27Q mutant, but the mutation of Lys27 in recombinant APE1 proteins does not affect acetylation by p300 at Lys6 in vitro
K299A/R301A
-
the mutation diminishes mitochondrial translocation of APE1
K3l/R4L/K6L/K7L
-
as the wild-type enzyme the mutant enzyme is predominantly localitzed in the nucleus
K6A/K7A
mutation targeting the gene regulation function. Mutant shows a diffuse nuclear staining, with a minimal localization in nucleoli. Mutant produces mitotic defects in Ape1-depleted cells, particularly promoting the formation of binucleated cells. Expression of the mutant protein increases the frequency of end-to-end fusions
K6R/K7R
-
no significant difference in nuclear localization between wild-type enzyme and mutant enzyme
N226A
increased cleavage rate at apurinic/apyrimidinic sites, ability to bind to damaged DNA decreases
N226A/N229A
ability of the mutant to bind damaged DNA is decreased, Vmax is almost identical to that of the wild-type enzyme
N229A
increased cleavage rate at apurinic/apyrimidinic sites, ability to bind to damaged DNA decreases
P211R
-
kinetic parameters similar to wild-type enzyme, decreased specificity of binding
Q315A
DNA glycosylase activity is reduced 1.6fold, activity towards abasic sites is increased 1.18fold
R156Q
-
100fold reduced DNA binding capacity
Y171A
-
enhancement by imidazole (in absence of tyrosine) is lower than that of wild-type enzyme. The ratio of turnover number to Km-value for DNA containing an abasic site is 50000fold lower than wild-type value at low salt concentration and 7500fold lower than wild-type value at high salt concentrations
Y171F/P173L/N174K
-
mutation results in 20000fold decrease in the reaction rate and reduced binding affinity
Y171H
-
mutant enzyme is not enhanceed by imidazole (in absence of tyrosine). The ratio of turnover number to Km-value for DNA containing an abasic site is 50000fold lower than wild-type value at low salt concentration
Y269A
-
the ratio of turnover number to Km-value for DNA containing an abasic site is 12.5fold lower than wild-type value at low salt concentration and 21.4fold lower than wild-type value at high salt concentrations
W199S
-
mutant is designed in order to investigate the involvement of the tryptophan residues in AP site recognition
W199S/W213S
-
mutant is designed in order to investigate the involvement of the tryptophan residues in AP site recognition
W213S
-
mutant is designed in order to investigate the involvement of the tryptophan residues in AP site recognition
A138D
-
production by site-directed mutagenesis
D335N
mutant retains its capacity to bind to AP sites in DNA, but loses its endonuclease activity
D251A
site-directed mutagenesis, the mutant shows a 3fold decline in the endonucleolytic cleavage activity
E57A
site-directed mutagenesis, the mutant shows a 2fold decline in the endonucleolytic cleavage activity
E57A/D251A
site-directed mutagenesis, the double mutant shows no 3'-5' exonuclease activity
F242S
site-directed mutagenesis, the mutant shows increased 3'-5' exonuclease catalytic efficiency compared to wild-type
W235S
site-directed mutagenesis, the mutant shows decreased 3'-5' exonuclease catalytic efficiency compared to wild-type
Y137S
site-directed mutagenesis, the mutant shows decreased 3'-5' exonuclease catalytic efficiency compared to wild-type
Y234S
site-directed mutagenesis, the mutant shows decreased 3'-5' exonuclease catalytic efficiency compared to wild-type
Y234S/W235S
site-directed mutagenesis, the mutant shows decreased 3'-5' exonuclease catalytic efficiency compared to wild-type
Y237S
site-directed mutagenesis, the mutant shows no 3'-5' exonuclease activity
D166N
mutant enzyme shows wild-type activity
K147Q
activity of mutant enzyme is severely attenuated
Q31E/D218S
almost no glycosylase activity
Q31S
significantly reduced glycosylase activity
W222A
almost no glycosylase activity
W222F
mutant is similarly active as wild type on 8-oxoguanine/C substrates
W69F
mutant is similarly active as wild type on 8-oxoguanine/C substrates
D166N
-
mutant enzyme shows wild-type activity
-
D172Q
-
binds to 8-oxoguanine containing single-stranded DNA more tightly than double-stranded DNA containing a 8-oxoguanine/cytosine base pair
-
K140Q
-
inactive mutant enzyme
-
K147Q
-
activity of mutant enzyme is severely attenuated
-
W222A
-
almost no glycosylase activity
-
W222F
-
mutant is similarly active as wild type on 8-oxoguanine/C substrates
-
W69F
-
mutant is similarly active as wild type on 8-oxoguanine/C substrates
-
Y127F
-
decreased endonuclease activity, Tyr 127 is essential to the binding and stabilization of the Fe3+ ion, mutation do not affect DNA binding
E261A
the mutant retains some activity
H70A/H110A
the mutant retains residual enzyme activity
H70A/H110A/E261A
the mutant completely loses the activity
C65A
-
redox deficient-DNA repair competent (adenovirus infected)
N226A/R177A
-
DNA repair-deficient-redox competent Ape1 does not protect rat neurons from cisplatin toxicity (adenovirus infected)
K364R
-
ntg1, localized to both nuclei and mitochondria
E233S
site-directed mutagenesis
Y105A
site-directed mutagenesis
E233S
-
site-directed mutagenesis
-
Y105A
-
site-directed mutagenesis
-
W200S
-
mutant is designed in order to investigate the involvement of the tryptophan residues in AP site recognition
W200S/W214S
-
mutant is designed in order to investigate the involvement of the tryptophan residues in AP site recognition
W214S
-
mutant is designed in order to investigate the involvement of the tryptophan residues in AP site recognition
C65A
-
redox deficient mutant
C65A
-
site-directed mutagenesis of a pET28A vector encoding human Ape1 (40-318) is performed, mutant is redox inactive
C65S
-
repair activity is not affected
C65S
mutation targeting the Ref-1 redox functions. Mutant form is detected in cytoplasmic vesicles indicating altered turnover. The endonuclease domain of Ape1 is required for successful mitotic progression
D210N
-
catalytically inactive
D210N
-
mutant enzyme is catalytically inactive against abasic sites in double-stranded DNA and single-stranded DNA
D210N
-
loss of abasic dsDNA incision, complete loss of endoribonuclease activity against c-myc CRD
D283N
-
loss of abasic dsDNA incision, no change in endoribonuclease activity against c-myc CRD
D283N
-
retaines endoribonuclease and abasic single-stranded RNA cleavage activities, with concurrent loss of apurinic/apyrimidinic site cleavage activities on double-stranded DNA and single-stranded DNA
D308A
-
altered kinetic values compared to wild-type enzyme
D308A
-
1.4fold reduction in abasic dsDNA incision, complete loss of endoribonuclease activity against c-myc CRD
D308A
replacement of Asp308 with alanine results in decrease in endonuclease activity, but the DNA binding activity is preserved compared to wild-type
D70A
-
mutant increases capacity to remove 3'-blocking ends in vitro
D70A
-
6.7fold reduction in abasic dsDNA incision, complete loss of endoribonuclease activity against c-myc CRD
E96A
-
exonuclease deficient mutant
E96A
-
APE-1 mutant displays a significantly reduced DNA-repair activity when compared with the wild-type protein
E96A
-
the mutant does not exhibit any nuclease activity against 88-nt RNA substrate
E96A
-
no reduction in abasic dsDNA incision, complete loss of endoribonuclease activity against c-myc CRD
E96A
replacement of Glu96 with alanine results in decrease in endonuclease activity, but the DNA binding activity is preserved compared to wild-type
E96Q
-
binding affinity nearly identical with wild-type enzyme, reduced specific endonuclease activity
E96Q
-
exonuclease deficient mutant
E96Q
the mutant is expressed well in both TB and autoinducing media, the E96Q mutation prevents Mg2+ binding at this site
H309N
-
altered kinetic values compared to wild-type enzyme
H309N
-
reduced single-turnover rate
H309N
-
the mutant does not exhibit any nuclease activity against 88-nt RNA substrate
H309N
site-directed mutagenesis, the mutant still binds to chromatin and gets acetylated
N212A
mutation targeting the endonuclease function. Mutant shows mainly nuclear staining, with a focal accumulation in nucleoli. Expression of the mutant protein increases the frequency of end-to-end fusions
N212A
simulations with substitution of Asn212 by Ala show a Mg2+-ion coordination comparable to that of the wild-type
N68A
-
binding affinity nearly identical with wild-type enzyme, reduced specific endonuclease activity, at Mg2+ concentrations below 1 mM the activity of the mutant sharply decreases
N68A
-
loss of abasic dsDNA incision, complete loss of endoribonuclease activity against c-myc CRD
R177A
APE1's high affinity for DNA single-strand breaks requires Arg177, poly(ADP-ribose)polymerase 1, PARP1, activation is not suppressed by the mutant
R177A
he turnover number of the endonuclease reaction catalyzed by APE1 increases compared to wild-type when Arg177 is replaced by alanine
Y128A
-
100fold reduced DNA binding capacity
Y128A
-
the ratio of turnover number to Km-value for DNA containing an abasic site is 33fold lower than wild-type value at low salt concentration and 7.5fold lower than wild-type value at high salt concentrations
Y171F
-
the ratio of turnover number to Km-value for DNA containing an abasic site is 25000fold lower than wild-type value at low salt concentration
Y171F
-
loss of abasic dsDNA incision, complete loss of endoribonuclease activity against c-myc CRD
K129S
inactive mutant enzyme
K129S
-
inactive mutant enzyme
-
D172N
inactive mutant enzyme
D172N
binds to 8-oxoguanine containing single-stranded DNA more tightly than double-stranded DNA containing a 8-oxoguanine/cytosine base pair
D172Q
binds to 8-oxoguanine containing single-stranded DNA more tightly than double-stranded DNA containing a 8-oxoguanine/cytosine base pair
D172Q
no detectable glycosylase activity
K140Q
inactive mutant enzyme
K140Q
binds to 8-oxoguanine containing single-stranded DNA more tightly than double-stranded DNA containing a 8-oxoguanine/cytosine base pair
D172N
-
binds to 8-oxoguanine containing single-stranded DNA more tightly than double-stranded DNA containing a 8-oxoguanine/cytosine base pair
-
D172N
-
inactive mutant enzyme
-
H83A
site-directed mutagenesis, the mutation decrease the AP endonuclease activity of Apn1 owing to weak coordination of Zn2+ ions involved in enzymatic catalysis, suppressed enzymatic activity of H83A Apn1 results from the reduced number of active site Zn2+ ions. Analysis of kinetics of recognition, binding, and incision of DNA substrates of the H83A Apn1 mutant. Substitution of His83 with Ala influences catalytic complex formation and further incision of the damaged DNA strand. The H83A Apn1 catalysis depends not only on the location of the mismatch relative to the abasic site in DNA, but also on the nature of damage. H83A Apn1 appears to cleave substrates AP(2-aPu) and F(2-aPu) in several stages (F is tetrahydrofuran). Minimal kinetic mechanism of abasic site cleavage by H83A Apn1, molecular dynamics of H83A Apn1, overview. Molecular dynamics simulations of the H83A Apn1 structure containing the two Zn2+ ions reveal an insignificant movement of Zn2 relative to DNA and amino acid residues involved in Zn2 coordination. Structure of enzyme mutant H83A Apn1-substrate DNA complex with three Zn2+ ions containing Zn2+ ions per molecule of mutant enzyme, overview
H83A
site-directed mutagenesis, the mutation decrease the AP endonuclease activity of Apn1 owing to weak coordination of Zn2+ ions involved in enzymatic catalysis, suppressed enzymatic activity of H83A Apn1 results from the reduced number of active site Zn2+ ions. The active site of H83A Apn1 contains only two Zn2+ ions, with their positions being changed versus a trinuclear Zn2+ cluster of wild-type Apn1
H83A
-
site-directed mutagenesis, the mutation decrease the AP endonuclease activity of Apn1 owing to weak coordination of Zn2+ ions involved in enzymatic catalysis, suppressed enzymatic activity of H83A Apn1 results from the reduced number of active site Zn2+ ions. Analysis of kinetics of recognition, binding, and incision of DNA substrates of the H83A Apn1 mutant. Substitution of His83 with Ala influences catalytic complex formation and further incision of the damaged DNA strand. The H83A Apn1 catalysis depends not only on the location of the mismatch relative to the abasic site in DNA, but also on the nature of damage. H83A Apn1 appears to cleave substrates AP(2-aPu) and F(2-aPu) in several stages (F is tetrahydrofuran). Minimal kinetic mechanism of abasic site cleavage by H83A Apn1, molecular dynamics of H83A Apn1, overview. Molecular dynamics simulations of the H83A Apn1 structure containing the two Zn2+ ions reveal an insignificant movement of Zn2 relative to DNA and amino acid residues involved in Zn2 coordination. Structure of enzyme mutant H83A Apn1-substrate DNA complex with three Zn2+ ions containing Zn2+ ions per molecule of mutant enzyme, overview
-
H83A
-
site-directed mutagenesis, the mutation decrease the AP endonuclease activity of Apn1 owing to weak coordination of Zn2+ ions involved in enzymatic catalysis, suppressed enzymatic activity of H83A Apn1 results from the reduced number of active site Zn2+ ions. The active site of H83A Apn1 contains only two Zn2+ ions, with their positions being changed versus a trinuclear Zn2+ cluster of wild-type Apn1
-
additional information
protein with two additional amino acid residues and a truncated protein with deletion of 22 residues at the amino-terminus are equally active
additional information
-
protein with two additional amino acid residues and a truncated protein with deletion of 22 residues at the amino-terminus are equally active
additional information
APE1 lacking the first 34 amino acids at the Nterminus, unlike wild-type enzyme, is unable to form cross-links with BS-AP DNAs that testifies to the involvement of disordered N-terminal extension, which is enriched in lysine residues, in the interaction with AP sites.
additional information
-
APE1 lacking the first 34 amino acids at the Nterminus, unlike wild-type enzyme, is unable to form cross-links with BS-AP DNAs that testifies to the involvement of disordered N-terminal extension, which is enriched in lysine residues, in the interaction with AP sites.
additional information
apurinic/apyrimidinic endonuclease 1-siRNA-mediated downregulation in osteosarcoma cells inhibits expression of TGFbeta1. Apurinic/apyrimidinic endonuclease 1-siRNA inhibits the capability to enhance HUVEC migration and tube formation of tumor cells through the TGFbeta/Smad3 signaling pathway. Tumor angiogenesis and growth in xenografts are suppressed by APE1-siRNA
additional information
-
apurinic/apyrimidinic endonuclease 1-siRNA-mediated downregulation in osteosarcoma cells inhibits expression of TGFbeta1. Apurinic/apyrimidinic endonuclease 1-siRNA inhibits the capability to enhance HUVEC migration and tube formation of tumor cells through the TGFbeta/Smad3 signaling pathway. Tumor angiogenesis and growth in xenografts are suppressed by APE1-siRNA
additional information
construction of a redox-deficient truncated APE1 protein lacking the first N-terminal 61 amino acid residues (APE1-NDELTA61) the mutant cannot stimulate DNA glycosylase activities of OGG1, MBD4, and ANPG on duplex DNA substrates in contrast to the wild-type enzyme
additional information
-
construction of a redox-deficient truncated APE1 protein lacking the first N-terminal 61 amino acid residues (APE1-NDELTA61) the mutant cannot stimulate DNA glycosylase activities of OGG1, MBD4, and ANPG on duplex DNA substrates in contrast to the wild-type enzyme
additional information
downregulation of endogenous APE1 levels in HEK293T cells using small interfering RNA (siRNA). Mutant phenotypes, overview
additional information
-
downregulation of endogenous APE1 levels in HEK293T cells using small interfering RNA (siRNA). Mutant phenotypes, overview
additional information
-
deletion mutant delta369 and delta491, the C-terminal deletion does not affect the AP endonuclease activity, but the protein is defective in the removal of AP sites in vivo
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