3.1.21.2: deoxyribonuclease IV
This is an abbreviated version!
For detailed information about deoxyribonuclease IV, go to the full flat file.
Word Map on EC 3.1.21.2
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3.1.21.2
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exonuclease
-
ape1
-
glycosylase
-
abasic
-
strand
-
endonucleases
-
single-stranded
-
nick
-
uracil
-
duplex
-
phosphodiester
-
uracil-dna
-
methanesulfonate
-
3'-blocking
-
8-oxoguanine
-
3'-phosphatase
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depurinated
-
deoxyribose
-
3\'-hydroxyl
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xrcc1
-
diesterase
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incise
-
site-containing
-
base-excision
-
endonucleolytic
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8-oxog
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soxrs
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ap-site
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5'-deoxyribose
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cross-complementing
-
non-ltr
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repair-deficient
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exoiiis
-
5'-phosphorylated
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uracil-containing
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non-long
-
3'-phosphoglycolate
-
asp148glu
-
analysis
-
pharmacology
- 3.1.21.2
-
exonuclease
- ape1
- glycosylase
-
abasic
- strand
- endonucleases
-
single-stranded
- nick
- uracil
- duplex
-
phosphodiester
-
uracil-dna
- methanesulfonate
-
3'-blocking
- 8-oxoguanine
-
3'-phosphatase
-
depurinated
- deoxyribose
-
3\'-hydroxyl
- xrcc1
- diesterase
-
incise
-
site-containing
-
base-excision
-
endonucleolytic
-
8-oxog
-
soxrs
-
ap-site
-
5'-deoxyribose
-
cross-complementing
-
non-ltr
-
repair-deficient
- exoiiis
-
5'-phosphorylated
-
uracil-containing
-
non-long
-
3'-phosphoglycolate
-
asp148glu
- analysis
- pharmacology
Reaction
Endonucleolytic cleavage of ssDNA at apurinic/apyrimidinic sites to 5'-phosphooligonucleotide end-products =
Synonyms
apurinic/apyrimidinic endonuclease, coliphage T4 endonuclease II, deoxriboendonuclease, DNA-adenine-transferase, E. coli endonuclease IV, EC 3.1.4.30, End, Endo IV, endodeoxyribonuclease IV, EndoII, EndoIV, endonuclease II, endonuclease IV, exonuclease III, More, MtbEndo IV, MtbNfo, MtbXthA, Nfo, nuclease, endodeoxyribo-oder redoxyendonuclease, Rv0670, Sco4631, ScoA3McrA, T4 endonuclease IV, TthNfo, type IV methyl-dependent restriction endonuclease
ECTree
3.1.21.2 deoxyribonuclease IVAdvanced search results
results (
results (Substrates Products
Substrates Products on EC 3.1.21.2 - deoxyribonuclease IV
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SUBSTRATE 
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
double-stranded native DNA + H2O
5'-phosphooligonucleotides
-
endonucleolytic cleavage of DNA into 5'-phosphooligonucleotides, the enzyme makes predominantly single-strand break, and a few double-strand breaks, the ratio is 3.7:1
-
-
ir
double-stranded nativeDNA + H2O
5'-phosphooligonucleotides
-
endonucleolytic cleavage of DNA into 5'-phosphooligonucleotides
-
-
ir
single-stranded DNA + H2O
?
-
the enzyme cleaves apurinic/apyrimidinic sites in single-stranded DNA. DNA probe containing a tetrahydrofuranyl abasic site to mimic the natural apurinic/apyrimidinic site
-
-
?
5'-end-labeled 19 nucleotide single-stranded DNA + H2O
?
-
-
-
?
5'-end-labeled 19 nucleotide single-stranded DNA + H2O
?
-
-
-
?
5'-end-labeled 29 nucleotide double-stranded DNA + H2O
?
92% cleavage after 30 min
-
-
?
5'-end-labeled 29 nucleotide double-stranded DNA + H2O
?
92% cleavage after 30 min
-
-
?
double stranded DNA + H2O
?
-
the enzyme prefers to remove mismatched 3'-terminal nucleotides from 3'-recessed, nicked, and gapped double stranded DNA
-
-
?
double stranded DNA + H2O
?
the enzyme cleaves with good efficiency a DNA duplex containing the abasic site analogue tetrahydrofuran. The enzyme contains apurinic/apyrimidinic endonuclease activity and 3'-5' exonuclease activity
-
-
?
double stranded DNA + H2O
?
the enzyme cleaves with good efficiency a DNA duplex containing the abasic site analogue tetrahydrofuran. The enzyme contains apurinic/apyrimidinic endonuclease activity and 3'-5' exonuclease activity
-
-
?
double-stranded alkylated DNA + H2O
5'-phosphooligonucleotides
-
endonucleolytic cleavage of DNA into 5'-phosphooligonucleotides
-
-
ir
double-stranded alkylated DNA + H2O
5'-phosphooligonucleotides
-
endonucleolytic cleavage of DNA into 5'-phosphooligonucleotides, hydrolysis of a phosphodiester bond near an alkylated base in native DNA without single breaks in the region, the enzyme makes predominantly single-strand break, and a few double-strand breaks, the ratio is 3.7:1
-
-
ir
double-stranded alkylated DNA + H2O
5'-phosphooligonucleotides
Tequatrovirus T4
-
in vivo the enzyme produces mostly double-stranded fragments with a few internal nicks
-
-
ir
double-stranded alkylated DNA + H2O
5'-phosphooligonucleotides
Tequatrovirus T4
-
the enzyme cleaves sites of DNA with conserved sequence elements to both the left and the right of the cleaved bonds comprising 16 basepairs with some variability tolerated, nicking of a single and both strands, the latter in two nicking events, substrate specificity, overview, in vitro the enzyme produces mostly single-stranded nicks
-
-
ir
double-stranded DNA + H2O
?
-
Endo IV has considerably high cleaving activity to apurinic/apyrimidinic sites in ssDNA compared with that in double-stranded DNA
-
-
?
double-stranded DNA + H2O
?
-
the enzyme can cleave various apurinic/apyrimidinic site analogues in ssDNA and dsDNA. The apurinic/apyrimidinic endonuclease activity can incise DNA 5' to various apurinic/apyrimidinic site analogues, including the alkane chain Spacer and polyethylene glycol Spacer. The efficient cleavage at apurinic/apyrimidinic sites requires 2 or more normal nucleotides existing at the 5'-terminus. The enzyme also possesses 3'-exonuclease activity for removing 3'-blocking groups and normal nucleotides
-
-
?
plasmid containing AP sites + H2O
?
the enzyme has apurinic/apyrimidinic endonuclease activity, 3'-phosphatase activity, and 3'-repair diesterase activity for phosphoglycolates and trans-4-hydroxy-2-pentenal-5-phosphates
-
-
?
plasmid containing AP sites + H2O
?
the enzyme has apurinic/apyrimidinic endonuclease activity, 3'-phosphatase activity, and 3'-repair diesterase activity for phosphoglycolates and trans-4-hydroxy-2-pentenal-5-phosphates
-
-
?
single-stranded DNA + H2O
5'-phosphooligonucleotides
-
preference for single-stranded DNA
about 150 nucleotides long
ir
single-stranded DNA + H2O
5'-phosphooligonucleotides
-
denatured lambda-DNA, breaks exlusively adjacent to cytosine residues
about 150 nucleotides long
ir
single-stranded DNA + H2O
5'-phosphooligonucleotides
-
no activity on denatured T4 DNA
about 150 nucleotides long
ir
single-stranded DNA + H2O
5'-phosphooligonucleotides
-
breakdown of host cell DNA occuring after T4 phage infection
-
ir
single-stranded DNA + H2O
5'-phosphooligonucleotides
Escherichia coli B / ATCC 11303
-
preference for single-stranded DNA
about 150 nucleotides long
ir
single-stranded DNA + H2O
5'-phosphooligonucleotides
Escherichia coli B / ATCC 11303
-
denatured lambda-DNA, breaks exlusively adjacent to cytosine residues
about 150 nucleotides long
ir
single-stranded DNA + H2O
5'-phosphooligonucleotides
Escherichia coli B / ATCC 11303
-
no activity on denatured T4 DNA
about 150 nucleotides long
ir
single-stranded DNA + H2O
5'-phosphooligonucleotides
Escherichia coli B / ATCC 11303
-
breakdown of host cell DNA occuring after T4 phage infection
-
ir
single-stranded DNA + H2O
5'-phosphooligonucleotides
Tequatrovirus T4
-
the Ser176 of T4 endonuclease IV is crucial for the restricted and polarized dC-specific cleavage of single-stranded DNA implicated in restriction of dC-containing DNA in host Escherichia coli
-
-
?
single-stranded DNA + H2O
5'-phosphooligonucleotides
Tequatrovirus T4
-
Endo IV catalyzes specific endonucleolytic cleavage of the 5' phosphodiester bond of dC in ssDNA with an efficiency dependent on the surrounding nucleotide sequence. The enzyme preferentially targets 5'-dTdCdA-3' but tolerates various combinations of individual nucleotides flanking this trinucleotide sequence. Endo IV preferentially recognizes short nucleotide sequences containing 5'-TdCdA-3', which likely accounts for the limited digestion of ssDNA by the enzyme and may be responsible in part for the indispensability of a deficiency in denB for stable synthesis of dC-substituted T4 genomic DNA
-
-
?
single-stranded DNA + H2O
5'-phosphooligonucleotides
Tequatrovirus T4
-
endonuclease IV cleaves single-stranded (ss) DNA in a dC-specific manner. The Ser176 of T4 endonuclease IV is crucial for the restricted and polarized dC-specific cleavage of single-stranded DNA implicated in restriction of dC-containing DNA in host Escherichia coli
-
-
?
single-stranded DNA + H2O
5'-phosphooligonucleotides
Tequatrovirus T4
-
the enzyme cleaves single-stranded (ss) DNA in a dC-specific manner. Endo IV cleaves ssDNAs exclusively at the 5-proximal dC where a sequence comprises dC residues both at the 5 proximal and 3 proximal positions (a dCs tract-dependent cleavage). The dCs tract-dependent cleavage is efficient and occurs when a dCs tract has at least 6 bases. Some dCs tracts larger than 6 bases behave as that of 6 bases (an extended dCs tract), while some others do not. One decameric dCs tract is shown to be cleavable in a dCs tract-dependent manner, but that with 13 dCs is not. The dCs tract-dependent cleavage is enhanced by the presence of a third dC residue at least for a 6 or 7 dCs tract. In contrast to the dCs tract-dependent cleavage, a dCs tract-independent one is generally inefficient and if two modes are possible for a substrate DNA, a dCs tract-dependent mode prevails
-
-
?
additional information
?
-
-
the enzyme hydrolyzes the 3'-nucleotide in the following order: nick > 3'-blunt > 3'-recessed > single stranded DNA
-
-
?
additional information
?
-
role for Endo IV to counteract DNA damage induced by the oxidative counterpart of UVB in Escherichia coli
-
-
?
additional information
?
-
-
role for Endo IV to counteract DNA damage induced by the oxidative counterpart of UVB in Escherichia coli
-
-
?
additional information
?
-
reaction proceeds through a synchronous bimolecular (ANDN) mechanism with reaction free energy and barrier of -3.5 and 20.6 kcal/mol.In the course of the reaction the trinuclear active site of endonuclease IV undergoes dramatic local conformational changes: shifts in the mode of coordination of both substrate and first-shell ligands
-
-
?
additional information
?
-
-
Nfo-catalyzed nucleotide incision repair and exonuclease activities can generate a single-strand gap at the 5' side of 5,6-dihydrouracil residue
-
-
?
additional information
?
-
-
Nfo-catalyzed nucleotide incision repair and exonuclease activities can generate a single-strand gap at the 5' side of 5,6-dihydrouracil residue
-
-
?
additional information
?
-
endonuclease activity of the enzyme is about 2fold higher for double-stranded DNA in comparison to single-stranded DNA
-
-
?
additional information
?
-
-
endonuclease activity of the enzyme is about 2fold higher for double-stranded DNA in comparison to single-stranded DNA
-
-
?
additional information
?
-
the enzyme also shows 3'->5' exonuclease activity
-
-
?
additional information
?
-
-
the enzyme also shows 3'->5' exonuclease activity
-
-
?
additional information
?
-
endonuclease activity of the enzyme is about 2fold higher for double-stranded DNA in comparison to single-stranded DNA
-
-
?
additional information
?
-
the enzyme also shows 3'->5' exonuclease activity
-
-
?
additional information
?
-
-
a His-tagged derivative of ScoA3McrA cleaves S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites. Sco4631 cleaves DNA at multiple possible sites on either side of the S-modification. Double-strand cleavage occurs 16-28 nucleotides away from the phosphorothioate links
-
-
?
additional information
?
-
-
a His-tagged derivative of ScoA3McrA cleaves S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites. Sco4631 cleaves DNA at multiple possible sites on either side of the S-modification. Double-strand cleavage occurs 16-28 nucleotides away from the phosphorothioate links
-
-
?
additional information
?
-
Tequatrovirus T4
-
endonuclease IV encoded by denB of bacteriophage T4 is implicated in restriction of deoxycytidine (dC)-containing DNA in the host Escherichia coli
-
-
?
additional information
?
-
Tequatrovirus T4
-
EndoII primarily catalyzes single-stranded nicking of DNA, 5 to 10fold less frequently double-stranded breaks are produced
-
-
?
