Literature summary for 4.2.99.18 extracted from

Dyakonova, E.S.; Koval, V.V.; Lomzov, A.A.; Ishchenko, A.A.; Fedorova, O.S.
The role of His-83 of yeast apurinic/apyrimidinic endonuclease Apn1 in catalytic incision of abasic sites in DNA (2015), Biochim. Biophys. Acta, 1850, 1297-1309 .

Search for more literature for 4.2.99.18

Cloned(Commentary)

Cloned (Comment)	Organism
gene APN1, sequence comparisons, recombinant expression of His-tagged wild-type and mutant enzymes	Saccharomyces cerevisiae

Protein Variants

Protein Variants	Comment	Organism
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	Saccharomyces cerevisiae

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
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	Saccharomyces cerevisiae

Metals/Ions

Metals/Ions	Comment	Organism	Structure
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	Saccharomyces cerevisiae

Organism

Organism	UniProt	Comment	Textmining
Saccharomyces cerevisiae	P22936	-	-
Saccharomyces cerevisiae ATCC 204508 / S288c	P22936	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged wild-type and mutant enzymes by nickel affinity chromatography	Saccharomyces cerevisiae

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
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	Saccharomyces cerevisiae	?	-	?
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	Saccharomyces cerevisiae ATCC 204508 / S288c	?	-	?

Synonyms

Synonyms	Comment	Organism
APN1	-	Saccharomyces cerevisiae
apurinic/apyrimidinic endonuclease	-	Saccharomyces cerevisiae

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
25	-	assay at	Saccharomyces cerevisiae

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.6	-	assay at	Saccharomyces cerevisiae

General Information

General Information	Comment	Organism
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	Saccharomyces cerevisiae
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	Saccharomyces cerevisiae

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Release 2023.1 (January 2023)