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. 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 | Saccharomyces cerevisiae |
KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
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) | Saccharomyces cerevisiae |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
additional information | the nucleotide incision repair of the enzyme in presence of Mg2+ is unaltered, Mg2+ does not affect yeast Ape1 activity | Saccharomyces cerevisiae | |
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 | Saccharomyces cerevisiae |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
additional information | Saccharomyces cerevisiae | 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 | Saccharomyces cerevisiae ATCC 204508 / S288c | 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 | ? | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Saccharomyces cerevisiae | P22936 | - |
- |
Saccharomyces cerevisiae ATCC 204508 / S288c | P22936 | - |
- |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
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 | Saccharomyces cerevisiae | ? | - |
? | |
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 | Saccharomyces cerevisiae | ? | - |
? | |
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 | Saccharomyces cerevisiae ATCC 204508 / S288c | ? | - |
? | |
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 | Saccharomyces cerevisiae ATCC 204508 / S288c | ? | - |
? |
Synonyms | Comment | Organism |
---|---|---|
APN1 | - |
Saccharomyces cerevisiae |
apurinic/apyrimidinic endonuclease | - |
Saccharomyces cerevisiae |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
25 | - |
assay at | Saccharomyces cerevisiae |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
7.6 | - |
assay at | Saccharomyces cerevisiae |
General Information | Comment | Organism |
---|---|---|
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 | Saccharomyces cerevisiae |
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 | Saccharomyces cerevisiae |