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Catalytic Site Atlas

CSA LITERATURE entry for 1bix

E.C. nameDNA-(apurinic or apyrimidinic site) lyase
SpeciesHomo sapiens (Human)
E.C. Number (IntEnz) 4.2.99.18
CSA Homologues of 1bix
CSA Entries With UniProtID P27695
CSA Entries With EC Number 4.2.99.18
PDBe Entry 1bix
PDBSum Entry 1bix
MACiE Entry 1bix

Literature Report

IntroductionHuman apurinic/apyrimidinic endonuclease I (HAP1) sourced from Homo sapiens is an essential DNA repair enzyme that initiates the removal of apurinic/apyrimidinic sites from DNA, excises 3' replication-blocking moieties and modulates DNA binding activity of several transcriptional regulators. HAP1 recognises abasic sites in ds DNA and makes a single nick in the backbone 5' to the abasic site generating the 3' hydroxyl required by the repair polymerase. Abasic lesions arise at high frequency in DNA due to spontaneous, mutagen induced or glycosylase-mediated hydrolysis of the N-glycosylic bond and represent cytotoxic and mutagenic lesions if uncorrected. HAP1 also exhibits 3'phosphodiesterase, 3'->5' exonuclease and RNase H activity.
The Ref-1 (redox effector factor) activity of HAP1 is to regulate the DNA-binding affinity of transcription factors such as Jun/Fos and NF-kB through a redox mechanism.
Mechansim1. Mg2+ distorts the 5' phosphate of an abasic site, resulting in an electropositive phosphorous group open to attack by phenolate residue. His 309 contributes to polarisation of the DNA phosphate group. 2. Tyr 171 is in a deprotonated state due to the presence of the hydrogen bonding network in the active site. Tyr 171 nucleophilically attacks the scissile phosphate directly. The transition state is stabilised by His 309 and Mg2+. His 309 is stabilised by hydrogen bonding to Asp 283. 3. Asp 210 acts as a general base, deprotonating a water molecule which attacks the scissile phosphate, displacing the Tyr 171 residue. The transition state is stabilised by His 309 and Mg2+. 4. Asp 210 acts as a general acid and protonates the leaving group.

Catalytic Sites for 1bix

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA309309macie:sideChainHis 309 contributes to polarisation of the DNA phosphate group. His 309 also stabilises the transition state.
AspA283283macie:sideChainAsp 283 stabilises His 309 through hydrogen bonding.
AspA210210macie:sideChainAsp 210 acts as a general base, deprotonating a water molecule which attacks the scissile phosphate. Asp 210 also acts as a general acid and protonates the leaving group.
TyrA171171macie:sideChainTyr 171 nucleophilically attacks the scissile phosphate directly.

Literature References

Notes:It remains unclear how the leaving groups are stabilised.
Lowry DF
Investigation of the role of the histidine-aspartate pair in the human exonuclease III-like abasic endonuclease, Ape1.
J Mol Biol 2003 329 311-322
PubMed: 12758078
Erzberger JP
The role of Mg2+ and specific amino acid residues in the catalytic reaction of the major human abasic endonuclease: new insights from EDTA-resistant incision of acyclic abasic site analogs and site-directed mutagenesis.
J Mol Biol 1999 290 447-457
PubMed: 10390343
Mundle ST
Novel role of tyrosine in catalysis by human AP endonuclease 1.
DNA Repair (Amst) 2004 3 1447-1455
PubMed: 15380100
Rothwell DG
Substitution of Asp-210 in HAP1 (APE/Ref-1) eliminates endonuclease activity but stabilises substrate binding.
Nucleic Acids Res 2000 28 2207-2213
PubMed: 10871340
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