Get   for     ? 
 Site search     ? 
Catalytic Site Atlas Version 2.2.12
Find Annotated Site: PDB code:
Swiss-Prot code:
EC number:
Help
CSA entry for 1bix
Original Entry
Title:
Dna repair
Compound:
Ap endonuclease 1
Mutant:
No
UniProt/Swiss-Prot:
P27695-APE1_HUMAN
EC Class:
4.2.99.18
Other CSA Entries:
Overview of all sites for 1bix
Homologues of 1bix
Entries for UniProt/Swiss-Prot: P27695
Entries for EC: 4.2.99.18
Other Databases:
PDB entry: 1bix
PDBsum entry: 1bix
UniProt/Swiss-Prot: P27695
IntEnz entry: 4.2.99.18
Literature Report:
Introduction:
Human 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.
Mechanism:
1. 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.
Sites:

Click to Display Catalytic Site (Get help with this section)
Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
401 0Sidechain
ElectrostaticSubstrate
ElectrostaticTransition state
Mg2+ distorts the 5' phosphate of an abasic site, resulting in an electropositive phosphorous group open to attack by phenolate residue. Mg2+ also stabilises the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10390343 Current protein Mutagenesis of residue
PubMed ID 10390343 Current protein Kinetic studies
PubMed ID 10390343 Current protein Ligand is essential for catalysis
PubMed ID 15380100 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
TYRA 171 171Sidechain
NucleophileSubstrate
Tyr 171 nucleophilically attacks the scissile phosphate directly.
Evidence from paper Evidence concerns Evidence type
PubMed ID 15380100 Current protein pH dependence of reaction
PubMed ID 10390343 Current protein Mutagenesis of residue
PubMed ID 15380100 Current protein Kinetic studies
PubMed ID 15380100 Current protein Mutagenesis of residue
PubMed ID 15380100 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 210 210Sidechain
Acid/baseWater
Acid/baseSubstrate
Asp 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.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10871340 Current protein Mutagenesis of residue
PubMed ID 10390343 Current protein Kinetic studies
PubMed ID 10871340 Current protein Kinetic studies
PubMed ID 10390343 Current protein Mutagenesis of residue
PubMed ID 10871340 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 283 283Sidechain
ElectrostaticResidue
Asp 283 stabilises His 309 through hydrogen bonding.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12758078 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12758078 Current protein Conservation of residue
PubMed ID 15380100 Current protein Kinetic studies
PubMed ID 15380100 Current protein Mutagenesis of residue
PubMed ID 12758078 Current protein Mutagenesis of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 309 309Sidechain
ElectrostaticTransition state
ElectrostaticSubstrate
His 309 contributes to polarisation of the DNA phosphate group. His 309 also stabilises the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12758078 Current protein Mutagenesis of residue
PubMed ID 15380100 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12758078 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12758078 Current protein Conservation of residue
Notes:
It remains unclear how the leaving groups are stabilised.
References:
1
Novel role of tyrosine in catalysis by human AP endonuclease 1.
S. T. Mundle and M. H. Fattal and L. F. Melo and J. D. Coriolan and N. E. O'Regan and P. R. Strauss
DNA Repair (Amst) 3, (11) 1447-55, (2004).
15380100
2
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. P. Erzberger and D. M. Wilson
J Mol Biol 290, (2) 447-57, (1999).
10390343
3
Investigation of the role of the histidine-aspartate pair in the human exonuclease III-like abasic endonuclease, Ape1.
D. F. Lowry and D. W. Hoyt and F. A. Khazi and J. Bagu and A. G. Lindsey and D. M. Wilson
J Mol Biol 329, (2) 311-22, (2003).
12758078
4
Substitution of Asp-210 in HAP1 (APE/Ref-1) eliminates endonuclease activity but stabilises substrate binding.
D. G. Rothwell and B. Hang and M. A. Gorman and P. S. Freemont and B. Singer and I. D. Hickson
Nucleic Acids Res 28, (11) 2207-13, (2000).
10871340
Which EBI biological databases are available and how do I access them? EBI Site Map