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X-ray diffraction
2.65Å resolution

CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC DNA

Released:

Function and Biology Details

Reaction catalysed:
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-(apurinic or apyrimidinic site) lyase, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 279 amino acids
Theoretical weight: 31.48 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P27695 (Residues: 40-318; Coverage: 88%)
Gene names: APE, APE1, APEX, APEX1, APX, HAP1, REF1
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
5'-D(*GP*CP*GP*TP*CP*CP*(3DR)P*CP*GP*AP*CP*GP*AP*CP*G)-3' Chains: U, X
Molecule details ›
Chains: U, X
Length: 15 nucleotides
Theoretical weight: 4.45 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)-3' Chains: V, Y
Molecule details ›
Chains: V, Y
Length: 14 nucleotides
Theoretical weight: 4.34 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-1
Spacegroup: P21
Unit cell:
a: 71.221Å b: 72.249Å c: 93.749Å
α: 90° β: 94.292° γ: 90°
R-values:
R R work R free
0.195 0.195 0.286
Expression systems:
  • Escherichia coli
  • Not provided