› 1dew

X-ray diffraction
2.65Å resolution

CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC DNA

Released:
DOI: 10.2210/pdb1dew/pdb
PDB entry 1dew coloured by chain, front view.
PDB entry 1dew coloured by chain, side view.
PDB entry 1dew coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected].
Mol CD, Izumi T, Mitra S, Tainer JA
Nature 403 451-6 (2000)
PMID: 10667800

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113676 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA repair nuclease/redox regulator APEX1, 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:
Ligand SO4 1 x SO4
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

Quick links

Citations

92 review citations

Base excision repair.
Krokan et al. (2013)
91 more

32 mentions without citation

AdoMet-dependent methylation, DNA methyltransferases and base flipping.
Cheng et al. (2001)
31 more