› 2o3c

X-ray diffraction
2.3Å resolution

Crystal structure of zebrafish Ape

Released:
DOI: 10.2210/pdb2o3c/pdb
PDB entry 2o3c coloured by chain, front view.
PDB entry 2o3c coloured by chain, side view.
PDB entry 2o3c coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease.
Georgiadis MM, Luo M, Gaur RK, Delaplane S, Li X, Kelley MR
Mutat Res 643 54-63 (2008)
PMID: 18579163

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:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106134 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA repair nuclease APEX1 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 282 amino acids
Theoretical weight: 31.95 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: A0MTA1 (Residues: 33-310; Coverage: 90%)
Gene names: apex1, apex1a, apex1b, si:ch211-214j24.12, zgc:66204
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

1 bound ligand:
Ligand PB 3 x PB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P21
Unit cell:
a: 54.66Å b: 117.78Å c: 85.84Å
α: 90° β: 98.34° γ: 90°
R-values:
R R work R free
0.199 0.199 0.236
Expression system: Escherichia coli

Quick links

Citations

24 review citations

The many functions of APE1/Ref-1: not only a DNA repair enzyme.
Tell et al. (2009)
23 more

1 mention without citation

Insights into Mechanisms of Damage Recognition and Catalysis by APE1-like Enzymes.
Bulygin et al. (2022)