› 6wcd

X-ray diffraction
1.54Å resolution

Crystal Structure of Xenopus laevis APE2 Catalytic Domain

Released:
DOI: 10.2210/pdb6wcd/pdb
Model geometry
Fit model/data
PDB entry 6wcd coloured by chain, front view.
PDB entry 6wcd coloured by chain, side view.
PDB entry 6wcd coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Endogenous DNA 3' Blocks Are Vulnerabilities for BRCA1 and BRCA2 Deficiency and Are Reversed by the APE2 Nuclease.
Álvarez-Quilón A, Wojtaszek JL, Mathieu MC, Patel T, Appel CD, Hustedt N, Rossi SE, Wallace BD, Setiaputra D, Adam S, Ohashi Y, Melo H, Cho T, Gervais C, Muñoz IM, Grazzini E, Young JTF, Rouse J, Zinda M, Williams RS, Durocher D
Mol Cell 78 1152-1165.e8 (2020)
PMID: 32516598

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 analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179511 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA-(apurinic or apyrimidinic site) endonuclease 2 Chain: A
Molecule details ›
Chain: A
Length: 355 amino acids
Theoretical weight: 39.86 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6DDT4 (Residues: 1-355; Coverage: 69%)
Gene names: ape2, apex2, apex2.L, apexl2, xth2
Sequence domains: Endonuclease/Exonuclease/phosphatase family

Ligands and Environments

4 bound ligands:
Ligand MG 1 x MG
Ligand MES 1 x MES
Ligand BU1 3 x BU1
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 56.383Å b: 73.149Å c: 98.877Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.144 0.143 0.157
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Human topoisomerases and their roles in genome stability and organization.
Pommier et al. (2022)
13 more

1 mention without citation

Endogenous DNA 3' Blocks Are Vulnerabilities for BRCA1 and BRCA2 Deficiency and Are Reversed by the APE2 Nuclease.
Álvarez-Quilón et al. (2020)