› 2voa

X-ray diffraction
1.7Å resolution

Structure of an AP Endonuclease from Archaeoglobus fulgidus

Released:
DOI: 10.2210/pdb2voa/pdb
PDB entry 2voa coloured by chain, front view.
PDB entry 2voa coloured by chain, side view.
PDB entry 2voa coloured by chain, top view.
Source organisms:
Primary publication:
Structure and function of the abasic site specificity pocket of an AP endonuclease from Archaeoglobus fulgidus.
Schmiedel R, Kuettner EB, Keim A, Sträter N, Greiner-Stöffele T
DNA Repair (Amst) 8 219-31 (2009)
PMID: 19015049

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
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115880 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Endonuclease/exonuclease/phosphatase domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 257 amino acids
Theoretical weight: 29.81 KDa
Source organism: Archaeoglobus fulgidus
Expression system: Escherichia coli
UniProt:
  • Canonical: O29675 (Residues: 1-257; Coverage: 100%)
Gene name: AF_0580
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
5'-D(*GP*CP*GP*GP*TP*AP*GP*CP*CP*GP)-3' Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.09 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*CP*GP*GP*CP*TP*AP*CP*CP*GP*CP)-3' Chain: D
Molecule details ›
Chain: D
Length: 10 nucleotides
Theoretical weight: 3.01 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand OCS 2 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P21
Unit cell:
a: 67.786Å b: 60.817Å c: 72.349Å
α: 90° β: 91.22° γ: 90°
R-values:
R R work R free
0.198 0.198 0.23
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Base excision repair in Archaea: back to the future in DNA repair.
Grasso et al. (2014)
11 other articles

4 mentions without citation

Molecular dynamics using atomic-resolution structure reveal structural fluctuations that may lead to polymerization of human Cu-Zn superoxide dismutase.
Strange et al. (2007)
3 more