› 1xqp

X-ray diffraction
1.69Å resolution

Crystal structure of 8-oxoguanosine complexed Pa-AGOG, 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum

Released:
DOI: 10.2210/pdb1xqp/pdb
PDB entry 1xqp coloured by chain, front view.
PDB entry 1xqp coloured by chain, side view.
PDB entry 1xqp coloured by chain, top view.
Source organism: Pyrobaculum aerophilum
Primary publication:
A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure.
Lingaraju GM, Sartori AA, Kostrewa D, Prota AE, Jiricny J, Winkler FK
Structure 13 87-98 (2005)
PMID: 15642264

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 domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187416 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-glycosylase/DNA lyase Chain: A
Molecule details ›
Chain: A
Length: 256 amino acids
Theoretical weight: 29.51 KDa
Source organism: Pyrobaculum aerophilum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8ZVK6 (Residues: 1-256; Coverage: 100%)
Gene name: PAE2237
Sequence domains: N-glycosylase/DNA lyase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 8HG 2 x 8HG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ENRAF-NONIUS FR591
Spacegroup: P21212
Unit cell:
a: 72.22Å b: 98.11Å c: 36.17Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.183 0.225
Expression system: Escherichia coli

Quick links

Citations

3 review citations

DNA base damage recognition and removal: new twists and grooves.
Huffman et al. (2005)
2 more

2 mentions without citation

Recent advances in the structural mechanisms of DNA glycosylases.
Brooks et al. (2013)
1 more