› 1xqo

X-ray diffraction
1.03Å resolution

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

Released:
DOI: 10.2210/pdb1xqo/pdb
PDB entry 1xqo coloured by chain, front view.
PDB entry 1xqo coloured by chain, side view.
PDB entry 1xqo 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

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21212
Unit cell:
a: 70.89Å b: 97.69Å c: 36.1Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.159 0.158 0.183
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

9 mentions without citation

Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding.
Krishnamurthy et al. (2008)
8 more