› 3i0x

X-ray diffraction
1.8Å resolution

Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing adenine opposite to 8-oxoG

Released:
DOI: 10.2210/pdb3i0x/pdb
PDB entry 3i0x coloured by chain, front view.
PDB entry 3i0x coloured by chain, side view.
PDB entry 3i0x coloured by chain, top view.
Source organism: Clostridium acetobutylicum
Primary publication:
Structural basis for the lack of opposite base specificity of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase.
Faucher F, Wallace SS, Doublié S
DNA Repair (Amst) 8 1283-9 (2009)
PMID: 19747886

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116388 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-(apurinic or apyrimidinic site) lyase Chain: A
Molecule details ›
Chain: A
Length: 291 amino acids
Theoretical weight: 34.35 KDa
Source organism: Clostridium acetobutylicum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97FM4 (Residues: 1-291; Coverage: 100%)
Gene name: CA_C2707
Sequence domains:
Structure domains:
5'-D(*AP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.93 KDa
Source organism: Clostridium acetobutylicum
Expression system: Not provided
5'-D(*GP*GP*TP*AP*GP*AP*CP*AP*TP*GP*GP*A)-3' Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.75 KDa
Source organism: Clostridium acetobutylicum
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 1 x NA
1 modified residue:
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P6522
Unit cell:
a: 92.13Å b: 92.13Å c: 190.73Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.187 0.187 0.21
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

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

2 mentions without citation

8-oxoguanine DNA glycosylases: one lesion, three subfamilies.
Faucher et al. (2012)
1 more