› 3knt

X-ray diffraction
2.7Å resolution

Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine glycosylase/lyase in complex with 15mer DNA containing 8-oxoguanine

Released:
DOI: 10.2210/pdb3knt/pdb
PDB entry 3knt coloured by chain, front view.
PDB entry 3knt coloured by chain, side view.
PDB entry 3knt coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
The C-terminal lysine of Ogg2 DNA glycosylases is a major molecular determinant for guanine/8-oxoguanine distinction.
Faucher F, Wallace SS, Doublié S
J Mol Biol 397 46-56 (2010)
PMID: 20083120

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

Assemblies composition:
hetero dodecamer
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116494 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
8-oxoguanine DNA glycosylase/AP lyase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 207 amino acids
Theoretical weight: 24.87 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q58134 (Residues: 1-207; Coverage: 100%)
Gene names: MJ0724, ogg
Structure domains:
5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' Chains: E, G, I, K
Molecule details ›
Chains: E, G, I, K
Length: 15 nucleotides
Theoretical weight: 4.55 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Not provided
5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' Chains: F, H, J, L
Molecule details ›
Chains: F, H, J, L
Length: 15 nucleotides
Theoretical weight: 4.65 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 4 x NA
1 modified residue:
Ligand 8OG 4 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21
Unit cell:
a: 54.8Å b: 150.03Å c: 90.27Å
α: 90° β: 107.53° γ: 90°
R-values:
R R work R free
0.19 0.188 0.225
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Repair of 8-oxo-7,8-dihydroguanine in prokaryotic and eukaryotic cells: Properties and biological roles of the Fpg and OGG1 DNA N-glycosylases.
Boiteux et al. (2017)
1 more

7 mentions without citation

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