› 1rrs

X-ray diffraction
2.4Å resolution

MutY adenine glycosylase in complex with DNA containing an abasic site

Released:
DOI: 10.2210/pdb1rrs/pdb
PDB entry 1rrs coloured by chain, front view.
PDB entry 1rrs coloured by chain, side view.
PDB entry 1rrs coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase.
Fromme JC, Banerjee A, Huang SJ, Verdine GL
Nature 427 652-6 (2004)
PMID: 14961129

Function and Biology Details

Reaction catalysed: 
Hydrolyzes free adenine bases from 7,8-dihydro-8-oxoguanine:adenine mismatched double-stranded DNA, leaving an apurinic site.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114537 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Adenine DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 369 amino acids
Theoretical weight: 42.09 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P83847 (Residues: 1-365; Coverage: 100%)
Gene name: mutY
Sequence domains:
Structure domains:
5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.42 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
5'-D(*TP*GP*TP*CP*CP*AP*(HPD)P*GP*TP*CP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.21 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 1 x CA
Ligand SF4 1 x SF4
1 modified residue:
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 37.758Å b: 85.539Å c: 141.163Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.231 0.231 0.275
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

38 review citations

Base-excision repair of oxidative DNA damage.
David et al. (2007)
37 more

6 mentions without citation

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