› 5kn8

X-ray diffraction
1.81Å resolution

MutY N-terminal domain in complex with undamaged DNA

Released:
DOI: 10.2210/pdb5kn8/pdb
PDB 5kn8 coloured by chain and viewed from the front.
PDB 5kn8 coloured by chain and viewed from the side.
PDB 5kn8 coloured by chain and viewed from the top.
Source organism: Geobacillus stearothermophilus
Primary publication:
Structural Basis for the Lesion-scanning Mechanism of the Bacterial MutY DNA Glycosylase.
Wang L, Chakravarthy S, Verdine GL
J. Biol. Chem. (2017)
PMID: 28130451

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Adenine DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 232 amino acids
Theoretical weight: 26.63 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P83847 (Residues: 1-229; Coverage: 63%)
Gene name: mutY
Sequence domains:
Structure domains:
DNA (5'-D(*AP*TP*CP*CP*TP*GP*TP*GP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.01 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
DNA (5'-D(*AP*GP*CP*AP*CP*AP*GP*GP*AP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 10 nucleotides
Theoretical weight: 3.08 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SF4 1 x SF4
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 49.2Å b: 38.618Å c: 83.796Å
α: 90° β: 104° γ: 90°
R-values:
R R work R free
0.169 0.166 0.22
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 citation in other articles

An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation.
Nguyen et al. (2021)
10 more

1 mention without citation

Structural Basis for the Lesion-scanning Mechanism of the MutY DNA Glycosylase.
Wang et al. (2017)