› 4yph

X-ray diffraction
2.32Å resolution

Crystal Structure of MutY bound to its anti-substrate with the disulfide cross-linker reduced

Released:
DOI: 10.2210/pdb4yph/pdb
PDB entry 4yph coloured by chain, front view.
PDB entry 4yph coloured by chain, side view.
PDB entry 4yph coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase.
Wang L, Lee SJ, Verdine GL
J Biol Chem 290 17096-105 (2015)
PMID: 25995449

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 analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118335 (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: 42.1 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P83847 (Residues: 1-365; Coverage: 100%)
Gene name: mutY
Sequence domains:
Structure domains:
DNA (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: synthetic construct
Expression system: Not provided
DNA (5'-D(TP*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.3 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 37.636Å b: 83.757Å c: 142.735Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.187 0.259
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Repair of 8-oxoG:A mismatches by the MUTYH glycosylase: Mechanism, metals and medicine.
Banda et al. (2017)
1 more

4 mentions without citation

Searching for DNA Damage: Insights From Single Molecule Analysis.
Schaich et al. (2021)
3 more