› 4ypr

X-ray diffraction
2.59Å resolution

Crystal Structure of D144N MutY bound to its anti-substrate

Released:
DOI: 10.2210/pdb4ypr/pdb
PDB entry 4ypr coloured by chain, front view.
PDB entry 4ypr coloured by chain, side view.
PDB entry 4ypr 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-118336 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Adenine DNA glycosylase Chains: A, B
Molecule details ›
Chains: A, B
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(*T*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 11 nucleotides
Theoretical weight: 3.3 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 11 nucleotides
Theoretical weight: 3.42 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SF4 2 x SF4
1 modified residue:
Ligand 8OG 2 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P61
Unit cell:
a: 105.272Å b: 105.272Å c: 235.374Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.172 0.169 0.228
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

2 mentions without citation

Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase.
Wang et al. (2015)
1 more