› 6u7t

X-ray diffraction
2Å resolution

MutY adenine glycosylase bound to DNA containing a transition state analog (1N) paired with d(8-oxo-G)

Released:
DOI: 10.2210/pdb6u7t/pdb
PDB entry 6u7t coloured by chain, front view.
PDB entry 6u7t coloured by chain, side view.
PDB entry 6u7t coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for Finding OG Lesions and Avoiding Undamaged G by the DNA Glycosylase MutY.
Russelburg LP, O'Shea Murray VL, Demir M, Knutsen KR, Sehgal SL, Cao S, David SS, Horvath MP
ACS Chem Biol 15 93-102 (2020)
PMID: 31829624

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-120675 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Adenine DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 366 amino acids
Theoretical weight: 41.81 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P83847 (Residues: 1-365; Coverage: 100%)
Gene name: mutY
Sequence 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(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.19 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P212121
Unit cell:
a: 37.8Å b: 86.49Å c: 140.58Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.262 0.261 0.27
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

Noncatalytic Domains in DNA Glycosylases.
Torgasheva et al. (2022)
4 other articles

3 mentions without citation

Structural Basis for Finding OG Lesions and Avoiding Undamaged G by the DNA Glycosylase MutY.
Russelburg et al. (2020)
2 more