› 8dwf

X-ray diffraction
2.6Å resolution

Glycosylase MutY variant E43S in complex with DNA containing d(8-oxo-G) paired with substrate adenine

Released:
DOI: 10.2210/pdb8dwf/pdb
PDB entry 8dwf coloured by chain, front view.
PDB entry 8dwf coloured by chain, side view.
PDB entry 8dwf coloured by chain, top view.
Source organisms:
Entry authors: Russelburg LP, Demir M, David SS, Horvath MP

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-224771 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Adenine DNA glycosylase Chains: A, D
Molecule details ›
Chains: A, D
Length: 365 amino acids
Theoretical weight: 41.73 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') Chains: B, E
Molecule details ›
Chains: B, E
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*AP*GP*TP*CP*T)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 11 nucleotides
Theoretical weight: 3.32 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand SF4 2 x SF4
Ligand CA 4 x CA
Ligand EDO 2 x EDO
Ligand TRS 2 x TRS
1 modified residue:
Ligand 8OG 2 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P21
Unit cell:
a: 49.08Å b: 137.9Å c: 74.52Å
α: 90° β: 101.44° γ: 90°
R-values:
R R work R free
0.208 0.207 0.253
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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