› 3ktu

X-ray diffraction
2.3Å resolution

Structure of human 8-oxoGuanine Glycosylase 1 bound to fluorninated oxoG-containing DNA

Released:
DOI: 10.2210/pdb3ktu/pdb
PDB entry 3ktu coloured by chain, front view.
PDB entry 3ktu coloured by chain, side view.
PDB entry 3ktu coloured by chain, top view.
Source organisms:
Entry authors: Verdine GL, Lee SM

Function and Biology Details

Reaction catalysed: 
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116506 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
N-glycosylase/DNA lyase Chain: A
Molecule details ›
Chain: A
Length: 317 amino acids
Theoretical weight: 35.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O15527 (Residues: 12-325; Coverage: 91%)
Gene names: MMH, MUTM, OGG1, OGH1
Sequence domains:
Structure domains:
DNA (5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.02 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*TP*CP*CP*AP*(FDG)P*GP*TP*CP*TP*AP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.67 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 2 x CA
1 modified residue:
Ligand FDG 1 x FDG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P6522
Unit cell:
a: 92.4Å b: 92.4Å c: 212.5Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.225 0.225 0.257
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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