› 1yqm

X-ray diffraction
2.5Å resolution

Catalytically inactive human 8-oxoguanine glycosylase crosslinked to 7-deazaguanine containing DNA

Released:
DOI: 10.2210/pdb1yqm/pdb
PDB entry 1yqm coloured by chain, front view.
PDB entry 1yqm coloured by chain, side view.
PDB entry 1yqm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.
Banerjee A, Yang W, Karplus M, Verdine GL
Nature 434 612-8 (2005)
PMID: 15800616

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 domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114868 (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: 319 amino acids
Theoretical weight: 35.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O15527 (Residues: 12-327; Coverage: 92%)
Gene names: MMH, MUTM, OGG1, OGH1
Sequence domains:
Structure domains:
5'-D(P*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: Homo sapiens
Expression system: Not provided
5'-D(P*GP*TP*CP*CP*AP*(7GU)P*GP*TP*CP*TP*AP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 2 x CA
1 modified residue:
Ligand 7GU 1 x 7GU

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P6522
Unit cell:
a: 92.508Å b: 92.508Å c: 210.649Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.212 0.212 0.261
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

37 review citations

CHARMM: the biomolecular simulation program.
Brooks et al. (2009)
36 more

2 mentions without citation

Recent advances in the structural mechanisms of DNA glycosylases.
Brooks et al. (2013)
1 more