› 2hhw

X-ray diffraction
1.88Å resolution

ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation

Released:
DOI: 10.2210/pdb2hhw/pdb
PDB entry 2hhw coloured by chain, front view.
PDB entry 2hhw coloured by chain, side view.
PDB entry 2hhw coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
The structural basis for the mutagenicity of O(6)-methyl-guanine lesions.
Warren JJ, Forsberg LJ, Beese LS
Proc Natl Acad Sci U S A 103 19701-6 (2006)
PMID: 17179038

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115345 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase I Chains: A, D
Molecule details ›
Chains: A, D
Length: 580 amino acids
Theoretical weight: 66.14 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q5KWC1 (Residues: 299-878; Coverage: 66%)
Gene names: GK2730, polA
Sequence domains: DNA polymerase family A
Structure domains:
5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3' Chains: B, E
Molecule details ›
Chains: B, E
Length: 9 nucleotides
Theoretical weight: 2.68 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3' Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 4.03 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
3 bound ligands:
Ligand MN 2 x MN
Ligand SO4 3 x SO4
Ligand D3T 2 x D3T
2 modified residues:
Ligand DDG 2 x DDG
Ligand 6OG 2 x 6OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 93.834Å b: 108.897Å c: 150.111Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.196 0.225
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

21 review citations

DNA mismatch repair: molecular mechanism, cancer, and ageing.
Hsieh et al. (2008)
20 more

2 mentions without citation

The structural basis for the mutagenicity of O(6)-methyl-guanine lesions.
Warren et al. (2006)
1 more