› 2hhu

X-ray diffraction
1.8Å resolution

C:O6-methyl-guanine in the polymerase postinsertion site (-1 basepair position)

Released:
DOI: 10.2210/pdb2hhu/pdb
PDB entry 2hhu coloured by chain, front view.
PDB entry 2hhu coloured by chain, side view.
PDB entry 2hhu 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-115343 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 580 amino acids
Theoretical weight: 66.23 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q5KWC1 (Residues: 300-878; Coverage: 66%)
Gene names: GK2730, polA
Sequence domains: DNA polymerase family A
Structure domains:
5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*CP*CP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.32 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
5'-D(*GP*TP*AP*CP*(6OG)P*GP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.95 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
3 bound ligands:
Ligand DCP 1 x DCP
Ligand SO4 4 x SO4
Ligand MG 1 x MG
1 modified residue:
Ligand 6OG 1 x 6OG

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 87.801Å b: 93.415Å c: 105.247Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.203 0.232
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

1 mention without citation

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