› 2hvi

X-ray diffraction
1.98Å resolution

ddCTP:G pair in the polymerase active site (0 position)

Released:
DOI: 10.2210/pdb2hvi/pdb
PDB entry 2hvi coloured by chain, front view.
PDB entry 2hvi coloured by chain, side view.
PDB entry 2hvi 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-115372 (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: 66.2 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q5KWC1 (Residues: 300-878; Coverage: 66%)
Gene names: GK2730, polA
Sequence domains:
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(*C*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3' Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 4.02 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
3 bound ligands:
Ligand DCT 3 x DCT
Ligand MG 2 x MG
Ligand SO4 1 x SO4
1 modified residue:
Ligand DDG 2 x DDG

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 93.795Å b: 108.492Å c: 149.403Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.199 0.231
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

10 mentions without citation

Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.
Wang et al. (2011)
9 more