› 3ht3

X-ray diffraction
1.7Å resolution

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus V713P mutant bound to G:dCTP

Released:
DOI: 10.2210/pdb3ht3/pdb
PDB entry 3ht3 coloured by chain, front view.
PDB entry 3ht3 coloured by chain, side view.
PDB entry 3ht3 coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism.
Wu EY, Beese LS
J Biol Chem 286 19758-67 (2011)
PMID: 21454515

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 analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112994 (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: 579 amino acids
Theoretical weight: 66.06 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: D9N168 (Residues: 1-579; Coverage: 100%)
Gene names: DPO1, polA
Sequence domains: DNA polymerase family A
Structure domains:
5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-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(*AP*CP*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3' Chains: C, F
Molecule details ›
Chains: C, F
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P212121
Unit cell:
a: 93.28Å b: 108.79Å c: 152.09Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.21 0.247
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

Alternating-laser excitation: single-molecule FRET and beyond.
Hohlbein et al. (2014)
10 more

5 mentions without citation

Recent progress in dissecting molecular recognition by DNA polymerases with non-native substrates.
Pugliese et al. (2017)
4 more