› 3hp6

X-ray diffraction
1.81Å resolution

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus F710Y mutant bound to G:T mismatch

Released:
DOI: 10.2210/pdb3hp6/pdb
PDB entry 3hp6 coloured by chain, front view.
PDB entry 3hp6 coloured by chain, side view.
PDB entry 3hp6 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-116372 (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: 66.22 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5KWC1 (Residues: 299-878; Coverage: 66%)
Gene names: GK2730, polA
Sequence domains: DNA polymerase family A
Structure domains:
5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DDG))-3' Chains: B, E
Molecule details ›
Chains: B, E
Length: 9 nucleotides
Theoretical weight: 2.72 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
5'-D(*AP*CP*GP*CP*CP*GP*TP*GP*AP*TP*CP*G)-3' Chains: C, F
Molecule details ›
Chains: C, F
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
3 bound ligands:
Ligand SO4 3 x SO4
Ligand MG 2 x MG
Ligand D3T 2 x D3T
2 modified residues:
Ligand CME 2 x CME
Ligand DDG 2 x DDG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 93.17Å b: 108.71Å c: 152.21Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.211 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

9 mentions without citation

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