› 3eyz

X-ray diffraction
2.1Å resolution

Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA (open form)

Released:
DOI: 10.2210/pdb3eyz/pdb
PDB entry 3eyz coloured by chain, front view.
PDB entry 3eyz coloured by chain, side view.
PDB entry 3eyz coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis.
Golosov AA, Warren JJ, Beese LS, Karplus M
Structure 18 83-93 (2010)
PMID: 20152155

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-116228 (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: 66.19 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P52026 (Residues: 297-876; Coverage: 66%)
Gene names: pol, polA
Sequence domains: DNA polymerase family A
Structure domains:
5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DGP*DC)-3' Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 2.98 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
5'-D(*DAP*DTP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DGP*DA)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 4.04 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
1 bound ligand:
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P212121
Unit cell:
a: 86.663Å b: 94.053Å c: 106.925Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.211 0.245
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Biomolecularmodeling and simulation: a field coming of age.
Schlick et al. (2011)
4 more

2 mentions without citation

Structural comparison of DNA polymerase architecture suggests a nucleotide gateway to the polymerase active site.
Wu et al. (2014)
1 more