› 1l5u

X-ray diffraction
1.95Å resolution

Crystal Structure of Bacillus DNA Polymerase I Fragment product complex with 12 base pairs of duplex DNA following addition of a dTTP, a dATP, and a dCTP residue.

Released:
DOI: 10.2210/pdb1l5u/pdb
PDB entry 1l5u coloured by chain, front view.
PDB entry 1l5u coloured by chain, side view.
PDB entry 1l5u coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.
Johnson SJ, Taylor JS, Beese LS
Proc Natl Acad Sci U S A 100 3895-900 (2003)
PMID: 12649320

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-114117 (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: 66.17 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P52026 (Residues: 297-876; Coverage: 66%)
Gene names: pol, polA
Sequence domains:
Structure domains:
5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*AP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.65 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.92 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 87.469Å b: 93.418Å c: 105.67Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.195 0.229
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

37 review citations

Structure-function relationships among RNA-dependent RNA polymerases.
Ng et al. (2008)
36 more

10 mentions without citation

Lesion processing: high-fidelity versus lesion-bypass DNA polymerases.
Broyde et al. (2008)
9 more