› 1lv5

X-ray diffraction
1.95Å resolution

Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP

Released:
DOI: 10.2210/pdb1lv5/pdb
PDB entry 1lv5 coloured by chain, front view.
PDB entry 1lv5 coloured by chain, side view.
PDB entry 1lv5 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-114150 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I Chains: A, B
Molecule details ›
Chains: A, B
Length: 580 amino acids
Theoretical weight: 66.13 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(*GP*GP*AP*TP*CP*AP*GP*CP*GP*A)-3' Chains: C, E
Molecule details ›
Chains: C, E
Length: 10 nucleotides
Theoretical weight: 3.09 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
5'-D(*AP*CP*GP*TP*CP*GP*CP*TP*GP*AP*TP*CP*CP*G)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 14 nucleotides
Theoretical weight: 4.26 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MN 2 x MN
Ligand MG 1 x MG
Ligand SO4 2 x SO4
Ligand DCP 2 x DCP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P31
Unit cell:
a: 91.681Å b: 91.681Å c: 190.116Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.264 0.218 0.261
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

35 review citations

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

32 mentions without citation

Translesion and Repair DNA Polymerases: Diverse Structure and Mechanism.
Yang et al. (2018)
31 more