› 1nkc

X-ray diffraction
1.8Å resolution

A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER FIVE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, DTTP, AND DATP.

Released:
DOI: 10.2210/pdb1nkc/pdb
PDB entry 1nkc coloured by chain, front view.
PDB entry 1nkc coloured by chain, side view.
PDB entry 1nkc coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
Structures of mismatch replication errors observed in a DNA polymerase.
Johnson SJ, Beese LS
Cell 116 803-16 (2004)
PMID: 15035983

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-114264 (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: DNA polymerase family A
Structure domains:
DNA PRIMER STRAND Chain: B
Molecule details ›
Chain: B
Length: 15 nucleotides
Theoretical weight: 4.59 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
DNA TEMPLATE STRAND Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.6 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: 87.802Å b: 93.491Å c: 105.475Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.186 0.218
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

24 review citations

Structural insights into translational fidelity.
Ogle et al. (2005)
23 more

2 mentions without citation

DNA conformations and their sequence preferences.
Svozil et al. (2008)
1 more