› 3ktq

X-ray diffraction
2.3Å resolution

CRYSTAL STRUCTURE OF AN ACTIVE TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS

Released:
DOI: 10.2210/pdb3ktq/pdb
PDB entry 3ktq coloured by chain, front view.
PDB entry 3ktq coloured by chain, side view.
PDB entry 3ktq coloured by chain, top view.
Source organism: Thermus aquaticus
Primary publication:
Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.
Li Y, Korolev S, Waksman G
EMBO J 17 7514-25 (1998)
PMID: 9857206

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-507649 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I, thermostable Chain: A
Molecule details ›
Chain: A
Length: 540 amino acids
Theoretical weight: 60.94 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P19821 (Residues: 293-832; Coverage: 65%)
Gene names: pol1, polA
Sequence domains:
Structure domains:
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOC)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: Thermus aquaticus
Expression system: Not provided
DNA (5'-D(*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.34 KDa
Source organism: Thermus aquaticus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand DCT 1 x DCT
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P3121
Unit cell:
a: 108.028Å b: 108.028Å c: 90.167Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.218 0.218 0.275
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

56 review citations

Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function.
Prakash et al. (2005)
55 more

47 mentions without citation

Unlocking the sugar "steric gate" of DNA polymerases.
Brown et al. (2011)
46 more