› 1qtm

X-ray diffraction
2.3Å resolution

DDTTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS

Released:
DOI: 10.2210/pdb1qtm/pdb
PDB entry 1qtm coloured by chain, front view.
PDB entry 1qtm coloured by chain, side view.
PDB entry 1qtm coloured by chain, top view.
Source organism: Thermus aquaticus
Primary publication:
Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation.
Li Y, Mitaxov V, Waksman G
Proc Natl Acad Sci U S A 96 9491-6 (1999)
PMID: 10449720

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-114472 (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: 539 amino acids
Theoretical weight: 60.81 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P19821 (Residues: 293-831; Coverage: 65%)
Gene names: pol1, polA
Sequence domains:
Structure domains:
5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DT))-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.63 KDa
Source organism: Thermus aquaticus
Expression system: Not provided
5'-D(*AP*AP*AP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.31 KDa
Source organism: Thermus aquaticus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand TTP 1 x TTP
1 modified residue:
Ligand 2DT 1 x 2DT

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P3121
Unit cell:
a: 107.988Å b: 107.988Å c: 90.201Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.227 0.227 0.28
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

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

14 mentions without citation

Structural and Molecular Kinetic Features of Activities of DNA Polymerases.
Kuznetsova et al. (2022)
13 more