› 1qss

X-ray diffraction
2.3Å resolution

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

Released:
DOI: 10.2210/pdb1qss/pdb
PDB entry 1qss coloured by chain, front view.
PDB entry 1qss coloured by chain, side view.
PDB entry 1qss 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-114469 (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: 60.87 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*(DDG))-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: Thermus aquaticus
Expression system: Not provided
5'-D(*AP*CP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.26 KDa
Source organism: Thermus aquaticus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand DG3 1 x DG3
1 modified residue:
Ligand DDG 1 x DDG

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P3121
Unit cell:
a: 108.557Å b: 108.557Å c: 90.527Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.228 0.228 0.285
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

6 mentions without citation

Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
Batra et al. (2006)
5 more