› 3rr8

X-ray diffraction
2.4Å resolution

Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddGTP

Released:
DOI: 10.2210/pdb3rr8/pdb
PDB entry 3rr8 coloured by chain, front view.
PDB entry 3rr8 coloured by chain, side view.
PDB entry 3rr8 coloured by chain, top view.
Source organism: Thermus aquaticus
Primary publication:
Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
Obeid S, Welte W, Diederichs K, Marx A
J Biol Chem 287 14099-108 (2012)
PMID: 22318723

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 analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116837 (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 BL21(DE3)
UniProt:
  • Canonical: P19821 (Residues: 293-832; 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*AP*AP*(3DR)P*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.78 KDa
Source organism: Thermus aquaticus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DG3 1 x DG3
Ligand GOL 4 x GOL
1 modified residue:
Ligand DDG 1 x DDG

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P3121
Unit cell:
a: 108.965Å b: 108.965Å c: 90.406Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.201 0.256
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

The Structural Basis for Processing of Unnatural Base Pairs by DNA Polymerases.
Marx et al. (2020)
16 other articles

1 mention without citation

Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
Obeid et al. (2012)