› 1tkd

X-ray diffraction
2.49Å resolution

T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site

Released:
DOI: 10.2210/pdb1tkd/pdb
PDB entry 1tkd coloured by chain, front view.
PDB entry 1tkd coloured by chain, side view.
PDB entry 1tkd coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.
Brieba LG, Eichman BF, Kokoska RJ, Doublié S, Kunkel TA, Ellenberger T
EMBO J 23 3452-61 (2004)
PMID: 15297882

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114648 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA-directed DNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 698 amino acids
Theoretical weight: 79.09 KDa
Source organism: Escherichia phage T7
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P00581 (Residues: 1-704; Coverage: 99%)
Gene name: 5
Sequence domains: DNA polymerase family A
Structure domains:
Thioredoxin 1 Chain: B
Molecule details ›
Chain: B
Length: 108 amino acids
Theoretical weight: 11.69 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0AA25 (Residues: 2-109; Coverage: 99%)
Gene names: JW5856, b3781, fipA, trxA, tsnC
Sequence domains: Thioredoxin
Structure domains: Glutaredoxin
DNA (5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DOC))-3') Chain: P
Molecule details ›
Chain: P
Length: 22 nucleotides
Theoretical weight: 6.72 KDa
DNA (5'-D(*CP*CP*CP*AP*(8OG)P*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 26 nucleotides
Theoretical weight: 7.96 KDa

Ligands and Environments

5 bound ligands:
Ligand MG 3 x MG
Ligand SO4 3 x SO4
Ligand D3T 1 x D3T
Ligand MES 1 x MES
Ligand 1PE 1 x 1PE
2 modified residues:
Ligand DOC 1 x DOC
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X26C
Spacegroup: P21212
Unit cell:
a: 105.514Å b: 215.112Å c: 52.035Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.262 0.202 0.265
Expression system: Escherichia coli BL21

Quick links

Citations

24 review citations

The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases.
McCulloch et al. (2008)
23 more

4 mentions without citation

Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.
Brieba et al. (2004)
3 more