› 1t8e

X-ray diffraction
2.54Å resolution

T7 DNA Polymerase Ternary Complex with dCTP at the Insertion Site.

Released:
DOI: 10.2210/pdb1t8e/pdb
PDB entry 1t8e coloured by chain, front view.
PDB entry 1t8e coloured by chain, side view.
PDB entry 1t8e 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-114633 (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(DE3)
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(DE3)
UniProt:
  • Canonical: P0AA25 (Residues: 2-109; Coverage: 99%)
Gene names: JW5856, b3781, fipA, trxA, tsnC
Sequence domains: Thioredoxin
Structure domains: Glutaredoxin
5'-D(P*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(2DT))-3' Chain: C
Molecule details ›
Chain: C
Length: 22 nucleotides
Theoretical weight: 6.74 KDa
25-MER Chain: D
Molecule details ›
Chain: D
Length: 26 nucleotides
Theoretical weight: 8.03 KDa

Ligands and Environments

5 bound ligands:
Ligand MG 3 x MG
Ligand SO4 1 x SO4
Ligand DCT 1 x DCT
Ligand MES 1 x MES
Ligand PG4 1 x PG4
1 modified residue:
Ligand 2DT 1 x 2DT

Experiments and Validation Details

Entry percentile scores
Spacegroup: P21212
Unit cell:
a: 106.285Å b: 218.121Å c: 52.133Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.255 0.22 0.255
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

23 review citations

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

19 mentions without citation

Clustering of Alpers disease mutations and catalytic defects in biochemical variants reveal new features of molecular mechanism of the human mitochondrial replicase, Pol γ.
Euro et al. (2011)
18 more