› 6p7e

X-ray diffraction
3Å resolution

Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase

Released:
DOI: 10.2210/pdb6p7e/pdb
PDB entry 6p7e coloured by chain, front view.
PDB entry 6p7e coloured by chain, side view.
PDB entry 6p7e coloured by chain, top view.
Source organisms:
Primary publication:
Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome.
Foster BM, Rosenberg D, Salvo H, Stephens KL, Bintz BJ, Hammel M, Ellenberger T, Gainey MD, Wallen JR
Biochemistry 58 4466-4479 (2019)
PMID: 31659895

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero pentamer (preferred)
hetero tetramer
PDBe Complex ID:
PDB-CPX-120441 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
DNA-directed DNA polymerase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 704 amino acids
Theoretical weight: 79.7 KDa
Source organism: Escherichia phage T7
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00581 (Residues: 1-704; Coverage: 100%)
Gene name: 5
Sequence domains: DNA polymerase family A
Thioredoxin 1 Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 109 amino acids
Theoretical weight: 11.82 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AA25 (Residues: 1-109; Coverage: 100%)
Gene names: JW5856, b3781, fipA, trxA, tsnC
Sequence domains: Thioredoxin
ASP-THR-ASP-PHE peptide Chains: U, V
Molecule details ›
Chains: U, V
Length: 4 amino acids
Theoretical weight: 496 Da
Source organism: Escherichia phage T7
Expression system: Not provided
THR-ASP-PHE peptide Chain: W
Molecule details ›
Chain: W
Length: 3 amino acids
Theoretical weight: 381 Da
Source organism: Escherichia phage T7
Expression system: Not provided
DNA (5'-D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)-3') Chains: I, K, M, O
Molecule details ›
Chains: I, K, M, O
Length: 21 nucleotides
Theoretical weight: 6.55 KDa
DNA (25-MER) Chains: J, L, N, P
Molecule details ›
Chains: J, L, N, P
Length: 25 nucleotides
Theoretical weight: 7.52 KDa

Ligands and Environments

2 bound ligands:
Ligand TTP 8 x TTP
Ligand MG 12 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P1
Unit cell:
a: 100.724Å b: 102.698Å c: 148.885Å
α: 91.36° β: 96.83° γ: 113.11°
R-values:
R R work R free
0.216 0.214 0.248
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology.
Hammel et al. (2021)
1 other article

3 mentions without citation

Conformational dynamics during high-fidelity DNA replication and translocation defined using a DNA polymerase with a fluorescent artificial amino acid.
Dangerfield et al. (2021)
2 more