› 4yfu

X-ray diffraction
1.5Å resolution

Crystal structure of open Bacillus fragment DNA polymerase bound to DNA and dTTP

Released:
DOI: 10.2210/pdb4yfu/pdb
PDB entry 4yfu coloured by chain, front view.
PDB entry 4yfu coloured by chain, side view.
PDB entry 4yfu coloured by chain, top view.
Source organisms:
Primary publication:
The Closing Mechanism of DNA Polymerase I at Atomic Resolution.
Miller BR, Beese LS, Parish CA, Wu EY
Structure 23 1609-1620 (2015)
PMID: 26211612

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-118314 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase I Chains: A, D
Molecule details ›
Chains: A, D
Length: 580 amino acids
Theoretical weight: 66.28 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: E1C9K5 (Residues: 2-580; Coverage: 100%)
Gene name: polA
Sequence domains: DNA polymerase family A
Structure domains:
Primer DNA Chains: B, E
Molecule details ›
Chains: B, E
Length: 9 nucleotides
Theoretical weight: 2.71 KDa
Source organism: synthetic construct
Expression system: Not provided
Template DNA Chains: C, F
Molecule details ›
Chains: C, F
Length: 14 nucleotides
Theoretical weight: 4.33 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
2 bound ligands:
Ligand TTP 1 x TTP
Ligand SO4 1 x SO4
2 modified residues:
Ligand CME 2 x CME
Ligand 2DT 2 x 2DT

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 93.23Å b: 108.1Å c: 151.34Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.195 0.23
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

DNA Polymerase θ: A Cancer Drug Target with Reverse Transcriptase Activity.
Chen et al. (2021)
2 more

4 mentions without citation

The Closing Mechanism of DNA Polymerase I at Atomic Resolution.
Miller et al. (2015)
3 more