› 5yus

X-ray diffraction
1.94Å resolution

DNA polymerase IV - DNA ternary complex 2

Released:
DOI: 10.2210/pdb5yus/pdb
PDB entry 5yus coloured by chain, front view.
PDB entry 5yus coloured by chain, side view.
PDB entry 5yus coloured by chain, top view.
Source organisms:
Primary publication:
Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction.
Kottur J, Nair DT
Nucleic Acids Res 46 5875-5885 (2018)
PMID: 29850882

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

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119449 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA polymerase IV Chains: A, F
Molecule details ›
Chains: A, F
Length: 352 amino acids
Theoretical weight: 39.59 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q47155 (Residues: 2-351; Coverage: 100%)
Gene names: JW0221, b0231, dinB, dinP
Sequence domains:
Structure domains:
DTN Chains: B, C, G, H
Molecule details ›
Chains: B, C, G, H
Length: 18 nucleotides
Theoretical weight: 5.49 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand TTP 2 x TTP
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21
Unit cell:
a: 86.84Å b: 57.12Å c: 110.55Å
α: 90° β: 95° γ: 90°
R-values:
R R work R free
0.192 0.19 0.228
Expression systems:
  • Escherichia coli K-12
  • Not provided

Quick links

Citations

4 review citations

Two-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion.
Wang et al. (2022)
3 more

1 mention without citation

Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction.
Kottur et al. (2018)