› 4ird

X-ray diffraction
2.48Å resolution

Structure of Polymerase-DNA complex

Released:
DOI: 10.2210/pdb4ird/pdb
PDB entry 4ird coloured by chain, front view.
PDB entry 4ird coloured by chain, side view.
PDB entry 4ird coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli.
Sharma A, Kottur J, Narayanan N, Nair DT
Nucleic Acids Res 41 5104-14 (2013)
PMID: 23525461

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-218970 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase IV Chains: A, F
Molecule details ›
Chains: A, F
Length: 342 amino acids
Theoretical weight: 38.3 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: Q47155 (Residues: 2-341; Coverage: 97%)
Gene names: JW0221, b0231, dinB, dinP
Sequence domains:
Structure domains:
DNA (5'-D(*TP*CP*TP*TP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') Chains: B, G
Molecule details ›
Chains: B, G
Length: 18 nucleotides
Theoretical weight: 5.48 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') Chain: H
Molecule details ›
Chain: H
Length: 14 nucleotides
Theoretical weight: 4.28 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 17 nucleotides
Theoretical weight: 5.19 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DZ4 2 x DZ4
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 86.69Å b: 56.88Å c: 110.93Å
α: 90° β: 93.99° γ: 90°
R-values:
R R work R free
0.216 0.213 0.277
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Engineering Polymerases for New Functions.
Coulther et al. (2019)
3 more

2 mentions without citation

cryo-EM structures of the E. coli replicative DNA polymerase reveal its dynamic interactions with the DNA sliding clamp, exonuclease and τ.
Fernandez-Leiro et al. (2015)
1 more