› 4irk

X-ray diffraction
2.32Å resolution

structure of Polymerase-DNA complex, dna

Released:
DOI: 10.2210/pdb4irk/pdb
PDB entry 4irk coloured by chain, front view.
PDB entry 4irk coloured by chain, side view.
PDB entry 4irk 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-117659 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, B
Molecule details ›
Chains: A, B
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*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 18 nucleotides
Theoretical weight: 5.49 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3') Chains: G, H
Molecule details ›
Chains: G, H
Length: 17 nucleotides
Theoretical weight: 5.17 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DCP 2 x DCP
Ligand MG 2 x MG
1 modified residue:
Ligand DOC 2 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 86.65Å b: 57.08Å c: 110.23Å
α: 90° β: 94.92° γ: 90°
R-values:
R R work R free
0.211 0.209 0.262
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

A rescue act: Translesion DNA synthesis past N(2) -deoxyguanosine adducts.
Nair et al. (2015)
2 more

2 mentions without citation

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