› 4ir9

X-ray diffraction
2.33Å resolution

Polymerase-DNA complex

Released:
DOI: 10.2210/pdb4ir9/pdb
PDB entry 4ir9 coloured by chain, front view.
PDB entry 4ir9 coloured by chain, side view.
PDB entry 4ir9 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-218965 (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: 352 amino acids
Theoretical weight: 39.59 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: Q47155 (Residues: 2-351; Coverage: 100%)
Gene names: JW0221, b0231, dinB, dinP
Sequence domains:
Structure domains:
DNA (5'-D(P*TP*CP*TP*CP*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: 5.47 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(P*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
DNA (5'-D(P*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

Ligands and Environments

2 bound ligands:
Ligand XG4 2 x XG4
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: 86.76Å b: 57.04Å c: 110.7Å
α: 90° β: 94.76° γ: 90°
R-values:
R R work R free
0.214 0.211 0.272
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

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

5 mentions without citation

DNA polymerase mu: An inflexible scaffold for substrate flexibility.
Kaminski et al. (2020)
4 more