› 4i3h

X-ray diffraction
3.7Å resolution

A three-gate structure of topoisomerase IV from Streptococcus pneumoniae

Released:
DOI: 10.2210/pdb4i3h/pdb
PDB entry 4i3h coloured by chain, front view.
PDB entry 4i3h coloured by chain, side view.
PDB entry 4i3h coloured by chain, top view.
Source organism: Streptococcus pneumoniae TIGR4
Primary publication:
Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.
Laponogov I, Veselkov DA, Crevel IM, Pan XS, Fisher LM, Sanderson MR
Nucleic Acids Res 41 9911-23 (2013)
PMID: 23965305

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117631 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA topoisomerase 4 subunit A; DNA topoisomerase 4 subunit B Chains: A, B
Molecule details ›
Chains: A, B
Length: 1144 amino acids
Theoretical weight: 128.32 KDa
Source organism: Streptococcus pneumoniae TIGR4
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59961 (Residues: 1-647; Coverage: 100%)
  • Canonical: P72525 (Residues: 1-490; Coverage: 60%)
Gene names: SP_0852, SP_0855, parC, parE
Sequence domains:
Structure domains:
DNA (5'-D(*CP*AP*AP*AP*GP*GP*CP*GP*GP*TP*AP*AP*TP*AP*CP*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*AP*AP*TP*CP*AP*GP*G)-3') Chains: E, G
Molecule details ›
Chains: E, G
Length: 34 nucleotides
Theoretical weight: 10.53 KDa
DNA (5'-D(*CP*CP*TP*GP*AP*TP*TP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*CP*CP*GP*CP*CP*TP*TP*TP*G)-3') Chains: F, H
Molecule details ›
Chains: F, H
Length: 34 nucleotides
Theoretical weight: 10.39 KDa

Ligands and Environments

1 bound ligand:
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P42212
Unit cell:
a: 160.6Å b: 160.6Å c: 280.56Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.186 0.248
Expression system: Escherichia coli

Quick links

Citations

13 review citations

Fluoroquinolone resistance: mechanisms, impact on bacteria, and role in evolutionary success.
Redgrave et al. (2014)
12 more

10 mentions without citation

The Blueprint of a Minimal Cell: MiniBacillus.
Reuß et al. (2016)
9 more