› 3ksb

X-ray diffraction
3.5Å resolution

Detailed structural insight into the DNA cleavage complex of type IIA topoisomerases (re-sealed form)

Released:
DOI: 10.2210/pdb3ksb/pdb
PDB entry 3ksb coloured by chain, front view.
PDB entry 3ksb coloured by chain, side view.
PDB entry 3ksb coloured by chain, top view.
Source organism: Streptococcus pneumoniae
Primary publication:
Structural basis of gate-DNA breakage and resealing by type II topoisomerases.
Laponogov I, Pan XS, Veselkov DA, McAuley KE, Fisher LM, Sanderson MR
PLoS One 5 e11338 (2010)
PMID: 20596531

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-116504 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA topoisomerase 4 subunit A Chains: A, B
Molecule details ›
Chains: A, B
Length: 496 amino acids
Theoretical weight: 56.46 KDa
Source organism: Streptococcus pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: P72525 (Residues: 1-488; Coverage: 59%)
Gene names: SP_0855, parC
Sequence domains: DNA gyrase/topoisomerase IV, subunit A
DNA topoisomerase 4 subunit B Chains: C, D
Molecule details ›
Chains: C, D
Length: 268 amino acids
Theoretical weight: 30.42 KDa
Source organism: Streptococcus pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59961 (Residues: 404-647; Coverage: 38%)
Gene names: SP_0852, parE
Sequence domains:
Structure domains: Rossmann fold
5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*TP*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3' Chain: E
Molecule details ›
Chain: E
Length: 34 nucleotides
Theoretical weight: 10.49 KDa
5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*TP*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3' Chain: F
Molecule details ›
Chain: F
Length: 34 nucleotides
Theoretical weight: 10.42 KDa

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P32
Unit cell:
a: 116.757Å b: 116.757Å c: 182.811Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.186 0.181 0.226
Expression system: Escherichia coli

Quick links

Citations

21 review citations

Mechanism of quinolone action and resistance.
Aldred et al. (2014)
20 more

4 mentions without citation

Structural basis of gate-DNA breakage and resealing by type II topoisomerases.
Laponogov et al. (2010)
3 more