› 3ksa

X-ray diffraction
3.3Å resolution

Detailed structural insight into the DNA cleavage complex of type IIA topoisomerases (cleaved form)

Released:
DOI: 10.2210/pdb3ksa/pdb
PDB entry 3ksa coloured by chain, front view.
PDB entry 3ksa coloured by chain, side view.
PDB entry 3ksa 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 octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116503 (preferred)
Entry contents:
2 distinct polypeptide molecules
4 distinct DNA molecules
Macromolecules (6 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*T)-3' Chain: E
Molecule details ›
Chain: E
Length: 15 nucleotides
Theoretical weight: 4.6 KDa
5'-D(P*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: 19 nucleotides
Theoretical weight: 5.81 KDa
5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*T)-3' Chain: G
Molecule details ›
Chain: G
Length: 15 nucleotides
Theoretical weight: 4.57 KDa
5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3' Chain: H
Molecule details ›
Chain: H
Length: 19 nucleotides
Theoretical weight: 5.85 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: 116.911Å b: 116.911Å c: 183.759Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.18 0.176 0.218
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

DNA Topoisomerase Inhibitors: Trapping a DNA-Cleaving Machine in Motion.
Bax et al. (2019)
3 more