› 3k9f

X-ray diffraction
2.9Å resolution

Detailed structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases

Released:
DOI: 10.2210/pdb3k9f/pdb
PDB entry 3k9f coloured by chain, front view.
PDB entry 3k9f coloured by chain, side view.
PDB entry 3k9f 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-116471 (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
DNA (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
DNA (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
DNA (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
DNA (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

2 bound ligands:
Ligand MG 2 x MG
Ligand LFX 2 x LFX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P32
Unit cell:
a: 122.407Å b: 122.407Å c: 178.287Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.187 0.183 0.218
Expression system: Escherichia coli

Quick links

Citations

21 review citations

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

13 mentions without citation

DNA topoisomerases and their poisoning by anticancer and antibacterial drugs.
Pommier et al. (2010)
12 more