3RAE

Quinolone(Levofloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from Klebsiella pneumoniae and comparison with a related Streptococcus pneumoniae complex.

Veselkov, D.A.Laponogov, I.Pan, X.S.Selvarajah, J.Skamrova, G.B.Branstrom, A.Narasimhan, J.Prasad, J.V.Fisher, L.M.Sanderson, M.R.

(2016) Acta Crystallogr.,Sect.D 72: 488-496

  • DOI: 10.1107/S2059798316001212
  • Primary Citation of Related Structures:  5EIX

  • PubMed Abstract: 
  • Klebsiella pneumoniae is a Gram-negative bacterium that is responsible for a range of common infections, including pulmonary pneumonia, bloodstream infections and meningitis. Certain strains of Klebsiella have become highly resistant to antibiotics. ...

    Klebsiella pneumoniae is a Gram-negative bacterium that is responsible for a range of common infections, including pulmonary pneumonia, bloodstream infections and meningitis. Certain strains of Klebsiella have become highly resistant to antibiotics. Despite the vast amount of research carried out on this class of bacteria, the molecular structure of its topoisomerase IV, a type II topoisomerase essential for catalysing chromosomal segregation, had remained unknown. In this paper, the structure of its DNA-cleavage complex is reported at 3.35 Å resolution. The complex is comprised of ParC breakage-reunion and ParE TOPRIM domains of K. pneumoniae topoisomerase IV with DNA stabilized by levofloxacin, a broad-spectrum fluoroquinolone antimicrobial agent. This complex is compared with a similar complex from Streptococcus pneumoniae, which has recently been solved.


    Organizational Affiliation

    Randall Division of Cell and Molecular Biophysics, King's College London, 3rd Floor, New Hunt's House, Guy's Campus, London SE1 1UL, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 4 subunit A
A, B
496Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Gene Names: parC
EC: 5.99.1.3
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  P72525
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 4 subunit B
C, D
268Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Gene Names: parE
EC: 5.99.1.3
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  Q59961
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*AP*TP*GP*AP*AP*T)-3'E7N/A
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*G)-3'F11N/A
Entity ID: 5
MoleculeChainsLengthOrganism
5'-D(*CP*GP*TP*GP*CP*AP*T)-3'G7N/A
Entity ID: 6
MoleculeChainsLengthOrganism
5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*G)-3'H11N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
LFX
Query on LFX

Download SDF File 
Download CCD File 
F, H
(3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid
Levofloxacin
C18 H20 F N3 O4
GSDSWSVVBLHKDQ-JTQLQIEISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 157.831α = 90.00
b = 157.831β = 90.00
c = 211.147γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
GDEdata collection
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2016-04-20
    Type: Database references