5EIX

QUINOLONE-STABILIZED CLEAVAGE COMPLEX OF TOPOISOMERASE IV FROM KLEBSIELLA PNEUMONIAE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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 D Struct Biol 72: 488-496

  • DOI: https://doi.org/10.1107/S2059798316001212
  • Primary Citation of Related Structures:  
    3RAE, 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. 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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit AA,
D [auth B],
G,
J		741Klebsiella pneumoniaeMutation(s): 0 
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for R4YHS8 (Klebsiella pneumoniae subsp. rhinoscleromatis SB3432)
Explore R4YHS8 
Go to UniProtKB:  R4YHS8
Find proteins for R4YE07 (Klebsiella pneumoniae subsp. rhinoscleromatis SB3432)
Explore R4YE07 
Go to UniProtKB:  R4YE07
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsR4YHS8R4YE07
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
SYMMETRISED E-SITE (PRE-CUT)B [auth E],
E [auth C],
H,
K		8synthetic construct
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
SYMMETRISED E-SITE (PRE-CUT)C [auth F],
F [auth D],
I,
L		12synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.07α = 90
b = 161.53β = 94.22
c = 138.6γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K010069/1
PTC fundingUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-05-18
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence, Derived calculations