3FOE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.001 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

Laponogov, I.Sohi, M.K.Veselkov, D.A.Pan, X.-S.Sawhney, R.Thompson, A.W.McAuley, K.E.Fisher, L.M.Sanderson, M.R.

(2009) Nat.Struct.Mol.Biol. 16: 667-669

  • DOI: 10.1038/nsmb.1604
  • Primary Citation of Related Structures:  3FOF
  • Also Cited By: 3K9F, 3KSA, 3KSB, 3LTN

  • PubMed Abstract: 
  • Type II topoisomerases alter DNA topology by forming a covalent DNA-cleavage complex that allows DNA transport through a double-stranded DNA break. We present the structures of cleavage complexes formed by the Streptococcus pneumoniae ParC breakage-r ...

    Type II topoisomerases alter DNA topology by forming a covalent DNA-cleavage complex that allows DNA transport through a double-stranded DNA break. We present the structures of cleavage complexes formed by the Streptococcus pneumoniae ParC breakage-reunion and ParE TOPRIM domains of topoisomerase IV stabilized by moxifloxacin and clinafloxacin, two antipneumococcal fluoroquinolones. These structures reveal two drug molecules intercalated at the highly bent DNA gate and help explain antibacterial quinolone action and resistance.


    Organizational Affiliation

    Randall Division of Cell and Molecular Biophysics, King's College London, University of London, London, UK.




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
DNA (5'-D(P*AP*CP*CP*AP*AP*GP*GP*TP*CP*AP*TP*GP*AP*AP*T)-3')E15N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3')F19N/A
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*TP*GP*TP*TP*TP*TP*AP*CP*GP*TP*GP*CP*AP*T)-3')G15N/A
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3')H19N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NFX
Query on NFX

Download SDF File 
Download CCD File 
F, H
7-[(3R)-3-aminopyrrolidin-1-yl]-8-chloro-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
Clinafloxacin
C17 H17 Cl F N3 O3
QGPKADBNRMWEQR-MRVPVSSYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.001 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.258 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 121.676α = 90.00
b = 121.676β = 90.00
c = 179.393γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance