3FOE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.264 

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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:  
    3FOE, 3FOF

  • 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-reunion and ParE TOPRIM domains of topoisomerase IV stabilized by moxifloxacin and clinafloxacin, two antipneumococcal fluoroquinolones ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit AA, B496Streptococcus pneumoniaeMutation(s): 0 
Gene Names: parCSP_0855
EC: 5.99.1 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P72525 
Go to UniProtKB:  P72525
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit BC, D268Streptococcus pneumoniaeMutation(s): 0 
Gene Names: parESP_0852
EC: 5.99.1 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q59961 
Go to UniProtKB:  Q59961
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*CP*CP*AP*AP*GP*GP*TP*CP*AP*TP*GP*AP*AP*T)-3')E15N/A
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    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      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
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      • Entity ID: 5
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*CP*TP*GP*TP*TP*TP*TP*AP*CP*GP*TP*GP*CP*AP*T)-3')G15N/A
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        • Entity ID: 6
          MoleculeChainsLengthOrganismImage
          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
          Protein Feature View
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          • Reference Sequence
          Small Molecules
          Ligands 1 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          NFX (Subject of Investigation/LOI)
          Query on NFX

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

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 4.00 Å
          • R-Value Free: 0.313 
          • R-Value Work: 0.258 
          • R-Value Observed: 0.264 
          • Space Group: P 32
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 121.676α = 90
          b = 121.676β = 90
          c = 179.393γ = 120
          Software Package:
          Software NamePurpose
          PHASERphasing
          PHENIXrefinement
          HKL-2000data reduction
          HKL-2000data scaling

          Structure Validation

          View Full Validation Report



          Ligand Structure Quality Assessment  



          Entry History 

          Deposition Data

          Revision History  (Full details and data files)

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