2XCS

The 2.1A crystal structure of S. aureus Gyrase complex with GSK299423 and DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents.

Bax, B.D.Chan, P.F.Eggleston, D.S.Fosberry, A.Gentry, D.R.Gorrec, F.Giordano, I.Hann, M.M.Hennessy, A.Hibbs, M.Huang, J.Jones, E.Jones, J.Brown, K.K.Lewis, C.J.May, E.W.Saunders, M.R.Singh, O.Spitzfaden, C.Shen, C.Shillings, A.Theobald, A.F.Wohlkonig, A.Pearson, N.D.Gwynn, M.N.

(2010) Nature 466: 935

  • DOI: 10.1038/nature09197
  • Primary Citation of Related Structures:  
    2XCO, 2XCQ, 2XCR, 2XCS, 2XCT

  • PubMed Abstract: 
  • Despite the success of genomics in identifying new essential bacterial genes, there is a lack of sustainable leads in antibacterial drug discovery to address increasing multidrug resistance. Type IIA topoisomerases cleave and religate DNA to regulate DNA topology and are a major class of antibacterial and anticancer drug targets, yet there is no well developed structural basis for understanding drug action ...

    Despite the success of genomics in identifying new essential bacterial genes, there is a lack of sustainable leads in antibacterial drug discovery to address increasing multidrug resistance. Type IIA topoisomerases cleave and religate DNA to regulate DNA topology and are a major class of antibacterial and anticancer drug targets, yet there is no well developed structural basis for understanding drug action. Here we report the 2.1 A crystal structure of a potent, new class, broad-spectrum antibacterial agent in complex with Staphylococcus aureus DNA gyrase and DNA, showing a new mode of inhibition that circumvents fluoroquinolone resistance in this clinically important drug target. The inhibitor 'bridges' the DNA and a transient non-catalytic pocket on the two-fold axis at the GyrA dimer interface, and is close to the active sites and fluoroquinolone binding sites. In the inhibitor complex the active site seems poised to cleave the DNA, with a single metal ion observed between the TOPRIM (topoisomerase/primase) domain and the scissile phosphate. This work provides new insights into the mechanism of topoisomerase action and a platform for structure-based drug design of a new class of antibacterial agents against a clinically proven, but conformationally flexible, enzyme class.


    Organizational Affiliation

    Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK. benjamin.d.bax@gsk.com



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT AA [auth B], B [auth D]692Staphylococcus aureus subsp. aureus N315Mutation(s): 1 
Gene Names: gyrBSA0005gyrASA0006
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Explore Q99XG5 
Go to UniProtKB:  Q99XG5
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Explore P66937 
Go to UniProtKB:  P66937
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-5UA*D(GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP *CP*TP*AP*CP*GP*GP*CP*T)-3'C [auth E], D [auth F]20synthetic construct
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    RXV
    Query on RXV

    Download Ideal Coordinates CCD File 
    I [auth F]6-METHOXY-4-(2-{4-[([1,3]OXATHIOLO[5,4-C]PYRIDIN-6-YLMETHYL)AMINO]PIPERIDIN-1-YL}ETHYL)QUINOLINE-3-CARBONITRILE
    C25 H27 N5 O2 S
    NKXJSCXEAVZSMF-UHFFFAOYSA-N
     Ligand Interaction
    MN
    Query on MN

    Download Ideal Coordinates CCD File 
    E [auth B], F [auth B], G [auth D], H [auth E]MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    External Ligand Annotations 
    IDBinding Affinity (Sequence Identity %)
    RXVIC50 :  14   nM  PDBBind
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.10 Å
    • R-Value Free: 0.214 
    • R-Value Work: 0.183 
    • R-Value Observed: 0.184 
    • Space Group: P 61
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 93.318α = 90
    b = 93.318β = 90
    c = 412.812γ = 120
    Software Package:
    Software NamePurpose
    REFMACrefinement
    MOSFLMdata reduction
    SCALAdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Revision History  (Full details and data files)

    • Version 1.0: 2010-08-04
      Type: Initial release
    • Version 1.1: 2011-09-28
      Changes: Database references