2XCO

The 3.1A crystal structure of the catalytic core (B'A' region) of Staphylococcus aureus DNA Gyrase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  
  • Also Cited By: 4BUL

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
A
726Staphylococcus aureus (strain N315)Mutation(s): 0 
Gene Names: gyrA, gyrB
EC: 5.6.2.3 5.6.2.3
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  Q99XG5
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  P66937
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.217 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 89.917α = 90.00
b = 89.917β = 90.00
c = 410.583γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance