2XCS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 

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, 2XCT
  • 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
B, D
692Staphylococcus aureus (strain N315)Gene Names: gyrA, gyrB
EC: 5.99.1.3 5.99.1.3
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  Q99XG5
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  P66937
Entity ID: 2
MoleculeChainsLengthOrganism
5'-5UA*D(GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP *CP*TP*AP*CP*GP*GP*CP*T)-3'E,F20synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
B, D, E
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
RXV
Query on RXV

Download SDF File 
Download CCD File 
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5UA
Query on 5UA
E, F
DNA LINKINGC11 H13 N5 O5

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RXVIC50: 14 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 93.318α = 90.00
b = 93.318β = 90.00
c = 412.812γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

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: 2011-09-28
    Type: Database references