Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.38 kDa 
• Atom Count: 4,943 
• Modelled Residue Count: 638 
• Deposited Residue Count: 726 
• Unique protein chains: 1

 2XCO

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

• PDB DOI:  https://doi.org/10.2210/pdb2XCO/pdb

• Classification: ISOMERASE
• Organism(s): Staphylococcus aureus subsp. aureus N315
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-24 Released: 2010-08-04 
• Deposition Author(s): 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., Singh, O., Spitzfaden, C., Shen, C., Shillings, A., Theobald, A.F., Wohlkonig, A., Pearson, N.D., Gwynn, M.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.285 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

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

• PubMed: 20686482 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A	A	726	Staphylococcus aureus subsp. aureus N315	Mutation(s): 0  Gene Names: gyrA, SA0006, gyrB, SA0005 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
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
UniProt Groups	Q99XG5P66937

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.285 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.917	α = 90
b = 89.917	β = 90
c = 410.583	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-04 
Deposition Author(s): 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., Singh, O., Spitzfaden, C., Shen, C., Shillings, A., Theobald, A.F., Wohlkonig, A., Pearson, N.D., Gwynn, M.N.

Revision History  

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