5CDR

2.65 structure of S.aureus DNA gyrase and artificially nicked DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin.

Chan, P.F.Srikannathasan, V.Huang, J.Cui, H.Fosberry, A.P.Gu, M.Hann, M.M.Hibbs, M.Homes, P.Ingraham, K.Pizzollo, J.Shen, C.Shillings, A.J.Spitzfaden, C.E.Tanner, R.Theobald, A.J.Stavenger, R.A.Bax, B.D.Gwynn, M.N.

(2015) Nat Commun 6: 10048-10048

  • DOI: 10.1038/ncomms10048
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • New antibacterials are needed to tackle antibiotic-resistant bacteria. Type IIA topoisomerases (topo2As), the targets of fluoroquinolones, regulate DNA topology by creating transient double-strand DNA breaks. Here we report the first co-crystal struc ...

    New antibacterials are needed to tackle antibiotic-resistant bacteria. Type IIA topoisomerases (topo2As), the targets of fluoroquinolones, regulate DNA topology by creating transient double-strand DNA breaks. Here we report the first co-crystal structures of the antibacterial QPT-1 and the anticancer drug etoposide with Staphylococcus aureus DNA gyrase, showing binding at the same sites in the cleaved DNA as the fluoroquinolone moxifloxacin. Unlike moxifloxacin, QPT-1 and etoposide interact with conserved GyrB TOPRIM residues rationalizing why QPT-1 can overcome fluoroquinolone resistance. Our data show etoposide's antibacterial activity is due to DNA gyrase inhibition and suggests other anticancer agents act similarly. Analysis of multiple DNA gyrase co-crystal structures, including asymmetric cleavage complexes, led to a 'pair of swing-doors' hypothesis in which the movement of one DNA segment regulates cleavage and religation of the second DNA duplex. This mechanism can explain QPT-1's bacterial specificity. Structure-based strategies for developing topo2A antibacterials are suggested.


    Related Citations: 
    • Crystallization and initial crystallographic analysis of covalent DNA-cleavage complexes of Staphyloccocus aureus DNA gyrase with QPT-1, moxifloxacin and etoposide.
      Srikannathasan, V.,Wohlkonig, A.,Shillings, A.,Singh, O.,Chan, P.F.,Huang, J.,Gwynn, M.N.,Fosberry, A.P.,Homes, P.,Hibbs, M.,Theobald, A.J.,Spitzfaden, C.,Bax, B.D.
      (2015) Acta Crystallogr F Struct Biol Commun 71: 1242


    Organizational Affiliation

    Antibacterial Discovery Performance Unit, Infectious Diseases, Therapy Area Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit A
A, C
483Staphylococcus aureus (strain N315)Mutation(s): 1 
Gene Names: gyrA
EC: 5.6.2.3
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  Q99XG5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B,DNA gyrase subunit B
B, D
190Staphylococcus aureus (strain N315)Mutation(s): 0 
Gene Names: gyrB
EC: 5.6.2.3
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  P66937
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*)-3')E8synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')G13synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')F20synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Download SDF File 
Download CCD File 
A, C, E, G
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.188 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 93.395α = 90.00
b = 93.395β = 90.00
c = 410.583γ = 120.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release