5CDQ

2.95A structure of Moxifloxacin with S.aureus DNA gyrase and DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    5CDO, 5CDN, 5CDQ, 5CDP, 5CDR, 5CDM

  • 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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit AA, C, R, T481Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: gyrA, SA0006
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit BB, D, S, U193Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: gyrB, SA0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Explore P66937 
Go to UniProtKB:  P66937
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*GP*CP*TP*T)-3')E, F, V, W20synthetic construct
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MFX
    Query on MFX
    Download Ideal Coordinates CCD File 
    E, F, V, W
    		1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
    C21 H24 F N3 O4
    FABPRXSRWADJSP-MEDUHNTESA-N    		 Ligand Interaction
    GOL
    Query on GOL
    Download Ideal Coordinates CCD File 
    A, C, R, T
    		GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N    		 Ligand Interaction
    MG
    Query on MG
    Download Ideal Coordinates CCD File 
    A, B, C, D, F, R, S, T, U, W
    		MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N    		 Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    PTR
    Query on PTR    		A,C,R,TL-PEPTIDE LINKINGC9 H12 N O6 PTYR
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.95 Å
    • R-Value Free: 0.218 
    • R-Value Work: 0.174 
    • R-Value Observed: 0.177 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 87.93α = 90
    b = 170.55β = 103.3
    c = 125.67γ = 90
    Software Package:
    Software NamePurpose
    Aimlessdata scaling
    BUSTER-TNTrefinement
    PDB_EXTRACTdata extraction
    PHENIXphasing

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2015-12-16
      Type: Initial release
    • Version 1.1: 2016-12-21
      Changes: Atomic model