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 
  • R-Value Observed: 0.189 

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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 AAC483Staphylococcus aureus subsp. aureus N315Mutation(s): 1 
Gene Names: gyrASA0006
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 BBD190Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: gyrBSA0005
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(*AP*GP*CP*CP*GP*TP*AP*)-3')E8synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')G13synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 5
        MoleculeChainsLengthOrganismImage
        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
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.65 Å
        • R-Value Free: 0.210 
        • R-Value Work: 0.188 
        • R-Value Observed: 0.189 
        • Space Group: P 61
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 93.395α = 90
        b = 93.395β = 90
        c = 410.583γ = 120
        Software Package:
        Software NamePurpose
        SCALEPACKdata scaling
        BUSTER-TNTrefinement
        PDB_EXTRACTdata extraction
        REFMACphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

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