5CDO

3.15A structure of QPT-1 with S.aureus DNA gyrase and DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report



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 structure ...

    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 A ACRT482Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
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 B BDSU188Staphylococcus 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(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')E, F, V, W20synthetic construct
    Small Molecules
    Ligands 7 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    53M
    Query on 53M

    Download Ideal Coordinates CCD File 
    E, W
    (2R,4S,4aS)-4',6'-dihydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidin]-2'-one
    C17 H18 N4 O6
    DJZPHYIXNUOVJU-VYUIOLGVSA-N
     Ligand Interaction
    53L
    Query on 53L

    Download Ideal Coordinates CCD File 
    F
    (2R,4S,4aS,5S)-6'-hydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4'(3'H)-dione
    C17 H18 N4 O6
    DJZPHYIXNUOVJU-VYUIOLGVSA-N
     Ligand Interaction
    50M
    Query on 50M

    Download Ideal Coordinates CCD File 
    S
    (2R,4S,4aS,5R)-6'-hydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4'(3'H)-dione
    C17 H18 N4 O6
    DJZPHYIXNUOVJU-VYUIOLGVSA-N
     Ligand Interaction
    SO4
    Query on SO4

    Download Ideal Coordinates CCD File 
    A, T
    SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 
    A, D, U
    GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    MN
    Query on MN

    Download Ideal Coordinates CCD File 
    B, D, S, U
    MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    NA
    Query on NA

    Download Ideal Coordinates CCD File 
    A, C, R, T
    SODIUM ION
    Na
    FKNQFGJONOIPTF-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: 3.15 Å
    • R-Value Free: 0.246 
    • R-Value Work: 0.215 
    • R-Value Observed: 0.216 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 90.472α = 90
    b = 170.211β = 102.75
    c = 124.579γ = 90
    Software Package:
    Software NamePurpose
    Aimlessdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

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