5CDM

2.5A structure of QPT-1 with S.aureus DNA gyrase and DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 

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

    Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK.,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 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: 2
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit A
A, C
482Staphylococcus aureus (strain N315)Mutation(s): 0 
Gene Names: gyrA
EC: 5.6.2.3
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  Q99XG5
Entity ID: 3
MoleculeChainsLengthOrganism
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,F8synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
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')I,N12synthetic construct
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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B, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
54Q
Query on 54Q

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I, N
(2R,4S,4aS)-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',6'(1'H,3'H)-trione
C17 H18 N4 O6
DJZPHYIXNUOVJU-VYUIOLGVSA-N
 Ligand Interaction
DT
Query on DT

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N
THYMIDINE-5'-MONOPHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, C
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 93.884α = 90.00
b = 93.884β = 90.00
c = 412.482γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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