5CDP

2.45A structure of etoposide with S.aureus DNA gyrase and DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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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:  
    5CDM, 5CDN, 5CDO, 5CDP, 5CDQ, 5CDR

  • 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 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 ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit AA, C483Staphylococcus aureus subsp. aureus N315Mutation(s): 1 
Gene Names: gyrA, SA0006
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Explore Q99XG5 
Go to UniProtKB:  Q99XG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99XG5
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit BB, D190Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: gyrB, SA0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Explore P66937 
Go to UniProtKB:  P66937
Entity Groups  
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UniProt GroupP66937
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')E,
G [auth F]		8synthetic construct
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')F [auth G],
H		13synthetic construct
Protein Feature View
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EVP
Query on EVP
Download Ideal Coordinates CCD File 
M [auth H](5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside
C29 H32 O13
VJJPUSNTGOMMGY-MRVIYFEKSA-N		 Ligand Interaction
MN
Query on MN
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J [auth B],
K [auth D],
L [auth G]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
I [auth A],
N [auth H]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.364α = 90
b = 93.364β = 90
c = 411.244γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
PHENIXphasing
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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