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 

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Ligand Structure Quality Assessment 


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: https://doi.org/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. 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.


  • 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
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit AA,
C,
G [auth R],
I [auth T]
481Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: gyrASA0006
EC: 5.99.1.3
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit BB,
D,
H [auth S],
J [auth U]
193Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: gyrBSA0005
EC: 5.99.1.3
UniProt
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Explore P66937 
Go to UniProtKB:  P66937
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP66937
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
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,
K [auth V],
L [auth W]
20synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MFX
Query on MFX

Download Ideal Coordinates CCD File 
JA [auth V]
KA [auth W]
MA [auth W]
W [auth E]
X [auth F]
JA [auth V],
KA [auth W],
MA [auth W],
W [auth E],
X [auth F],
Z [auth F]
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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth R]
CA [auth R]
DA [auth R]
HA [auth T]
O [auth A]
BA [auth R],
CA [auth R],
DA [auth R],
HA [auth T],
O [auth A],
P [auth A],
T [auth C],
U [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth R]
EA [auth S]
FA [auth T]
GA [auth T]
IA [auth U]
AA [auth R],
EA [auth S],
FA [auth T],
GA [auth T],
IA [auth U],
LA [auth W],
M [auth A],
N [auth A],
NA [auth W],
Q [auth B],
R [auth C],
S [auth C],
V [auth D],
Y [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A,
C,
G [auth R],
I [auth T]
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
MFX BindingDB:  5CDQ IC50: min: 7700, max: 1.27e+6 (nM) from 7 assay(s)
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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