6FQM

3.06A COMPLEX OF S.AUREUS GYRASE with imidazopyrazinone T1 AND DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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Literature

A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance.

Germe, T., Voros, J., Jeannot, F., Taillier, T., Stavenger, R.A., Bacque, E., Maxwell, A., Bax, B.D.

(2018) Nucleic Acids Res 46: 4114-4128

  • DOI: https://doi.org/10.1093/nar/gky181
  • Primary Citation of Related Structures:  
    6FQM, 6FQS, 6FQV

  • PubMed Abstract: 

    • Imidazopyrazinones (IPYs) are a new class of compounds that target bacterial topoisomerases as a basis for their antibacterial activity. We have characterized the mechanism of these compounds through structural/mechanistic studies showing they bind and stabilize a cleavage complex between DNA gyrase and DNA ('poisoning') in an analogous fashion to fluoroquinolones, but without the requirement for the water-metal-ion bridge ...

    Imidazopyrazinones (IPYs) are a new class of compounds that target bacterial topoisomerases as a basis for their antibacterial activity. We have characterized the mechanism of these compounds through structural/mechanistic studies showing they bind and stabilize a cleavage complex between DNA gyrase and DNA ('poisoning') in an analogous fashion to fluoroquinolones, but without the requirement for the water-metal-ion bridge. Biochemical experiments and structural studies of cleavage complexes of IPYs compared with an uncleaved gyrase-DNA complex, reveal conformational transitions coupled to DNA cleavage at the DNA gate. These involve movement at the GyrA interface and tilting of the TOPRIM domains toward the scissile phosphate coupled to capture of the catalytic metal ion. Our experiments show that these structural transitions are involved generally in poisoning of gyrase by therapeutic compounds and resemble those undergone by the enzyme during its adenosine triphosphate-coupled strand-passage cycle. In addition to resistance mutations affecting residues that directly interact with the compounds, we characterized a mutant (D82N) that inhibits formation of the cleavage complex by the unpoisoned enzyme. The D82N mutant appears to act by stabilizing the binary conformation of DNA gyrase with uncleaved DNA without direct interaction with the compounds. This provides general insight into the resistance mechanisms to antibiotics targeting bacterial type II topoisomerases.

    Organizational Affiliation: 

    Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit BA [auth B],
G [auth b],
I [auth d]		201Staphylococcus 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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP66937
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit AB [auth A],
D [auth C],
H [auth a],
J [auth c]		490Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
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
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit BC [auth D]202Staphylococcus 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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP66937
Protein Feature View
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*AP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*TP*CP*T)-3')E,
F,
K [auth e],
L [auth f]		20synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E32 (Subject of Investigation/LOI)
Query on E32
Download Ideal Coordinates CCD File 
P [auth E],
R [auth E],
S [auth F],
W [auth e],
X [auth f],
P [auth E],
R [auth E],
S [auth F],
W [auth e],
X [auth f],
Y [auth f]
7-[(3~{S})-3-azanylpyrrolidin-1-yl]-5-cyclopropyl-8-fluoranyl-imidazo[1,2-a]quinoxalin-4-one
C17 H18 F N5 O
FBYRCTKKXBIHCM-JTQLQIEISA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
O [auth C],
V [auth c]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
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Q [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
MN
Query on MN
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M [auth B],
N [auth D],
T [auth b],
U [auth d]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		B [auth A],
D [auth C],
H [auth a],
J [auth c]		L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.34α = 90
b = 171.71β = 102.86
c = 124.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Innovative Medicines Initiative Joint Undertaking115583

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references