8RCW | pdb_00008rcw

Crystal structure of the Mycobacterium tuberculosis regulator VirS (N-terminal fragment 4-208) in complex with the lead compound SMARt751


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.217 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.200 (DCC) 

Starting Model: in silico
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Literature

Crystal structure of the Mycobacterium tuberculosis VirS regulator reveals its interaction with the lead compound SMARt751.

Grosse, C.Sigoillot, M.Megalizzi, V.Tanina, A.Willand, N.Baulard, A.R.Wintjens, R.

(2024) J Struct Biol 216: 108090-108090

  • DOI: https://doi.org/10.1016/j.jsb.2024.108090
  • Primary Citation of Related Structures:  
    8RCW

  • PubMed Abstract: 

    Ethionamide (ETO) is a prodrug that is primarily used as a second-line agent in the treatment of tuberculosis. Among the bacterial ETO activators, the monooxygenase MymA has been recently identified, and its expression is regulated by the mycobacterial regulator VirS. The discovery of VirS ligands that can enhance mymA expression and thereby increase the antimycobacterial efficacy of ETO, has led to the development of a novel therapeutic strategy against tuberculosis. This strategy involves the selection of preclinical candidates, including SMARt751. We report the first crystal structure of the AraC-like regulator VirS, in complex with SMARt751, refined at 1.69 Å resolution. Crystals were obtained via an in situ proteolysis method in the requisite presence of SMARt751. The elucidated structure corresponds to the ligand-binding domain of VirS, adopting an α/β fold with structural similarities to H-NOX domains. Within the VirS structure, SMARt751 is situated in a completely enclosed hydrophobic cavity, where it forms hydrogen bonds with Asn11 and Asn149 as well as van der Waals contacts with various hydrophobic amino acids. Comprehensive structural comparisons within the AraC family of transcriptional regulators are conducted and analyzed to figure out the effects of the SMARt751 binding on the regulatory activity of VirS.


  • Organizational Affiliation
    • Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Department of Research in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, Belgium; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HTH-type transcriptional regulator VirS
A, B
229Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: virSRv3082cMTV013.03c
UniProt
Find proteins for P9WMJ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WMJ3 
Go to UniProtKB:  P9WMJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WMJ3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.200 (DCC) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.332α = 90
b = 115.332β = 90
c = 70.987γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata processing
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
autoPROCdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fonds National de la Recherche Scientifique (FNRS)BelgiumCR40003580
Agence Nationale de la Recherche (ANR)FranceANR-20-PAMR-0005

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release