Toxin VapC21 from Mycobacterium tuberculosis

Experimental Data Snapshot

  • Resolution: 1.31 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 

Starting Model: experimental
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Crystal structure of VapC21 from Mycobacterium tuberculosis at 1.31 angstrom resolution.

Jardim, P.Santos, I.C.Barbosa, J.A.R.G.de Freitas, S.M.Valadares, N.F.

(2016) Biochem Biophys Res Commun 478: 1370-1375

  • DOI: https://doi.org/10.1016/j.bbrc.2016.08.130
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Persisters are individual bacterial cells that exhibit a phenotype characterized by slow growth, low metabolic rate and multidrug tolerance. The processes that drive cells into a persistence state constitute an active but incipient research field, and structural data regarding its components are scarce. The molecular targets of many therapeutic drugs are involved in cell wall synthesis and cell division, and these cellular processes are down-regulated in persister cells, consequently these cells are more likely to survive antibiotic treatment. Toxin-antitoxin systems were shown to have a leading role in the formation of persisters, and several pathogenic bacteria display a wide array of these systems. The Mycobacterium tuberculosis H37Rv genome presents 88 toxin-antitoxin loci, of which 47 code for members of the VapBC protein family. To date, only four crystal structures of Mycobacterium tuberculosis VapBC complexes are available, and all of them present the toxin bound to and inhibited by the antitoxin. We present the 1.31 Å resolution structure of VapC21, the first structure of a Mycobacterium tuberculosis VapC toxin in the absence of its cognate inhibitory antitoxin. Our data show that VapC21 is a dimer in solution, with conserved active site architecture and an extensive antitoxin binding groove. Additionally, the strategy used to mutate a putative catalytic residue allowing the expression and purification of soluble VapC21 will pave the way for the resolution of more toxin structures in the absence of antitoxins. Taken together, our findings represent an important step in unraveling the molecular mechanisms related to persistence, which will contribute for the design of faster and more efficient therapeutic approaches for the treatment of tuberculosis, particularly for infections with multidrug-resistant strains.

  • Organizational Affiliation

    Laboratory of Molecular Biophysics, Department of Cell Biology, University of Brasília, Brasília, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease VapC21146Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: vapC21Rv2757c
EC: 3.1
Find proteins for P9WF91 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WF91 
Go to UniProtKB:  P9WF91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WF91
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.31 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.339α = 90
b = 44.351β = 101.72
c = 56.53γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-09-28
    Changes: Database references
  • Version 1.2: 2017-06-21
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description