7AWK | pdb_00007awk

Crystal structure of the HigB1 toxin mutant K95A from Mycobacterium tuberculosis (Rv1955)

• PDB DOI: https://doi.org/10.2210/pdb7AWK/pdb

• Classification: TOXIN
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-11-08 Released: 2021-11-24 
• Deposition Author(s): Bigot, D.J., Guillet, V., Mourey, L.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.273 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.221 (DCC) 

Starting Model: other

Literature

Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis.

Mansour, M., Giudice, E., Xu, X., Akarsu, H., Bordes, P., Guillet, V., Bigot, D.J., Slama, N., D'urso, G., Chat, S., Redder, P., Falquet, L., Mourey, L., Gillet, R., Genevaux, P.

(2022) Nat Commun 13: 2641-2641

• PubMed: 35552387 
• DOI: https://doi.org/10.1038/s41467-022-30373-w
• Primary Citation Related Structures: 
  7AWK, 7NBU


• PubMed Abstract: 
  

  Toxins of toxin-antitoxin systems use diverse mechanisms to control bacterial growth. Here, we focus on the deleterious toxin of the atypical tripartite toxin-antitoxin-chaperone (TAC) system of Mycobacterium tuberculosis, whose inhibition requires the concerted action of the antitoxin and its dedicated SecB-like chaperone. We show that the TAC toxin is a bona fide ribonuclease and identify exact cleavage sites in mRNA targets on a transcriptome-wide scale in vivo. mRNA cleavage by the toxin occurs after the second nucleotide of the ribosomal A-site codon during translation, with a strong preference for CCA codons in vivo. Finally, we report the cryo-EM structure of the ribosome-bound TAC toxin in the presence of native M. tuberculosis cspA mRNA, revealing the specific mechanism by which the TAC toxin interacts with the ribosome and the tRNA in the P-site to cleave its mRNA target.

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Organizational Affiliation: 
• Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France.
Institut de Génétique et Développement de Rennes (IGDR), UMR6290, Université de Rennes, CNRS, Rennes, France.
Department of Biology, University of Fribourg & Swiss Institute of Bioinformatics, Fribourg, Switzerland.
Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland.
Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
Institut de Génétique et Développement de Rennes (IGDR), UMR6290, Université de Rennes, CNRS, Rennes, France. [e-mail].
Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.92 kDa 
• Atom Count: 1,049 
• Modeled Residue Count: 120 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable endoribonuclease HigB1	A	130	Mycobacterium tuberculosis H37Rv	Mutation(s): 1  Gene Names: higB1, higB, Rv1955 EC: 3.1
UniProt
Find proteins for P9WJA5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJA5  Go to UniProtKB:  P9WJA5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.273 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.221 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.975	α = 90
b = 82.054	β = 90
c = 38.047	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Bigot, D.J., Guillet, V., Mourey, L.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-189-CE12-0026-03

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2022-05-18
  Changes: Database references
• Version 1.2: 2022-05-25
  Changes: Database references
• Version 1.3: 2024-06-19
  Changes: Data collection, Derived calculations
• Version 1.4: 2026-03-04
  Changes: Refinement description, Structure summary