8RR5

MenT1 toxin (rv0078a) from Mycobacterium tuberculosis H37Rv, phosphorylated at T39

• PDB DOI: https://doi.org/10.2210/pdb8RR5/pdb

• Classification: TOXIN
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-01-22 Released: 2024-09-11 
• Deposition Author(s): Arrowsmith, T.J., Blower, T.R.
• Funding Organization(s): Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Inducible auto-phosphorylation regulates a widespread family of nucleotidyltransferase toxins.

Arrowsmith, T.J., Xu, X., Xu, S., Usher, B., Stokes, P., Guest, M., Bronowska, A.K., Genevaux, P., Blower, T.R.

(2024) Nat Commun 15: 7719-7719

• PubMed: 39231966 
• DOI: https://doi.org/10.1038/s41467-024-51934-1
• Primary Citation of Related Structures:  
  8RR5, 8RR6


• PubMed Abstract: 
  

  Nucleotidyltransferases (NTases) control diverse physiological processes, including RNA modification, DNA replication and repair, and antibiotic resistance. The Mycobacterium tuberculosis NTase toxin family, MenT, modifies tRNAs to block translation. MenT toxin activity can be stringently regulated by diverse MenA antitoxins. There has been no unifying mechanism linking antitoxicity across MenT homologues. Here we demonstrate through structural, biochemical, biophysical and computational studies that despite lacking kinase motifs, antitoxin MenA ₁ induces auto-phosphorylation of MenT ₁ by repositioning the MenT ₁ phosphoacceptor T39 active site residue towards bound nucleotide. Finally, we expand this predictive model to explain how unrelated antitoxin MenA ₃ is similarly able to induce auto-phosphorylation of cognate toxin MenT ₃ . Our study reveals a conserved mechanism for the control of tuberculosis toxins, and demonstrates how active site auto-phosphorylation can regulate the activity of widespread NTases.

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Organizational Affiliation: 

Department of Biosciences, Durham University, Durham, UK.

Biological Assembly 1  

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

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 21.59 kDa 
• Atom Count: 1,360 
• Modelled Residue Count: 176 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotidyl transferase AbiEii/AbiGii toxin family protein	A	196	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv0078A
UniProt
Find proteins for L7N686 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore L7N686  Go to UniProtKB:  L7N686

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.001	α = 90
b = 127.001	β = 90
c = 68.776	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Arrowsmith, T.J., Blower, T.R.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/S022791/1

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary