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 6Y5U | pdb_00006y5u

MenT3 (aka TglT), nucleotidyltransferase toxin Rv1045 from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6Y5U

This is version 1.4 of the entry. See complete history. 

Literature

A nucleotidyltransferase toxin inhibits growth of Mycobacterium tuberculosis through inactivation of tRNA acceptor stems.

Cai, Y., Usher, B., Gutierrez, C., Tolcan, A., Mansour, M., Fineran, P.C., Condon, C., Neyrolles, O., Genevaux, P., Blower, T.R.

(2020) Sci Adv 6: eabb6651-eabb6651

  • DOI: https://doi.org/10.1126/sciadv.abb6651
  • Primary Citation Related Structures: 
    6Y56, 6Y5U

  • PubMed Abstract: 

    Toxin-antitoxin systems are widespread stress-responsive elements, many of whose functions remain largely unknown. Here, we characterize the four DUF1814-family nucleotidyltransferase-like toxins (MenT 1-4 ) encoded by the human pathogen Mycobacterium tuberculosis . Toxin MenT 3 inhibited growth of M. tuberculosis when not antagonized by its cognate antitoxin, MenA 3 . We solved the structures of toxins MenT 3 and MenT 4 to 1.6 and 1.2 Å resolution, respectively, and identified the biochemical activity and target of MenT 3 . MenT 3 blocked in vitro protein expression and prevented tRNA charging in vivo. MenT 3 added pyrimidines (C or U) to the 3'-CCA acceptor stems of uncharged tRNAs and exhibited strong substrate specificity in vitro, preferentially targeting tRNA Ser from among the 45 M . tuberculosis tRNAs. Our study identifies a previously unknown mechanism that expands the range of enzymatic activities used by bacterial toxins, uncovering a new way to block protein synthesis and potentially treat tuberculosis and other infections.


  • Organizational Affiliation: 
    • Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31400 Toulouse, France.

Macromolecule Content 

  • Total Structure Weight: 31.98 kDa 
  • Atom Count: 2,494 
  • Modeled Residue Count: 288 
  • Deposited Residue Count: 292 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rv1045292Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv1045
UniProt
Find proteins for P96356 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P96356 
Go to UniProtKB:  P96356
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP96356
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.41α = 90
b = 95.41β = 90
c = 69.026γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2020-09-30
    Changes: Database references
  • Version 1.3: 2021-01-20
    Changes: Structure summary
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Structure summary