7DU4

The structure of the M.tb MazF-mt9 toxin in complex with a fragment of cognate antitoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanistic Insight into the Peptide Binding Modes to Two M. tb MazF Toxins.

Chen, R.Zhou, J.Xie, W.

(2021) Toxins (Basel) 13

  • DOI: https://doi.org/10.3390/toxins13050319
  • Primary Citation of Related Structures:  
    7DU4, 7DU5

  • PubMed Abstract: 

    Tuberculosis (TB) is a contagious disease caused by Mycobacterium tuberculosis ( M. tb ). It is regarded as a major health threat all over the world, mainly because of its high mortality and drug-resistant nature. Toxin-antitoxin (TA) systems are modules ubiquitously found in prokaryotic organisms, and the well-studied MazEF systems (MazE means "what is it?" in Hebrew) are implicated in the formation of "persister cells" in the M. tb pathogen. Here, we report cocrystal structures of M. tb MazF-mt1 and -mt9, two important MazF members responsible for specific mRNA and tRNA cleavages, respectively, in complexes with truncated forms of their cognate antitoxin peptides. These peptides bind to the toxins with comparable affinities to their full-length antitoxins, which would reduce the RNA-cleavage capacities of the toxins in vitro. After structural analysis of the binding modes, we systemically tested the influence of the substitutions of individual residues in the truncated MazE-mt9 peptide on its affinity. This study provides structural insight into the binding modes and the inhibition mechanisms between the MazE/F-mt TA pairs. More importantly, it contributes to the future design of peptide-based antimicrobial agents against TB and potentially relieves the drug-resistance problems by targeting novel M. tb proteins.


  • Organizational Affiliation

    MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou 510006, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable endoribonuclease MazF7
A, B
140Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: mazF7Rv2063A
EC: 3.1
UniProt
Find proteins for P0CL62 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P0CL62 
Go to UniProtKB:  P0CL62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CL62
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptideC [auth Q]15Mycobacterium tuberculosis H37RvMutation(s): 0 
UniProt
Find proteins for P9WJ85 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WJ85 
Go to UniProtKB:  P9WJ85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WJ85
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.61α = 90
b = 74.61β = 90
c = 104.354γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870782

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references, Refinement description
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description