9IKD | pdb_00009ikd

The apo structure of the MazF-mt3 toxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 
    0.279 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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Literature

Long Dynamic beta 1-beta 2 Loops in M. tb MazF Toxins Affect the Interaction Modes and Strengths of the Toxin-Antitoxin Pairs.

Tang, Z.Jiang, P.Xie, W.

(2024) Int J Mol Sci 25

  • DOI: https://doi.org/10.3390/ijms25179630
  • Primary Citation of Related Structures:  
    8ZWS, 9IKD

  • PubMed Abstract: 

    Tuberculosis is a worldwide plague caused by the pathogen Mycobacterium tuberculosis ( M. tb ). Toxin-antitoxin (TA) systems are genetic elements abundantly present in prokaryotic organisms and regulate important cellular processes. MazEF is a TA system implicated in the formation of "persisters cells" of M. tb , which contain more than 10 such members. However, the exact function and inhibition mode of each MazF are not fully understood. Here we report crystal structures of MazF-mt3 in its apo form and in complex with the C-terminal half of MazE-mt3. Structural analysis suggested that two long but disordered β1-β2 loops would interfere with the binding of the cognate MazE-mt3 antitoxin. Similar loops are also present in the MazF-mt1 and -mt9 but are sustainably shortened in other M. tb MazF members, and these TA pairs behave distinctly in terms of their binding modes and their RNase activities. Systematic crystallographic and biochemical studies further revealed that the biochemical activities of M. tb toxins were combined results between the interferences from the characteristic loops and the electrostatic interactions between the cognate TA pairs. This study provides structural insight into the binding mode and the inhibition mechanism of the MazE/F TA pairs, which facilitate the structure-based peptide designs.


  • Organizational Affiliation
    • MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoribonuclease MazF6118Mycobacterium tuberculosis CDC1551Mutation(s): 0 
Gene Names: mazF6MT2046
EC: 3.1.27
UniProt
Find proteins for P9WII3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WII3 
Go to UniProtKB:  P9WII3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WII3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free:  0.279 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.795α = 90
b = 110.795β = 90
c = 271.217γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release