5WYG

The crystal structure of the apo form of Mtb MazF

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

  • Deposited: 2017-01-13 Released: 2017-04-12 
  • Deposition Author(s): Xie, W., Chen, R., Tu, J.
  • Funding Organization(s): the Science and Technology Program of Guangzhou, the Fundamental Research Funds for the Central Universities, Guangdong Innovative Research Team Program

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure of the MazF-mt9 toxin, a tRNA-specific endonuclease from Mycobacterium tuberculosis

Chen, R., Tu, J., Liu, Z., Meng, F., Ma, P., Ding, Z., Yang, C., Chen, L., Deng, X., Xie, W.

(2017) Biochem Biophys Res Commun 486: 804-810

  • DOI: https://doi.org/10.1016/j.bbrc.2017.03.132
  • Primary Citation of Related Structures:  
    5WYG

  • PubMed Abstract: 

    Tuberculosis (TB) is a severe disease caused by Mycobacterium tuberculosis (M. tb) and the well-characterized M. tb MazE/F proteins play important roles in stress adaptation. Recently, the MazF-mt9 toxin has been found to display endonuclease activities towards tRNAs but the mechanism is unknown. We hereby present the crystal structure of apo-MazF-mt9. The enzyme recognizes tRNA Lys with a central UUU motif within the anticodon loop, but is insensitive to the sequence context outside of the loop. Based on our crystallographic and biochemical studies, we identified key residues for catalysis and proposed the potential tRNA-binding site.

    • Organizational Affiliation: 

    State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, People's Republic of China.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable endoribonuclease MazF7A,
B [auth C]		140Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: mazF7, Rv2063A
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.468α = 90
b = 74.468β = 90
c = 105.114γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
the Science and Technology Program of GuangzhouChina201504010025
the Fundamental Research Funds for the Central UniversitiesChina16lgjc76
Guangdong Innovative Research Team ProgramChinaNO. 2011Y038

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description