6M6V

Crystal structure the toxin-antitoxin MntA-HepT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Novel polyadenylylation-dependent neutralization mechanism of the HEPN/MNT toxin/antitoxin system.

Yao, J.Zhen, X.Tang, K.Liu, T.Xu, X.Chen, Z.Guo, Y.Liu, X.Wood, T.K.Ouyang, S.Wang, X.

(2020) Nucleic Acids Res 48: 11054-11067

  • DOI: 10.1093/nar/gkaa855
  • Primary Citation of Related Structures:  
    7BXO, 6M6W, 6M6V, 6M6U

  • PubMed Abstract: 
  • The two-gene module HEPN/MNT is predicted to be the most abundant toxin/antitoxin (TA) system in prokaryotes. However, its physiological function and neutralization mechanism remains obscure. Here, we discovered that the MntA antitoxin (MNT-domain pr ...

    The two-gene module HEPN/MNT is predicted to be the most abundant toxin/antitoxin (TA) system in prokaryotes. However, its physiological function and neutralization mechanism remains obscure. Here, we discovered that the MntA antitoxin (MNT-domain protein) acts as an adenylyltransferase and chemically modifies the HepT toxin (HEPN-domain protein) to block its toxicity as an RNase. Biochemical and structural studies revealed that MntA mediates the transfer of three AMPs to a tyrosine residue next to the RNase domain of HepT in Shewanella oneidensis. Furthermore, in vitro enzymatic assays showed that the three AMPs are transferred to HepT by MntA consecutively with ATP serving as the substrate, and this polyadenylylation is crucial for reducing HepT toxicity. Additionally, the GSX10DXD motif, which is conserved among MntA proteins, is the key active motif for polyadenylylating and neutralizing HepT. Thus, HepT/MntA represents a new type of TA system, and the polyadenylylation-dependent TA neutralization mechanism is prevalent in bacteria and archaea.


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing, China.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Toxin-antitoxin system antidote Mnt familyA139Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: SO_3165
Find proteins for Q8ECH7 (Shewanella oneidensis (strain MR-1))
Explore Q8ECH7 
Go to UniProtKB:  Q8ECH7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Toxin-antitoxin system toxin HepN familyBCD133Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: SO_3166
Find proteins for Q8ECH6 (Shewanella oneidensis (strain MR-1))
Explore Q8ECH6 
Go to UniProtKB:  Q8ECH6
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*AP*AP*A)-3')E, F, G3Escherichia coli
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.08 Å
    • R-Value Free: 0.277 
    • R-Value Work: 0.221 
    • R-Value Observed: 0.223 
    • Space Group: P 21 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 56.56α = 90
    b = 225.7β = 90
    c = 52.74γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data reduction
    MOLREPphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


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

    Revision History 

    • Version 1.0: 2020-09-30
      Type: Initial release
    • Version 1.1: 2020-10-21
      Changes: Database references, Structure summary
    • Version 1.2: 2020-11-18
      Changes: Database references