7AER

Rebuilt and re-refined PDB entry 5yep: tri-AMPylated Shewanella oneidensis HEPN toxin in complex with MNT antitoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5YEP


Literature

HEPN-MNT Toxin-Antitoxin System: The HEPN Ribonuclease Is Neutralized by OligoAMPylation.

Songailiene, I.Juozapaitis, J.Tamulaitiene, G.Ruksenaite, A.Sulcius, S.Sasnauskas, G.Venclovas, C.Siksnys, V.

(2020) Mol Cell 80: 955-970.e7

  • DOI: https://doi.org/10.1016/j.molcel.2020.11.034
  • Primary Citation of Related Structures:  
    7AE2, 7AE6, 7AE8, 7AE9, 7AER

  • PubMed Abstract: 

    Prokaryotic toxin-antitoxin (TA) systems are composed of a toxin capable of interfering with key cellular processes and its neutralizing antidote, the antitoxin. Here, we focus on the HEPN-MNT TA system encoded in the vicinity of a subtype I-D CRISPR-Cas system in the cyanobacterium Aphanizomenon flos-aquae. We show that HEPN acts as a toxic RNase, which cleaves off 4 nt from the 3' end in a subset of tRNAs, thereby interfering with translation. Surprisingly, we find that the MNT (minimal nucleotidyltransferase) antitoxin inhibits HEPN RNase through covalent di-AMPylation (diadenylylation) of a conserved tyrosine residue, Y109, in the active site loop. Furthermore, we present crystallographic snapshots of the di-AMPylation reaction at different stages that explain the mechanism of HEPN RNase inactivation. Finally, we propose that the HEPN-MNT system functions as a cellular ATP sensor that monitors ATP homeostasis and, at low ATP levels, releases active HEPN toxin.


  • Organizational Affiliation

    Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, 10257 Vilnius, Lithuania.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin-antitoxin system antidote Mnt family139Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: SO_3165
UniProt
Find proteins for Q8ECH7 (Shewanella oneidensis (strain MR-1))
Explore Q8ECH7 
Go to UniProtKB:  Q8ECH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ECH7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin-antitoxin system toxin HepN family
B, C, D
139Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: SO_3166
UniProt
Find proteins for Q8ECH6 (Shewanella oneidensis (strain MR-1))
Explore Q8ECH6 
Go to UniProtKB:  Q8ECH6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ECH6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.61α = 90
b = 224.38β = 90
c = 53.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
SHELXCDphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release