Structure of the Salmonella tRNA pyrophosphokinase CapRel

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Direct activation of a bacterial innate immune system by a viral capsid protein.

Zhang, T.Tamman, H.Coppieters 't Wallant, K.Kurata, T.LeRoux, M.Srikant, S.Brodiazhenko, T.Cepauskas, A.Talavera, A.Martens, C.Atkinson, G.C.Hauryliuk, V.Garcia-Pino, A.Laub, M.T.

(2022) Nature 612: 132-140

  • DOI: https://doi.org/10.1038/s41586-022-05444-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Bacteria have evolved diverse immunity mechanisms to protect themselves against the constant onslaught of bacteriophages 1-3 . Similar to how eukaryotic innate immune systems sense foreign invaders through pathogen-associated molecular patterns 4 (PAMPs), many bacterial immune systems that respond to bacteriophage infection require phage-specific triggers to be activated. However, the identities of such triggers and the sensing mechanisms remain largely unknown. Here we identify and investigate the anti-phage function of CapRel SJ46 , a fused toxin-antitoxin system that protects Escherichia coli against diverse phages. Using genetic, biochemical and structural analyses, we demonstrate that the C-terminal domain of CapRel SJ46 regulates the toxic N-terminal region, serving as both antitoxin and phage infection sensor. Following infection by certain phages, newly synthesized major capsid protein binds directly to the C-terminal domain of CapRel SJ46 to relieve autoinhibition, enabling the toxin domain to pyrophosphorylate tRNAs, which blocks translation to restrict viral infection. Collectively, our results reveal the molecular mechanism by which a bacterial immune system directly senses a conserved, essential component of phages, suggesting a PAMP-like sensing model for toxin-antitoxin-mediated innate immunity in bacteria. We provide evidence that CapRels and their phage-encoded triggers are engaged in a 'Red Queen conflict' 5 , revealing a new front in the intense coevolutionary battle between phages and bacteria. Given that capsid proteins of some eukaryotic viruses are known to stimulate innate immune signalling in mammalian hosts 6-10 , our results reveal a deeply conserved facet of immunity.

  • Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RelA/SpoT family protein
A, B
373Salmonella phage SJ46Mutation(s): 0 
Gene Names: J46_0058
Find proteins for A0A1B0VBT5 (Salmonella phage SJ46)
Explore A0A1B0VBT5 
Go to UniProtKB:  A0A1B0VBT5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B0VBT5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.573α = 90
b = 136.196β = 102.7
c = 57.782γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Fonds National de la Recherche Scientifique (FNRS)Belgium--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2022-12-14
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description