8JHU

Legionella effector protein SidI


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.

Subramanian, A.Wang, L.Moss, T.Voorhies, M.Sangwan, S.Stevenson, E.Pulido, E.H.Kwok, S.Chalkley, R.J.Li, K.H.Krogan, N.J.Swaney, D.L.Burlingame, A.L.Floor, S.N.Sil, A.Walter, P.Mukherjee, S.

(2023) Nat Cell Biol 25: 1600-1615

  • DOI: https://doi.org/10.1038/s41556-023-01248-z
  • Primary Citation of Related Structures:  
    8JHU

  • PubMed Abstract: 

    A widespread strategy employed by pathogens to establish infection is to inhibit host-cell protein synthesis. Legionella pneumophila, an intracellular bacterial pathogen and the causative organism of Legionnaires' disease, secretes a subset of protein effectors into host cells that inhibit translation elongation. Mechanistic insights into how the bacterium targets translation elongation remain poorly defined. We report here that the Legionella effector SidI functions in an unprecedented way as a transfer-RNA mimic that directly binds to and glycosylates the ribosome. The 3.1 Å cryo-electron microscopy structure of SidI reveals an N-terminal domain with an 'inverted L' shape and surface-charge distribution characteristic of tRNA mimicry, and a C-terminal domain that adopts a glycosyl transferase fold that licenses SidI to utilize GDP-mannose as a sugar precursor. This coupling of tRNA mimicry and enzymatic action endows SidI with the ability to block protein synthesis with a potency comparable to ricin, one of the most powerful toxins known. In Legionella-infected cells, the translational pausing activated by SidI elicits a stress response signature mimicking the ribotoxic stress response, which is activated by elongation inhibitors that induce ribosome collisions. SidI-mediated effects on the ribosome activate the stress kinases ZAKα and p38, which in turn drive an accumulation of the protein activating transcription factor 3 (ATF3). Intriguingly, ATF3 escapes the translation block imposed by SidI, translocates to the nucleus and orchestrates the transcription of stress-inducible genes that promote cell death, revealing a major role for ATF3 in the response to collided ribosome stress. Together, our findings elucidate a novel mechanism by which a pathogenic bacterium employs tRNA mimicry to hijack a ribosome-to-nuclear signalling pathway that regulates cell fate.


  • Organizational Affiliation

    G.W. Hooper Foundation, University of California at San Francisco, San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Legionella pneumophila effector protein SidI1,172Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
EC: 2.5.1.18
UniProt
Find proteins for P08515 (Schistosoma japonicum)
Explore P08515 
Go to UniProtKB:  P08515
Find proteins for Q5ZSL3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZSL3 
Go to UniProtKB:  Q5ZSL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ5ZSL3P08515
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Damon Runyon Cancer Research FoundationUnited StatesDRG-2312-17
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM032384
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM140440
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1K99GM143527-01A1
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19 AI135990
The Pew Charitable TrustsUnited StatesA129837

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Database references