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- PDB-8jhu: Legionella effector protein SidI -

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Basic information

Entry
Database: PDB / ID: 8jhu
TitleLegionella effector protein SidI
ComponentsLegionella pneumophila effector protein SidI
KeywordsTOXIN / mannosyltransferase
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Glutathione S-transferase class-mu 26 kDa isozyme / Uncharacterized protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang, L. / Subramanian, A. / Mukherjee, S. / Walter, P.
Funding support United States, 6items
OrganizationGrant numberCountry
Damon Runyon Cancer Research FoundationDRG-2312-17 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM032384 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM140440 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1K99GM143527-01A1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI135990 United States
The Pew Charitable TrustsA129837 United States
CitationJournal: Nat Cell Biol / Year: 2023
Title: A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.
Authors: Advait Subramanian / Lan Wang / Tom Moss / Mark Voorhies / Smriti Sangwan / Erica Stevenson / Ernst H Pulido / Samentha Kwok / Robert J Chalkley / Kathy H Li / Nevan J Krogan / Danielle L ...Authors: Advait Subramanian / Lan Wang / Tom Moss / Mark Voorhies / Smriti Sangwan / Erica Stevenson / Ernst H Pulido / Samentha Kwok / Robert J Chalkley / Kathy H Li / Nevan J Krogan / Danielle L Swaney / Alma L Burlingame / Stephen N Floor / Anita Sil / Peter Walter / Shaeri Mukherjee /
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 ...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.
History
DepositionMay 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Legionella pneumophila effector protein SidI


Theoretical massNumber of molelcules
Total (without water)134,8831
Polymers134,8831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Legionella pneumophila effector protein SidI / GST 26 / Sj26 antigen / SjGST


Mass: 134883.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: lpg2504 / Production host: Escherichia coli (E. coli)
References: UniProt: P08515, UniProt: Q5ZSL3, glutathione transferase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Legionella pneumophila effector proein SidICOMPLEXall0RECOMBINANT
2Legionella pneumophila effector protein SidICOMPLEX1RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.1 MDaYES
210.1 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Legionella pneumophila (bacteria)446
32Legionella pneumophila (bacteria)446
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 749000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026668
ELECTRON MICROSCOPYf_angle_d0.4668988
ELECTRON MICROSCOPYf_dihedral_angle_d3.338873
ELECTRON MICROSCOPYf_chiral_restr0.038991
ELECTRON MICROSCOPYf_plane_restr0.0051162

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