6S5T

Legionella pneumophila SidJ-Human calmodulin complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.15 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

Inhibition of bacterial ubiquitin ligases by SidJ-calmodulin catalysed glutamylation.

Bhogaraju, S.Bonn, F.Mukherjee, R.Adams, M.Pfleiderer, M.M.Galej, W.P.Matkovic, V.Lopez-Mosqueda, J.Kalayil, S.Shin, D.Dikic, I.

(2019) Nature 572: 382-386

  • DOI: 10.1038/s41586-019-1440-8

  • PubMed Abstract: 
  • The family of bacterial SidE enzymes catalyses phosphoribosyl-linked (PR) serine ubiquitination and promotes infectivity of Legionella pneumophilia, a pathogenic bacterium causing Legionnaires' disease <sup>1-3 </sup>. SidEs share the genetic locus w ...

    The family of bacterial SidE enzymes catalyses phosphoribosyl-linked (PR) serine ubiquitination and promotes infectivity of Legionella pneumophilia, a pathogenic bacterium causing Legionnaires' disease 1-3 . SidEs share the genetic locus with the Legionella effector SidJ that spatiotemporally opposes their toxicity in yeast and mammalian cells, through an unknown mechanism 4-6 . Deletion of SidJ leads to a significant defect in the growth of Legionella in both its natural host amoeba and in murine macrophages 4,5 . Here, we demonstrate that SidJ is a glutamylase that modifies the catalytic glutamate in the mono-ADPribosyl transferase (mART) domain of SdeA thus blocking its ubiquitin (Ub) ligase activity. SidJ glutamylation activity requires interaction with calmodulin (CaM), a eukaryotic specific co-factor, and can be regulated by intracellular changes in Ca 2+ concentrations. The cryo-EM structure of SidJ/human apo-CaM complex revealed the architecture of this unique heterodimeric glutamylase. In infected cells, we show that SidJ mediates glutamylation of SidEs on the surface of Legionella-containing vacuoles (LCVs). Using quantitative proteomics, we also uncovered multiple host proteins as putative targets of SidJ-mediated glutamylation. Collectively, this study reveals the mechanism of SidE ligases inhibition by a SidJ/CaM glutamylase and opens new avenues for studying protein glutamylation, an understudied protein modification in higher eukaryotes.


    Organizational Affiliation

    Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany. bhogaraju@embl.fr.,Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany. bhogaraju@embl.fr.,European Molecular Biology Laboratory, Grenoble, France. bhogaraju@embl.fr.,Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,European Molecular Biology Laboratory, Grenoble, France.,Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.,Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany. dikic@biochem2.uni-frankfurt.de.,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany. dikic@biochem2.uni-frankfurt.de.,Max Planck Institute of Biophysics, Frankfurt am Main, Germany. dikic@biochem2.uni-frankfurt.de.,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SidJ
A
873Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)Mutation(s): 0 
Gene Names: sidJ
EC: 6.-.-.-
Find proteins for Q5ZTK6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Go to UniProtKB:  Q5ZTK6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calmodulin-2
B
149Homo sapiensMutation(s): 0 
Gene Names: CALM2 (CAM2, CAMB)
Find proteins for P0DP24 (Homo sapiens)
Go to Gene View: CALM2
Go to UniProtKB:  P0DP24
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 1177
German Research FoundationGermanyEXC115
European Research Council742720

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references
  • Version 1.2: 2019-08-28
    Type: Data collection, Database references