+Open data
-Basic information
Entry | Database: PDB / ID: 6s5t | ||||||||||||
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Title | Legionella pneumophila SidJ-Human calmodulin complex | ||||||||||||
Components |
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Keywords | TRANSFERASE / Bacterial glutamylase / pseudo kinase / calmodulin-dependent / Legionella / SidJ / SdeA / serine ubiquitination | ||||||||||||
Function / homology | Function and homology information Ligases / negative regulation of calcium ion transmembrane transporter activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / ligase activity / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity ...Ligases / negative regulation of calcium ion transmembrane transporter activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / ligase activity / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / : / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cysteine-type peptidase activity / : / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / response to calcium ion / positive regulation of protein serine/threonine kinase activity / G2/M transition of mitotic cell cycle / spindle pole / calcium-dependent protein binding / myelin sheath / transferase activity / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / centrosome / nucleotide binding / calcium ion binding / protein kinase binding / protein-containing complex / proteolysis / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Legionella pneumophila (bacteria) Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.15 Å | ||||||||||||
Authors | Bhogaraju, S. / Galej, W.P. / Pfleiderer, M.M. / Adams, M. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Nature / Year: 2019 Title: Inhibition of bacterial ubiquitin ligases by SidJ-calmodulin catalysed glutamylation. Authors: Sagar Bhogaraju / Florian Bonn / Rukmini Mukherjee / Michael Adams / Moritz M Pfleiderer / Wojciech P Galej / Vigor Matkovic / Jaime Lopez-Mosqueda / Sissy Kalayil / Donghyuk Shin / Ivan Dikic / Abstract: The family of bacterial SidE enzymes catalyses phosphoribosyl-linked serine ubiquitination and promotes infectivity of Legionella pneumophila, a pathogenic bacteria that causes Legionnaires' disease. ...The family of bacterial SidE enzymes catalyses phosphoribosyl-linked serine ubiquitination and promotes infectivity of Legionella pneumophila, a pathogenic bacteria that causes Legionnaires' disease. SidE enzymes share the genetic locus with the Legionella effector SidJ that spatiotemporally opposes the toxicity of these enzymes in yeast and mammalian cells, through a mechanism that is currently unknown. Deletion of SidJ leads to a substantial defect in the growth of Legionella in both its natural hosts (amoebae) and in mouse macrophages. Here we demonstrate that SidJ is a glutamylase that modifies the catalytic glutamate in the mono-ADP ribosyl transferase domain of the SdeA, thus blocking the ubiquitin ligase activity of SdeA. The glutamylation activity of SidJ requires interaction with the eukaryotic-specific co-factor calmodulin, and can be regulated by intracellular changes in Ca concentrations. The cryo-electron microscopy structure of SidJ in complex with human apo-calmodulin revealed the architecture of this heterodimeric glutamylase. We show that, in cells infected with L. pneumophila, SidJ mediates the glutamylation of SidE enzymes on the surface of vacuoles that contain Legionella. We used quantitative proteomics to uncover multiple host proteins as putative targets of SidJ-mediated glutamylation. Our study reveals the mechanism by which SidE ligases are inhibited by a SidJ-calmodulin glutamylase, and opens avenues for exploring an understudied protein modification (glutamylation) in eukaryotes. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6s5t.cif.gz | 189.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s5t.ent.gz | 145.4 KB | Display | PDB format |
PDBx/mmJSON format | 6s5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s5t_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6s5t_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6s5t_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 6s5t_validation.cif.gz | 52.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/6s5t ftp://data.pdbj.org/pub/pdb/validation_reports/s5/6s5t | HTTPS FTP |
-Related structure data
Related structure data | 10100MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 100338.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg2155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZTK6 |
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#2: Protein | Mass: 16852.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALM2, CAM2, CAMB / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP24 |
#3: Chemical | ChemComp-ANP / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 0.12 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Recombinant Legionella pneumophila SidJ -human calmodulin complex | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19851 / Symmetry type: POINT |