+Open data
-Basic information
Entry | Database: PDB / ID: 7pqe | ||||||
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Title | Structure of SidJ/CaM bound to SdeA in post-catalysis state | ||||||
Components |
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Keywords | LIGASE / Glutamylase / Pseudokinase / phosphoribosyl / ubiquitination / Complex | ||||||
Function / homology | Function and homology information Ligases / NAD+-protein-arginine ADP-ribosyltransferase / negative regulation of calcium ion transmembrane transporter activity / deNEDDylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / K63-linked deubiquitinase activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane ...Ligases / NAD+-protein-arginine ADP-ribosyltransferase / negative regulation of calcium ion transmembrane transporter activity / deNEDDylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / K63-linked deubiquitinase activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / protein deubiquitination / 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 / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cysteine-type peptidase activity / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / titin binding / 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 / nucleotidyltransferase activity / sarcomere / protein serine/threonine kinase activator activity / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / spindle microtubule / positive regulation of protein serine/threonine kinase activity / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / host cell / myelin sheath / transferase activity / vesicle / transmembrane transporter binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein ubiquitination / G protein-coupled receptor signaling pathway / nucleotide binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / proteolysis / extracellular region / 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: 3.7 Å | ||||||
Authors | Adams, M. / Bhogaraju, S. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for protein glutamylation by the Legionella pseudokinase SidJ. Authors: Michael Adams / Rahul Sharma / Thomas Colby / Felix Weis / Ivan Matic / Sagar Bhogaraju / Abstract: Legionella pneumophila (LP) avoids phagocytosis by secreting nearly 300 effector proteins into the host cytosol. SidE family of effectors (SdeA, SdeB, SdeC and SidE) employ phosphoribosyl ...Legionella pneumophila (LP) avoids phagocytosis by secreting nearly 300 effector proteins into the host cytosol. SidE family of effectors (SdeA, SdeB, SdeC and SidE) employ phosphoribosyl ubiquitination to target multiple host Rab GTPases and innate immune factors. To suppress the deleterious toxicity of SidE enzymes in a timely manner, LP employs a metaeffector named SidJ. Upon activation by host Calmodulin (CaM), SidJ executes an ATP-dependent glutamylation to modify the catalytic residue Glu860 in the mono-ADP-ribosyl transferase (mART) domain of SdeA. SidJ is a unique glutamylase that adopts a kinase-like fold but contains two nucleotide-binding pockets. There is a lack of consensus about the substrate recognition and catalytic mechanism of SidJ. Here, we determined the cryo-EM structure of SidJ in complex with its substrate SdeA in two different states of catalysis. Our structures reveal that both phosphodiesterase (PDE) and mART domains of SdeA make extensive contacts with SidJ. In the pre-glutamylation state structure of the SidJ-SdeA complex, adenylylated E860 of SdeA is inserted into the non-canonical (migrated) nucleotide-binding pocket of SidJ. Structure-based mutational analysis indicates that SidJ employs its migrated pocket for the glutamylation of SdeA. Finally, using mass spectrometry, we identified several transient autoAMPylation sites close to both the catalytic pockets of SidJ. Our data provide unique insights into the substrate recognition and the mechanism of protein glutamylation by the pseudokinase SidJ. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution Authors: Adams, P.D. / Afonine, P.V. / Bunkoczi, G. / Chen, V.B. / Davis, I.W. / Echols, N. / Headd, J.J. / Hung, L. / Kapral, G.J. / Grosse, R.W. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R. / Read, ...Authors: Adams, P.D. / Afonine, P.V. / Bunkoczi, G. / Chen, V.B. / Davis, I.W. / Echols, N. / Headd, J.J. / Hung, L. / Kapral, G.J. / Grosse, R.W. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R. / Read, R.J. / Richardson, D.C. / Richardson, J.S. / Terwilliger, T.C. / Zwart, P.H. | ||||||
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 | 7pqe.cif.gz | 271.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pqe.ent.gz | 199 KB | Display | PDB format |
PDBx/mmJSON format | 7pqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pqe_validation.pdf.gz | 768.4 KB | Display | wwPDB validaton report |
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Full document | 7pqe_full_validation.pdf.gz | 786.3 KB | Display | |
Data in XML | 7pqe_validation.xml.gz | 46.8 KB | Display | |
Data in CIF | 7pqe_validation.cif.gz | 71.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/7pqe ftp://data.pdbj.org/pub/pdb/validation_reports/pq/7pqe | HTTPS FTP |
-Related structure data
Related structure data | 13591MC 7ppoC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 110875.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: sdeA, lpg2157 / Production host: Escherichia coli (E. coli) References: UniProt: Q5ZTK4, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Transferases; Acyltransferases; Aminoacyltransferases, NAD+-protein-arginine ADP-ribosyltransferase |
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#2: Protein | Mass: 91826.992 Da / Num. of mol.: 1 / Mutation: E565A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: sidJ, lpg2155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZTK6, Ligases |
#3: Protein | Mass: 19066.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP24 |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-CA / |
Has ligand of interest | Y |
-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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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K |
-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 |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58448 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 3.7 Å / Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.32 Å2 | ||||||||||||||||||||||||
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