6K4L

Crystal structure of Se-labelled SidJ complex with CaM at 2.95 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.949 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase.

Gan, N.Zhen, X.Liu, Y.Xu, X.He, C.Qiu, J.Liu, Y.Fujimoto, G.M.Nakayasu, E.S.Zhou, B.Zhao, L.Puvar, K.Das, C.Ouyang, S.Luo, Z.Q.

(2019) Nature 572: 387-391

  • DOI: 10.1038/s41586-019-1439-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The bacterial pathogen Legionella pneumophila creates an intracellular niche permissive for its replication by extensively modulating host cell functions using hundreds of effector proteins delivered via its Dot/Icm secretion system <sup>1 </sup>. Am ...

    The bacterial pathogen Legionella pneumophila creates an intracellular niche permissive for its replication by extensively modulating host cell functions using hundreds of effector proteins delivered via its Dot/Icm secretion system 1 . Among these, members of the SidE family (SidEs) regulate multiple cellular processes by a unique phosphoribosyl ubiquitination mechanism that bypasses the canonical ubiquitination machinery 2-4 . The activity of SidEs is regulated by SidJ, another Dot/Icm effector 5 , but the mechanism of such regulation is not completely understood 6,7 . Here we demonstrate that SidJ inhibits the activity of SidEs by inducing covalent attachment of glutamate moieties to E860 of SdeA, which is one of the catalytic residues for the mono-ADP-ribosyltransferase activity involved in ubiquitin activation 2 . The inhibition by SidJ is spatially restricted in host cells because its activity requires the eukaryote-specific protein calmodulin (CaM). We solved a structure of SidJ-CaM in complex with adenosine monophosphate (AMP) and found that the ATP utilized is cleaved at the α phosphate position by SidJ which in the absence of glutamate or modifiable SdeA undergoes self-AMPylation. Our results reveal an unprecedented mechanism of regulation in bacterial pathogenicity in which a glutamylation reaction that inhibits the activity of virulence factors is activated by host factor-dependent acyl-adenylation.


    Organizational Affiliation

    Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China. ouyangsy@fjnu.edu.cn.,Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130001, China.,Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. ouyangsy@fjnu.edu.cn.,Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.,Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Department of Respiratory Medicine and Center of Infection and Immunity, The First Hospital of Jilin University, Changchun, 130021, China.,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA. luoz@purdue.edu.,The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SidJ
A, B
873Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)Mutation(s): 0 
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-1
C, D
149Homo sapiensMutation(s): 0 
Gene Names: CALM1 (CALM, CAM, CAM1)
Find proteins for P0DP23 (Homo sapiens)
Go to Gene View: CALM1
Go to UniProtKB:  P0DP23
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.949 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.060α = 90.00
b = 159.246β = 101.68
c = 135.809γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-05-24 
  • Released Date: 2019-07-24 
  • Deposition Author(s): Ouyang, S.Y.

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