6NJD

Crystal structure of RavD (residues 1-200) from Legionella pneumophila (strain Corby) complexed with Met-1 linked di-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A bacterial effector deubiquitinase specifically hydrolyses linear ubiquitin chains to inhibit host inflammatory signalling.

Wan, M.Wang, X.Huang, C.Xu, D.Wang, Z.Zhou, Y.Zhu, Y.

(2019) Nat Microbiol --: --

  • DOI: 10.1038/s41564-019-0454-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Linear ubiquitin (Ub) chains regulate many cellular processes, including NF-κB immune signalling. Pathogenic bacteria have evolved to secrete effector proteins that harbour deubiquitinase activity into host cells to disrupt host ubiquitination signal ...

    Linear ubiquitin (Ub) chains regulate many cellular processes, including NF-κB immune signalling. Pathogenic bacteria have evolved to secrete effector proteins that harbour deubiquitinase activity into host cells to disrupt host ubiquitination signalling. All previously identified effector deubiquitinases hydrolyse isopeptide-linked polyubiquitin (polyUb). It has been a long-standing question whether bacterial pathogens have evolved an effector deubiquitinase to directly cleave linear Ub chains. In this study, we performed extensive screening of bacterial pathogens and found that Legionella pneumophila-the causative agent of human Legionnaire's disease-encodes an effector protein, RavD, which harbours deubiquitinase activity exquisitely specific for linear Ub chains. RavD hydrolyses linear Ub chains but not any type of isopeptide-linked polyUb. The crystal structure of RavD with linear diubiquitin reveals that RavD adopts a papain-like fold with a Cys-His-Ser catalytic triad. The Ub-binding surface and specific interacting residues in RavD determine its specificity for Met1 linkages. RavD prevents the accumulation of linear Ub chains on Legionella-containing vacuoles established by the pathogen in host cells to inhibit the NF-κB pathway during infection. This study identified a unique linear Ub chain-specific effector deubiquitinase and indicates its potential application as a tool to dissect linear polyUb-mediated signalling in mammalian cells.


    Organizational Affiliation

    MOE Key Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signalling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China. zhuyongqun@zju.edu.cn.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signalling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China. zhuyongqun@zju.edu.cn.,Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Di-ubiquitin
A, C
157Homo sapiensMutation(s): 2 
Gene Names: UBC
Find proteins for F5H747 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  F5H747
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RavD
B, D
205N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.740α = 90.00
b = 102.090β = 90.00
c = 90.920γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81530068
National Natural Science Foundation of ChinaChina81322024
National Natural Science Foundation of ChinaChina31370722
National Natural Science Foundation of ChinaChina81561130162
National Natural Science Foundation of ChinaChina81501717
Ministry of Science and Technology (China)China2017YFA0503900
Royal SocietyUnited KingdomNA140239

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-05
    Type: Data collection, Database references