6KS5

Crystal structure of Legionella pneumophila deubiquitinase Ceg23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The bacterial deubiquitinase Ceg23 regulates the association of Lys-63-linked polyubiquitin molecules on theLegionellaphagosome.

Ma, K.Zhen, X.Zhou, B.Gan, N.Cao, Y.Fan, C.Ouyang, S.Luo, Z.Q.Qiu, J.

(2020) J Biol Chem 295: 1646-1657

  • DOI: https://doi.org/10.1074/jbc.RA119.011758
  • Primary Citation of Related Structures:  
    6KS5

  • PubMed Abstract: 

    Legionella pneumophila is the causative agent of the lung malady Legionnaires' disease, it modulates host function to create a niche termed the Legionella -containing vacuole (LCV) that permits intracellular L. pneumophila replication. One important aspect of such modulation is the co-option of the host ubiquitin network with a panel of effector proteins. Here, using recombinantly expressed and purified proteins, analytic ultracentrifugation, structural analysis, and computational modeling, along with deubiquitinase (DUB), and bacterial infection assays, we found that the bacterial defective in organelle trafficking/intracellular multiplication effector Ceg23 is a member of the ovarian tumor (OTU) DUB family. We found that Ceg23 displays high specificity toward Lys-63-linked polyubiquitin chains and is localized on the LCV, where it removes ubiquitin moieties from proteins ubiquitinated by the Lys-63-chain type. Analysis of the crystal structure of a Ceg23 variant lacking two putative transmembrane domains at 2.80 Å resolution revealed that despite very limited homology to established members of the OTU family at the primary sequence level, Ceg23 harbors a catalytic motif resembling those associated with typical OTU-type DUBs. ceg23 deletion increased the association of Lys-63-linked polyubiquitin with the bacterial phagosome, indicating that Ceg23 regulates Lys-63-linked ubiquitin signaling on the LCV. In summary, our findings indicate that Ceg23 contributes to the regulation of the association of Lys-63 type polyubiquitin with the Legionella phagosome. Future identification of host substrates targeted by Ceg23 could clarify the roles of these polyubiquitin chains in the intracellular life cycle of L. pneumophila and Ceg23's role in bacterial virulence.


  • Organizational Affiliation

    Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type IV secretion protein Dot
A, B
352Legionella pneumophilaMutation(s): 0 
Gene Names: C3927_07335
UniProt
Find proteins for Q5ZV21 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZV21 
Go to UniProtKB:  Q5ZV21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZV21
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.35α = 90
b = 71.61β = 90
c = 142.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
SHELXphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references