6JKY

Crystal structure of MvcA-UBE2N-Ub complex from Legionella pneumophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

Starting Models: experimental
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This is version 1.2 of the entry. See complete history


Literature

Legionella pneumophila regulates the activity of UBE2N by deamidase-mediated deubiquitination.

Gan, N.Guan, H.Huang, Y.Yu, T.Fu, J.Nakayasu, E.S.Puvar, K.Das, C.Wang, D.Ouyang, S.Luo, Z.Q.

(2020) EMBO J 39: e102806-e102806

  • DOI: https://doi.org/10.15252/embj.2019102806
  • Primary Citation of Related Structures:  
    6JKY, 6K11

  • PubMed Abstract: 

    The Legionella pneumophila effector MavC induces ubiquitination of the E2 ubiquitin-conjugating enzyme UBE2N by transglutamination, thereby abolishing its function in the synthesis of K 63 -type polyubiquitin chains. The inhibition of UBE2N activity creates a conundrum because this E2 enzyme is important in multiple signaling pathways, including some that are important for intracellular L. pneumophila replication. Here, we show that prolonged inhibition of UBE2N activity by MavC restricts intracellular bacterial replication and that the activity of UBE2N is restored by MvcA, an ortholog of MavC (50% identity) with ubiquitin deamidase activity. MvcA functions to deubiquitinate UBE2N-Ub using the same catalytic triad required for its deamidase activity. Structural analysis of the MvcA-UBE2N-Ub complex reveals a crucial role of the insertion domain in MvcA in substrate recognition. Our study establishes a deubiquitination mechanism catalyzed by a deamidase, which, together with MavC, imposes temporal regulation of the activity of UBE2N during L. pneumophila infection.


  • Organizational Affiliation

    Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MvcA
A, D
385Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 1 
Gene Names: lpg2148
UniProt
Find proteins for Q5ZTL3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZTL3 
Go to UniProtKB:  Q5ZTL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZTL3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 N
B, E
152Homo sapiensMutation(s): 1 
Gene Names: UBE2N
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
PHAROS:  P61088
GTEx:  ENSG00000177889 
Entity Groups  
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UniProt GroupP61088
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ub
C, F
79Schistosoma margrebowieiMutation(s): 0 
Gene Names: SMRZ_LOCUS12712
UniProt
Find proteins for A0A3P7ZMV6 (Schistosoma margrebowiei)
Explore A0A3P7ZMV6 
Go to UniProtKB:  A0A3P7ZMV6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3P7ZMV6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.325α = 90
b = 107.605β = 90
c = 263.845γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata collection
autoPROCdata scaling
Cootmodel building
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-04-15
    Changes: Database references, Structure summary
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description