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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.15252/embj.2019102806
  • Primary Citation of Related Structures:  
    6K11, 6JKY

  • 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
MvcAA, D385Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 1 
Gene Names: lpg2148
Find proteins for Q5ZTL3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZTL3 
Go to UniProtKB:  Q5ZTL3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 NB, E152Homo sapiensMutation(s): 1 
Gene Names: UBE2NBLU
EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
NIH Common Fund Data Resources
PHAROS:  P61088
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
UbC, F79Schistosoma margrebowieiMutation(s): 0 
Gene Names: SMRZ_LOCUS12712
Find proteins for A0A3P7ZMV6 (Schistosoma margrebowiei)
Explore A0A3P7ZMV6 
Go to UniProtKB:  A0A3P7ZMV6
Protein Feature View
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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

  • Deposited Date: 2019-03-03 
  • Released Date: 2019-12-18 
  • Deposition Author(s): Ouyang, S.Y., Guan, H.

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