7BXG

MavC-UBE2N-Ub complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.198 

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Literature

Insights into catalysis and regulation of non-canonical ubiquitination and deubiquitination by bacterial deamidase effectors.

Wang, Y., Zhan, Q., Wang, X., Li, P., Liu, S., Gao, G., Gao, P.

(2020) Nat Commun 11: 2751-2751

  • DOI: 10.1038/s41467-020-16587-w
  • Primary Citation of Related Structures:  
    7BXF, 7BXG, 7BXH

  • PubMed Abstract: 

    • The bacterial effector MavC catalyzes non-canonical ubiquitination of host E2 enzyme UBE2N without engaging any of the conventional ubiquitination machinery, thereby abolishing UBE2N's function in forming K63-linked ubiquitin (Ub) chains and dampening NF-кB signaling ...

    The bacterial effector MavC catalyzes non-canonical ubiquitination of host E2 enzyme UBE2N without engaging any of the conventional ubiquitination machinery, thereby abolishing UBE2N's function in forming K63-linked ubiquitin (Ub) chains and dampening NF-кB signaling. We now report the structures of MavC in complex with conjugated UBE2N~Ub and an inhibitor protein Lpg2149, as well as the structure of its ortholog, MvcA, bound to Lpg2149. Recognition of UBE2N and Ub depends on several unique features of MavC, which explains the inability of MvcA to catalyze ubiquitination. Unexpectedly, MavC and MvcA also possess deubiquitinase activity against MavC-mediated ubiquitination, highlighting MavC as a unique enzyme possessing deamidation, ubiquitination, and deubiquitination activities. Further, Lpg2149 directly binds and inhibits both MavC and MvcA by disrupting the interactions between enzymes and Ub. These results provide detailed insights into catalysis and regulation of MavC-type enzymes and the molecular mechanisms of this non-canonical ubiquitination machinery.

    Organizational Affiliation: 

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. gaopu@ibp.ac.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MavCA386Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: lpg2147
UniProt
Find proteins for Q5ZTL4 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZTL4 
Go to UniProtKB:  Q5ZTL4
Entity Groups  
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UniProt GroupQ5ZTL4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 NB153Homo sapiensMutation(s): 0 
Gene Names: UBE2N, BLU
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 
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UniProt GroupP61088
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-CC [auth D]77Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Entity Groups  
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UniProt GroupP0CG48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.198 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.527α = 90
b = 150.527β = 90
c = 58.372γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2020-04-19 
  • Released Date: 2020-05-20 
    • Deposition Author(s): Gao, P., Wang, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references