6KFP

Crystal structure of MavC ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the mechanism and inhibition of transglutaminase-induced ubiquitination by the Legionella effector MavC.

Mu, Y.Wang, Y.Huang, Y.Li, D.Han, Y.Chang, M.Fu, J.Xie, Y.Ren, J.Wang, H.Zhang, Y.Luo, Z.Q.Feng, Y.

(2020) Nat Commun 11: 1774-1774

  • DOI: 10.1038/s41467-020-15645-7
  • Primary Citation of Related Structures:  
    6K3B, 6KFP, 6KG6

  • PubMed Abstract: 
  • Protein ubiquitination is one of the most prevalent post-translational modifications, controlling virtually every process in eukaryotic cells. Recently, the Legionella effector MavC was found to mediate a unique ubiquitination through transglutamination, ...

    Protein ubiquitination is one of the most prevalent post-translational modifications, controlling virtually every process in eukaryotic cells. Recently, the Legionella effector MavC was found to mediate a unique ubiquitination through transglutamination, linking ubiquitin (Ub) to UBE2N through Ub Gln40 in a process that can be inhibited by another Legionella effector, Lpg2149. Here, we report the structures of MavC/UBE2N/Ub ternary complex, MavC/UBE2N-Ub (product) binary complex, and MavC/Lpg2149 binary complex. During the ubiquitination, the loop containing the modification site K92 of UBE2N undergoes marked conformational change, and Lpg2149 inhibits this ubiquitination through competing with Ub to bind MavC. Moreover, we found that MavC itself also exhibits weak deubiquitinase activity towards this non-canonical ubiquitination. Together, our study not only provides insights into the mechanism and inhibition of this transglutaminase-induced ubiquitination by MavC, but also sheds light on the future studies into UBE2N inhibition by this modification and deubiquitinases of this unique ubiquitination.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, 100029, Beijing, China. fengyue@mail.buct.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MavC A378Legionella pneumophilaMutation(s): 1 
Gene Names: C3927_10720
Find proteins for Q5ZTL4 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZTL4 
Go to UniProtKB:  Q5ZTL4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 N B152Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27a D77Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
Find proteins for P62979 (Homo sapiens)
Explore P62979 
Go to UniProtKB:  P62979
NIH Common Fund Data Resources
PHAROS:  P62979
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.704α = 90
b = 105.86β = 90
c = 125.391γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31822012

Revision History 

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references