6QH3

Catalytic domain of the human ubiquitin-conjugating enzyme UBE2S C118M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Autoinhibition Mechanism of the Ubiquitin-Conjugating Enzyme UBE2S by Autoubiquitination.

Liess, A.K.L.Kucerova, A.Schweimer, K.Yu, L.Roumeliotis, T.I.Diebold, M.Dybkov, O.Sotriffer, C.Urlaub, H.Choudhary, J.S.Mansfeld, J.Lorenz, S.

(2019) Structure 27: 1195-1210.e7

  • DOI: https://doi.org/10.1016/j.str.2019.05.008
  • Primary Citation of Related Structures:  
    6QH3, 6QHK

  • PubMed Abstract: 

    Ubiquitin-conjugating enzymes (E2s) govern key aspects of ubiquitin signaling. Emerging evidence suggests that the activities of E2s are modulated by posttranslational modifications; the structural underpinnings, however, are largely unclear. Here, we unravel the structural basis and mechanistic consequences of a conserved autoubiquitination event near the catalytic center of E2s, using the human anaphase-promoting complex/cyclosome-associated UBE2S as a model system. Crystal structures we determined of the catalytic ubiquitin carrier protein domain combined with MD simulations reveal that the active-site region is malleable, which permits an adjacent ubiquitin acceptor site, Lys +5 , to be ubiquitinated intramolecularly. We demonstrate by NMR that the Lys +5 -linked ubiquitin inhibits UBE2S by obstructing its reloading with ubiquitin. By immunoprecipitation, quantitative mass spectrometry, and siRNA-and-rescue experiments we show that Lys +5 ubiquitination of UBE2S decreases during mitotic exit but does not influence proteasomal turnover of this E2. These findings suggest that UBE2S activity underlies inherent regulation during the cell cycle.


  • Organizational Affiliation

    Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany. Electronic address: sonja.lorenz@virchow.uni-wuerzburg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 SA [auth B],
B [auth A]
156Homo sapiensMutation(s): 1 
Gene Names: UBE2SE2EPFOK/SW-cl.73
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q16763 (Homo sapiens)
Explore Q16763 
Go to UniProtKB:  Q16763
GTEx:  ENSG00000108106 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16763
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.619α = 90
b = 84.619β = 90
c = 87.832γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyEmmy Noether LO2003/1-1
German Research FoundationGRK 2243

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description