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 1.1 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: 10.1016/j.str.2019.05.008
  • Primary Citation of Related Structures:  
    6QHK, 6QH3

  • 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, w ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 SAB156Homo sapiensMutation(s): 1 
Gene Names: UBE2SE2EPFOK/SW-cl.73
EC: 2.3.2.23
Find proteins for Q16763 (Homo sapiens)
Explore Q16763 
Go to UniProtKB:  Q16763
NIH Common Fund Data Resources
PHAROS  Q16763
Protein Feature View
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  • Reference Sequence
Small Molecules
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 

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references