6QH3

Catalytic domain of the human ubiquitin-conjugating enzyme UBE2S C118M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 

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:  

  • 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.,Department for Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, 37077 Göttingen, Germany.,Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany. Electronic address: joerg.mansfeld@tu-dresden.de.,Group for Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, 37077 Göttingen, Germany; Proteomics Service Facility, Georg-August-Universität, Göttingen, 37077 Göttingen, Germany.,Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany.,Functional Proteomics Group, The Institute of Cancer Research, London SW3 6JB, UK.,Biopolymers, University of Bayreuth, 95447 Bayreuth, Germany.,Institute of Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany.,Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 S
B, A
156Homo sapiensMutation(s): 1 
Gene Names: UBE2S (E2EPF)
EC: 2.3.2.23
Find proteins for Q16763 (Homo sapiens)
Go to Gene View: UBE2S
Go to UniProtKB:  Q16763
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 84.619α = 90.00
b = 84.619β = 90.00
c = 87.832γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references