2VRR

Structure of SUMO modified Ubc9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Ubc9 sumoylation regulates SUMO target discrimination.

Knipscheer, P.Flotho, A.Klug, H.Olsen, J.V.van Dijk, W.J.Fish, A.Johnson, E.S.Mann, M.Sixma, T.K.Pichler, A.

(2008) Mol Cell 31: 371-382

  • DOI: https://doi.org/10.1016/j.molcel.2008.05.022
  • Primary Citation of Related Structures:  
    2VRR

  • PubMed Abstract: 

    Posttranslational modification with small ubiquitin-related modifier, SUMO, is a widespread mechanism for rapid and reversible changes in protein function. Considering the large number of known targets, the number of enzymes involved in modification seems surprisingly low: a single E1, a single E2, and a few distinct E3 ligases. Here we show that autosumoylation of the mammalian E2-conjugating enzyme Ubc9 at Lys14 regulates target discrimination. While not altering its activity toward HDAC4, E2-25K, PML, or TDG, sumoylation of Ubc9 impairs its activity on RanGAP1 and strongly activates sumoylation of the transcriptional regulator Sp100. Enhancement depends on a SUMO-interacting motif (SIM) in Sp100 that creates an additional interface with the SUMO conjugated to the E2, a mechanism distinct from Ubc9 approximately SUMO thioester recruitment. The crystal structure of sumoylated Ubc9 demonstrates how the newly created binding interface can provide a gain in affinity otherwise provided by E3 ligases.


  • Organizational Affiliation

    The Netherlands Cancer Institute and Center for Biomedical Genetics, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SUMO-CONJUGATING ENZYME UBC9158Mus musculusMutation(s): 0 
EC: 6.3.2.19
UniProt & NIH Common Fund Data Resources
Find proteins for P63280 (Mus musculus)
Explore P63280 
Go to UniProtKB:  P63280
IMPC:  MGI:107365
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63280
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SMALL UBIQUITIN-RELATED MODIFIER 179Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
PHAROS:  P63165
GTEx:  ENSG00000116030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63165
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.52α = 90
b = 66.61β = 90
c = 122.579γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Data collection
  • Version 1.4: 2018-03-28
    Changes: Database references, Source and taxonomy
  • Version 1.5: 2019-07-31
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.6: 2023-12-13
    Changes: Advisory, Data collection, Database references, Other, Refinement description