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 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1016/j.molcel.2008.05.022

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUMO-CONJUGATING ENZYME UBC9
A
158Mus musculusMutation(s): 0 
Gene Names: Ube2i (Ubc9, Ubce2i, Ubce9)
EC: 2.3.2.-
Find proteins for P63280 (Mus musculus)
Go to UniProtKB:  P63280
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SMALL UBIQUITIN-RELATED MODIFIER 1
B
79Homo sapiensMutation(s): 0 
Gene Names: SUMO1 (SMT3C, SMT3H3, UBL1)
Find proteins for P63165 (Homo sapiens)
Go to Gene View: SUMO1
Go to UniProtKB:  P63165
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 27.520α = 90.00
b = 66.610β = 90.00
c = 122.579γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-28
    Type: Data collection
  • Version 1.4: 2018-03-28
    Type: Database references, Source and taxonomy