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 1.5 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
  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-CONJUGATING ENZYME UBC9A158Mus musculusMutation(s): 0 
Gene Names: Ube2iUbc9Ubce2iUbce9
EC: 6.3.2.19 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for P63280 (Mus musculus)
Explore P63280 
Go to UniProtKB:  P63280
NIH Common Fund Data Resources
IMPC  MGI:107365
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SMALL UBIQUITIN-RELATED MODIFIER 1B79Homo sapiensMutation(s): 0 
Gene Names: SUMO1SMT3CSMT3H3UBL1OK/SW-cl.43
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
NIH Common Fund Data Resources
PHAROS  P63165
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-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 
  • 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

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Entry History 

Deposition Data

Revision History 

  • 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