3RCZ

Rad60 SLD2 Ubc9 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DNA repair and global sumoylation are regulated by distinct Ubc9 noncovalent complexes.

Prudden, J.Perry, J.J.Nie, M.Vashisht, A.A.Arvai, A.S.Hitomi, C.Guenther, G.Wohlschlegel, J.A.Tainer, J.A.Boddy, M.N.

(2011) Mol Cell Biol 31: 2299-2310

  • DOI: 10.1128/MCB.05188-11
  • Primary Citation of Related Structures:  
    3RCZ, 3RD2

  • PubMed Abstract: 
  • Global sumoylation, SUMO chain formation, and genome stabilization are all outputs generated by a limited repertoire of enzymes. Mechanisms driving selectivity for each of these processes are largely uncharacterized. Here, through crystallographic analyses we show that the SUMO E2 Ubc9 forms a noncovalent complex with a SUMO-like domain of Rad60 (SLD2) ...

    Global sumoylation, SUMO chain formation, and genome stabilization are all outputs generated by a limited repertoire of enzymes. Mechanisms driving selectivity for each of these processes are largely uncharacterized. Here, through crystallographic analyses we show that the SUMO E2 Ubc9 forms a noncovalent complex with a SUMO-like domain of Rad60 (SLD2). Ubc9:SLD2 and Ubc9:SUMO noncovalent complexes are structurally analogous, suggesting that differential recruitment of Ubc9 by SUMO or Rad60 provides a novel means for such selectivity. Indeed, deconvoluting Ubc9 function by disrupting either the Ubc9:SLD2 or Ubc9:SUMO noncovalent complex reveals distinct roles in facilitating sumoylation. Ubc9:SLD2 acts in the Nse2 SUMO E3 ligase-dependent pathway for DNA repair, whereas Ubc9:SUMO instead promotes global sumoylation and chain formation, via the Pli1 E3 SUMO ligase. Moreover, this Pli1-dependent SUMO chain formation causes the genome instability phenotypes of SUMO-targeted ubiquitin ligase (STUbL) mutants. Overall, we determine that, unexpectedly, Ubc9 noncovalent partner choice dictates the role of sumoylation in distinct cellular pathways.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein rad60A82Schizosaccharomyces pombeMutation(s): 0 
Gene Names: rad60SPBC1921.02
Find proteins for Q9USX3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9USX3 
Go to UniProtKB:  Q9USX3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-conjugating enzyme ubc9B163Schizosaccharomyces pombeMutation(s): 0 
Gene Names: hus5ubc9SPAC30D11.13
EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for P40984 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P40984 
Go to UniProtKB:  P40984
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.202 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.232α = 90
b = 115.232β = 90
c = 34.842γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-21
    Changes: Database references