5V3N

Structure of S. cerevisiae Ulp2-Tof2-Csm1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Recruitment of a SUMO isopeptidase to rDNA stabilizes silencing complexes by opposing SUMO targeted ubiquitin ligase activity.

Liang, J.Singh, N.Carlson, C.R.Albuquerque, C.P.Corbett, K.D.Zhou, H.

(2017) Genes Dev. 31: 802-815

  • DOI: 10.1101/gad.296145.117
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Post-translational modification by SUMO (small ubiquitin-like modifier) plays important but still poorly understood regulatory roles in eukaryotic cells, including as a signal for ubiquitination by SUMO targeted ubiquitin ligases (STUbLs). Here, we d ...

    Post-translational modification by SUMO (small ubiquitin-like modifier) plays important but still poorly understood regulatory roles in eukaryotic cells, including as a signal for ubiquitination by SUMO targeted ubiquitin ligases (STUbLs). Here, we delineate the molecular mechanisms for SUMO-dependent control of ribosomal DNA (rDNA) silencing through the opposing actions of a STUbL (Slx5:Slx8) and a SUMO isopeptidase (Ulp2). We identify a conserved region in the Ulp2 C terminus that mediates its specificity for rDNA-associated proteins and show that this region binds directly to the rDNA-associated protein Csm1. Two crystal structures show that Csm1 interacts with Ulp2 and one of its substrates, the rDNA silencing protein Tof2, through adjacent conserved interfaces in its C-terminal domain. Disrupting Csm1's interaction with either Ulp2 or Tof2 dramatically reduces rDNA silencing and causes a marked drop in Tof2 abundance, suggesting that Ulp2 promotes rDNA silencing by opposing STUbL-mediated degradation of silencing proteins. Tof2 abundance is rescued by deletion of the STUbL SLX5 or disruption of its SUMO-interacting motifs, confirming that Tof2 is targeted for degradation in a SUMO- and STUbL-dependent manner. Overall, our results demonstrate how the opposing actions of a localized SUMO isopeptidase and a STUbL regulate rDNA silencing by controlling the abundance of a key rDNA silencing protein, Tof2.


    Organizational Affiliation

    Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Monopolin complex subunit CSM1
A
113Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CSM1 (SPO86)
Find proteins for P25651 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25651
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ulp2p,Topoisomerase 1-associated factor 2 chimera
B
38Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Saccharomyces cerevisiae x Saccharomyces kudriavzevii (strain VIN7)
This entity is chimeric
Mutation(s): 0 
Gene Names: TOF2,
Find proteins for Q02208 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02208
Find proteins for H0GHZ9 (Saccharomyces cerevisiae x Saccharomyces kudriavzevii (strain VIN7))
Go to UniProtKB:  H0GHZ9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.684α = 90.00
b = 56.933β = 121.06
c = 40.992γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM104141

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-05-24
    Type: Database references
  • Version 1.2: 2017-05-31
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence