5V1A

Structure of S. cerevisiae Ulp2:Csm1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.4 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.,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like-specific protease 2
B
26Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ULP2 (SMT4)
EC: 3.4.22.-
Find proteins for P40537 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40537
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Monopolin complex subunit CSM1
A
122Saccharomyces 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
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 46.737α = 90.00
b = 46.737β = 90.00
c = 124.638γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PHASERphasing
HKL-2000data 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 Sciences (NIH/NIGMS)United 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
  • Version 1.4: 2020-01-01
    Type: Author supporting evidence