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 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/10.1101/gad.296145.117
  • Primary Citation of Related Structures:  
    5V1A, 5V3N

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like-specific protease 2A [auth B]26Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ULP2SMT4YIL031W
EC: 3.4.22.68
UniProt
Find proteins for P40537 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40537 
Go to UniProtKB:  P40537
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40537
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Monopolin complex subunit CSM1B [auth A]122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSM1SPO86YCR086WYCR86W
UniProt
Find proteins for P25651 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25651 
Go to UniProtKB:  P25651
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25651
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.737α = 90
b = 46.737β = 90
c = 124.638γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Database references
  • Version 1.2: 2017-05-31
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description