3M99

Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

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This is version 1.3 of the entry. See complete history


Literature

Structural basis for assembly and activation of the heterotetrameric SAGA histone H2B deubiquitinase module.

Kohler, A.Zimmerman, E.Schneider, M.Hurt, E.Zheng, N.

(2010) Cell 141: 606-617

  • DOI: https://doi.org/10.1016/j.cell.2010.04.026
  • Primary Citation of Related Structures:  
    3M99

  • PubMed Abstract: 

    Deubiquitinating enzymes (DUBs) regulate diverse cellular functions by cleaving ubiquitin from specific protein substrates. How their activities are modulated in various cellular contexts remains poorly understood. The yeast deubiquitinase Ubp8 protein is recruited and activated by the SAGA complex and, together with Sgf11, Sus1, and Sgf73, forms a DUB module responsible for deubiquitinating histone H2B during gene expression. Here, we report the crystal structure of the complete SAGA DUB module, which features two functional lobes structurally coupled by Sgf73. In the "assembly lobe," a long Sgf11 N-terminal helix is clamped onto the Ubp8 ZnF-UBP domain by Sus1. In the "catalytic lobe," an Sgf11 C-terminal zinc-finger domain binds to the Ubp8 catalytic domain next to its active site. Our structural and functional analyses reveal a central role of Sgf11 and Sgf73 in activating Ubp8 for deubiquitinating histone H2B and demonstrate how a DUB can be allosterically regulated by its nonsubstrate partners.


  • Organizational Affiliation

    Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany. alwin.koehler@mfpl.ac.at


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 8471Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: UBP8YM9959.05YMR223W
EC: 3.1.2.15
UniProt
Find proteins for P50102 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50102 
Go to UniProtKB:  P50102
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50102
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SAGA-associated factor 1199Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SGF11YPL047W
UniProt
Find proteins for Q03067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q03067
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UniProt GroupQ03067
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SUS196Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUS1YBR111W-A
UniProt
Find proteins for Q6WNK7 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ6WNK7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
SAGA-associated factor 73104Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SGF73SGF73 (AA 1-104)YGL066W
UniProt
Find proteins for P53165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53165 
Go to UniProtKB:  P53165
Entity Groups  
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UniProt GroupP53165
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.424α = 90
b = 103.519β = 108.09
c = 70.35γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description