4W4U

Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 2.3 of the entry. See complete history


Literature

Uncovering the role of Sgf73 in maintaining SAGA deubiquitinating module structure and activity.

Yan, M.Wolberger, C.

(2015) J Mol Biol 427: 1765-1778

  • DOI: https://doi.org/10.1016/j.jmb.2014.12.004
  • Primary Citation of Related Structures:  
    4W4U

  • PubMed Abstract: 

    The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex performs multiple functions in transcription activation including deubiquitinating histone H2B, which is mediated by a subcomplex called the deubiquitinating module (DUBm). The yeast DUBm comprises a catalytic subunit, Ubp8, and three additional subunits, Sgf11, Sus1 and Sgf73, all of which are required for DUBm activity. A portion of the non-globular Sgf73 subunit lies between the Ubp8 catalytic domain and the ZnF-UBP domain and has been proposed to contribute to deubiquitinating activity by maintaining the catalytic domain in an active conformation. We report structural and solution studies of the DUBm containing two different Sgf73 point mutations that disrupt deubiquitinating activity. We find that the Sgf73 mutations abrogate deubiquitinating activity by impacting the Ubp8 ubiquitin-binding fingers region and they have an unexpected effect on the overall folding and stability of the DUBm complex. Taken together, our data suggest a role for Sgf73 in maintaining both the organization and the ubiquitin-binding conformation of Ubp8, thereby contributing to overall DUBm activity.


  • Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolaseA,
E [auth D]
476Saccharomyces cerevisiae CEN.PK113-7DMutation(s): 0 
Gene Names: CENPK1137D_262
EC: 3.4.19.12
UniProt
Find proteins for N1P0J5 (Saccharomyces cerevisiae (strain CEN.PK113-7D))
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Go to UniProtKB:  N1P0J5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN1P0J5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription and mRNA export factor SUS1
B, F
96Saccharomyces cerevisiae CEN.PK113-7DMutation(s): 0 
Gene Names: SUS1CENPK1137D_4659
UniProt
Find proteins for N1P8F5 (Saccharomyces cerevisiae (strain CEN.PK113-7D))
Explore N1P8F5 
Go to UniProtKB:  N1P8F5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN1P8F5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SAGA-associated factor 11
C, G
99Saccharomyces cerevisiae CEN.PK113-7DMutation(s): 0 
Gene Names: SGF11CENPK1137D_1654
UniProt
Find proteins for N1NXA6 (Saccharomyces cerevisiae (strain CEN.PK113-7D))
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UniProt GroupN1NXA6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
SAGA-associated factor 73D [auth E],
H
96Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: SGF73YGL066W
UniProt
Find proteins for P53165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53165 
Go to UniProtKB:  P53165
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UniProt GroupP53165
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth E],
P [auth D],
Q [auth D],
R [auth D],
S [auth D],
T [auth D],
U [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.739α = 90
b = 67.273β = 106.84
c = 137.145γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
Cootmodel building
HKL-2000data scaling
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-095822

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 2.0: 2017-09-13
    Changes: Atomic model, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 2.1: 2017-11-22
    Changes: Refinement description
  • Version 2.2: 2019-12-25
    Changes: Author supporting evidence
  • Version 2.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description