4W4U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 2.2 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: 10.1016/j.jmb.2014.12.004

  • 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 ...

    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.,Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA. Electronic address: cwolberg@jhmi.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase
A, D
476Saccharomyces cerevisiae (strain CEN.PK113-7D)Mutation(s): 0 
EC: 3.4.19.12
Find proteins for N1P0J5 (Saccharomyces cerevisiae (strain CEN.PK113-7D))
Go to UniProtKB:  N1P0J5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcription and mRNA export factor SUS1
B, F
96Saccharomyces cerevisiae (strain CEN.PK113-7D)Mutation(s): 0 
Gene Names: SUS1
Find proteins for N1P8F5 (Saccharomyces cerevisiae (strain CEN.PK113-7D))
Go to UniProtKB:  N1P8F5
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SAGA-associated factor 11
C, G
99Saccharomyces cerevisiae (strain CEN.PK113-7D)Mutation(s): 0 
Gene Names: SGF11
Find proteins for N1NXA6 (Saccharomyces cerevisiae (strain CEN.PK113-7D))
Go to UniProtKB:  N1NXA6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
SAGA-associated factor 73
E, H
96Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: SGF73
Find proteins for P53165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53165
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, D, E, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.739α = 90.00
b = 67.273β = 106.84
c = 137.145γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
Cootmodel building
Blu-Icedata collection
PHENIXrefinement
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-08-15 
  • Released Date: 2015-07-01 
  • Deposition Author(s): Wolberger, C., Yan, M.

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

Revision History 

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