2QIY

yeast Deubiquitinase Ubp3 and Bre5 cofactor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis for bre5 cofactor recognition by the ubp3 deubiquitylating enzyme.

Li, K.Ossareh-Nazari, B.Liu, X.Dargemont, C.Marmorstein, R.

(2007) J Mol Biol 372: 194-204

  • DOI: 10.1016/j.jmb.2007.06.052
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Yeast Ubp3 and its co-factor Bre5 form a deubiquitylation complex to regulate protein transport between the endoplasmic reticulum and Golgi compartments of the cell. A novel N-terminal domain of the Ubp3 catalytic subunit forms a complex with the NTF ...

    Yeast Ubp3 and its co-factor Bre5 form a deubiquitylation complex to regulate protein transport between the endoplasmic reticulum and Golgi compartments of the cell. A novel N-terminal domain of the Ubp3 catalytic subunit forms a complex with the NTF2-like domain of the Bre5 regulatory subunit. Here, we report the X-ray crystal structure of an Ubp3-Bre5 complex and show that it forms a symmetric hetero-tetrameric complex in which the Bre5 NTF2-like domain dimer interacts with two L-shaped beta-strand-turn-alpha-helix motifs of Ubp3. The Ubp3 N-terminal domain binds within a hydrophobic cavity on the surface of the Bre5 NTF2-like domain subunit with conserved residues within both proteins interacting predominantly through antiparallel beta-sheet hydrogen bonds and van der Waals contacts. Structure-based mutagenesis and functional studies confirm the significance of the observed interactions for Ubp3-Bre5 association in vitro and Ubp3 function in vivo. Comparison of the structure to other protein complexes with NTF2-like domains shows that the Ubp3-Bre5 interface is novel. Together, these studies provide new insights into Ubp3 recognition by Bre5 and into protein recognition by NTF2-like domains.


    Related Citations: 
    • Structural basis for interaction between the Ubp3 deubiqutinating enzyme and its Bre5 cofactor
      Li, K., Zhao, K., Ossareh-Nazari, B., Da, G., Dargemont, C., Marmorstein, R.
      (2005) J Biol Chem 280: 29176

    Organizational Affiliation

    The Wistar Institute University of Pennsylvania, Philadelphia, PA 19104, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBP3-associated protein BRE5A, B154Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: BRE5
Find proteins for P53741 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53741 
Go to UniProtKB:  P53741
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 3C, D48Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: UBP3
EC: 3.1.2.15 (PDB Primary Data), 3.4.19.12 (UniProt)
Find proteins for Q01477 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01477 
Go to UniProtKB:  Q01477
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.1α = 90
b = 90.24β = 90
c = 101.48γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance