Molecular Basis for Bre5 Cofactor Recognition by the Ubp3 Deubiquitylating Enzyme

Keqin Li, Batool Ossareh-Nazari, Xin Liu, Catherine Dargemont, Ronen Marmorstein

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


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 β-strand-turn-α-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 β-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.

Original languageEnglish (US)
Pages (from-to)194-204
Number of pages11
JournalJournal of Molecular Biology
Issue number1
StatePublished - Sep 7 2007


  • deubiquitylation
  • nuclear transport factor 2 (NTF2)-like domain
  • protein-protein recognition
  • ubiquitin-specific processing proteases (UBPs)

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology


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