2QIY

yeast Deubiquitinase Ubp3 and Bre5 cofactor complex

Summary for 2QIY

• Entry DOI: 10.2210/pdb2qiy/pdb
• Related: 1ZX2
• Descriptor: UBP3-associated protein BRE5, Ubiquitin carboxyl-terminal hydrolase 3 (3 entities in total)
• Functional Keywords: deubiquitylation, ubiquitin-specific processing proteases(ubps), ntf2, protein-protein recognition, hydrolase, thiol protease, ubl conjugation pathway, phosphorylation, rna-binding, signaling protein-hydrolase complex, signaling protein/hydrolase
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 4
• Total formula weight: 45898.14

Authors

Li, K.,Liu, X.,Marmorstein, R. (deposition date: 2007-07-05, release date: 2007-10-30, Last modification date: 2023-08-30)

Primary citation

Li, K.,Ossareh-Nazari, B.,Liu, X.,Dargemont, C.,Marmorstein, R.
Molecular basis for bre5 cofactor recognition by the ubp3 deubiquitylating enzyme.
J.Mol.Biol., 372:194-204, 2007

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 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.

PubMed: 17632125
DOI: 10.1016/j.jmb.2007.06.052

Experimental method

X-RAY DIFFRACTION (1.69 Å)