Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein

Troy Eugene Messick, Nathaniel Scott Russell, Ayaka Jennifer Iwata, Kathryn Lorenz Sarachan, Ramin Shiekhattar, John R. Shanks, Francisca E. Reyes-Turcu, Keith D. Wilkinson, Ronen Marmorstein

Research output: Contribution to journalArticle

76 Scopus citations

Abstract

Ubiquitination of proteins modifies protein function by either altering their activities, promoting their degradation, or altering their subcellular localization. Deubiquitinating enzymes are proteases that reverse this ubiquitination. Previous studies demonstrate that proteins that contain an ovarian tumor (OTU) domain possess deubiquitinating activity. This domain of ∼130 amino acids is weakly similar to the papain family of proteases and is highly conserved from yeast to mammals. Here we report structural and functional studies on the OTU domain-containing protein from yeast, Otu1. We show that Otu1 binds polyubiquitin chain analogs more tightly than monoubiquitin and preferentially hydrolyzes longer polyubiquitin chains with Lys48 linkages, having little or no activity on Lys63- and Lys 29-linked chains. We also show that Otu1 interacts with Cdc48, a regulator of the ER-associated degradation pathway. We also report the x-ray crystal structure of the OTU domain of Otu1 covalently complexed with ubiquitin and carry out structure-guided mutagenesis revealing a novel mode of ubiquitin recognition and a variation on the papain protease catalytic site configuration that appears to be conserved within the OTU family of ubiquitin hydrolases. Together, these studies provide new insights into ubiquitin binding and hydrolysis by yeast Otu1 and other OTU domain-containing proteins.

Original languageEnglish (US)
Pages (from-to)11038-11049
Number of pages12
JournalJournal of Biological Chemistry
Volume283
Issue number16
DOIs
StatePublished - Apr 18 2008
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

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    Messick, T. E., Russell, N. S., Iwata, A. J., Sarachan, K. L., Shiekhattar, R., Shanks, J. R., Reyes-Turcu, F. E., Wilkinson, K. D., & Marmorstein, R. (2008). Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein. Journal of Biological Chemistry, 283(16), 11038-11049. https://doi.org/10.1074/jbc.M704398200