Deubiquitinating function of ataxin-3: Insights from the solution structure of the Josephin domain

^*Howard Hughes Medical Institute and Department of Cell Biology, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, CT 06510; ^¶Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06510; and ^†Istituto Fondazione Italiana per la Ricerca sul Cancro di Oncologia Molecolare, ^‡Istituto Oncologico Europeo, and ^§Dipartimento di Medicina, Chirurgia ed Odontoiatria, Universita' degli Studi di Milano, 20122 Milan, Italy

Contributed by Pietro De Camilli, July 25, 2005

Abstract

Spinocerebellar ataxia type 3 is a human neurodegenerative disease resulting from polyglutamine tract expansion. The affected protein, ataxin-3, which contains an N-terminal Josephin domain followed by tandem ubiquitin (Ub)-interacting motifs (UIMs) and a polyglutamine stretch, has been implicated in the function of the Ub proteasome system. NMR-based structural analysis has now revealed that the Josephin domain binds Ub and has a papain-like fold that is reminiscent of that of other deubiquitinases, despite primary sequence divergence but consistent with its deubiqutinating activity. Mutation of the catalytic Cys enhances the stability of a complex between ataxin-3 and polyubiquitinated proteins. This effect depends on the integrity of the UIM region, suggesting that the UIMs are bound to the substrate polyubiquitin during catalysis. We propose that ataxin-3 functions as a polyubiquitin chain-editing enzyme.

Footnotes

↵ ∥ To whom correspondence may be addressed. E-mail: michael.hodsdon{at}yale.edu or pietro.decamilli{at}yale.edu.
Author contributions: Y.M., F.S.-M., P.P.D.F., S.P., M.E.H., and P.D.C. designed research; Y.M., F.S.-M., S.P., and M.E.H. performed research; F.S.-M. and S.P. contributed new reagents/analytic tools; Y.M., F.S.-M., P.P.D.F., S.P., M.E.H., and P.D.C. analyzed data; and Y.M., M.E.H., and P.D.C. wrote the paper.
Abbreviations: JD, Josephin domain; NOE, nuclear Overhauser effect; polyQ, polyglutamine; Ub, ubiquitin; UIM, Ub-interacting motif; VCP, valosin-containing protein.
Data deposition: The JD chemical shift assignments have been deposited in the BioMagRes-Bank (BMRB accession no. 6742). Coordinates for the ensemble of the JD structures have been deposited in the Protein Data Bank (PDB ID code 2AGA).
Note. Shortly before submission, an independent solution structure of the ataxin-3 JD was published in PNAS (43). Comparison to the structure presented here reveals striking similarities in overall global conformation, with one significant and interesting difference involving a large rotation in the orientation of α3 relative to α2. Both studies found evidence for structural mobility of α3, which is consistent with the observation of variable conformations.
Freely available online through the PNAS open access option.