Ataxin-3 is an ubiquitously expressed protein which contains a poly-glutamine tract. Genetically abnormal expansion of the poly-glutamine repeats results in accumulation of ubiquitinated ataxin-3 protein aggregates and leads to a neurodegenerative disorder, Machado–Joseph disease (MJD). The protein has ubiquitin interacting motifs and a N-terminal Cysteine residue (C14) responsible for its deubiquitinating activity. Ataxin-3 binds and hydrolyzes polyubiquitinated proteins, and interacts with key proteasome components, such as p97/VCP and p45, indicating that Ataxin-3 may play functional roles in ubiquitin-proteasome system. The protein also act as a transcriptional repressor when interacting with transcriptional activators and coactivators.