UbcH6 is a member of an evolutionally conserved subfamily of E2 ubiquitin-conjugating enzymes. In this study, we report that UbcH6 interacts with and ubiquitinates ataxin-1, the spinocerebellar ataxia type 1 gene product. UbcH6 was identified as an ataxin-1-interacting protein using a yeast two-hybrid screen. UbcH6 co-immunoprecipitates and co-localizes with the ataxin-1 protein in the nucleus. Our binding assays showed that ataxin-1 interacts with UbcH6 through its AXH domain. Interestingly, UbcH6 could ubiquitinate ataxin-1 in the absence of an E3 ligase. The expression level of UbcH6 regulated the rate of ataxin-1 degradation. This study demonstrates that UbcH6 and ataxin-1 are E2-substrate cognate pairs in the ubiquitin-proteasome system. (C) 2008 Elsevier Inc. All rights reserved.