Hydrolase that can remove conjugated ubiquitin from proteins and may therefore play an important regulatory role at the level of protein turnover by preventing degradation. Participates in the regulation of the ubiquitin conjugation pathway involving CDC48 by hindering multiubiquitination of substrates at the CDC48 chaperone. May be indirectly involved in PIS1 gene expression. Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Forms a complex composed of CDC48, NPL4, UFD1, DOA1, SHP1 and deubiquitinase OTU1; within the complex interacts with CDC48 and DOA1/UFD3. The OTU domain mediates the hydrolase activity and the interaction with CDC48. Present with 2770 molecules/cell in log phase SD medium.