Has an ATP-independent isopeptidase activity, cleaving at the C-terminus of the ubiquitin moiety in natural or engineered linear fusion proteins, irrespective of their size or the presence of an N-terminal extension to ubiquitin (PubMed:12778054, PubMed:17632125). Plays a role in regulation of silencing by interacting with SIR4 (PubMed:8752220). Also, in conjunction with BRE5, cleaves ubiquitin, leading to the subsequent mono-ubiquitination of SEC23 (PubMed:12778054). Required for ribophagy, a process which relocalizes ribosomal particles into the vacuole for degradation in response to starvation (PubMed:20508643). 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). Heterotetramer with BRE5; contains two molecules of BRE5 and two molecules of UBP3 (PubMed:12778054, PubMed:17632125). Forms a complex composed of CDC48, DOA1, deubiquitinase UBP3 and probably BRE5. Within the complex interacts directly with DOA1 and CDC48 in a BRE5-independent manner (PubMed:20508643). Present with 2210 molecules/cell in log phase SD medium. Belongs to the peptidase C19 family.