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Deubiquitinating enzymes (DUBs), belonging to the superfamily of proteases, are a group of enzymes that catalyze the cleavage of ubiquitin from ubiquitin-linked molecules after the terminal carbonyl of the last residue of ubiquitin (Gly76). Based on the mechanism of catalysis, DUBs is divided into two classes, cysteine proteases, which interact with substrates through the thiol group of a cysteine in the active site, and metalloproteases, which form a noncovalent intermediate with the substrate through a Zn2+ bound polarized water molecule. The cysteine protease DUBs have different Ub-protease domains and hence are further divided into four subclasses, ubiquitin-specific protease (USP), ubiquitin C-terminal hydrolase (UCH), Otubain protease (OTU) and Machado-Joseph disease protease (MJD); while all metalloprotease DUBs have one Ub protease domain called JAMM (JAB1/MPN/Mov34 metalloenzyme).