Ubiquitin-Specific Proteases: Structure and Function

USPs were first discovered and cloned in Saccharomyces cerevisiae (Tobias & Varshavsky, 1991 (link)). They are the largest subfamily of DUBs having a total of 58 members. The number of USPs has increased since the evolution of E3 ubiquitin ligases (Semple, 2003 (link)). The size of USPs ranges from 330 amino acids to 3,500 amino acids with an average size of 800–1,000 amino acids for full-length enzymes. The catalytic structural domain of USPs contains 295-850 amino acids; the catalytic structural domain of 27 USPs contains 300–400 amino acids, while that of 29 USPs contains 400–850 amino acids (Ye et al., 2009 (link)). USPs have also other diverse domains in terms of size and structure (Hariri & St-Arnaud, 2021 (link)). However, there is a high degree of homology within the catalytic domain. The catalytic core of USPs contains three motifs, consisting of very conserved catalytic Cys residues, catalytic His residues, and catalytic Asp/Asn residues, which form the catalytic triad (Nijman et al., 2005 (link); Ye et al., 2009 (link)). In addition to the catalytic domain, USPs also have domains for subcellular localization, substrate specificity, zinc binding, and ubiquitin recognition (Hariri & St-Arnaud, 2021 (link); Nijman et al., 2005 (link); Ye et al., 2009 (link)). Figure 2A shows USP4, USP7, USP14, USP19, and USP44 as examples of USPs having major domains.
The ubiquitin-like (UBL) domain of USPs can regulate their catalytic activity; however, the mechanism of action of the UBL domain in each USP varies. For example, the UBL domain of USP14 is important for its localization on proteasome and might enhance its catalytic capability., while that of USP4 binds to the catalytic domain, showing a competitive relationship with ubiquitin. As shown in Fig. 2B, the UBL4 and UBL5 domains of USP7 are located on its C-terminal and can affect its deubiquitinating activity by promoting conformational changes and facilitating the formation of a catalytic center (Faesen, Luna-Vargas & Sixma, 2012 (link)).
Different USPs have specific substrate proteins; therefore, they can regulate different signaling pathways (Ye et al., 2009 (link)). USPs can stabilize various oncoproteins or alter their cellular localization by deubiquitination, which can cause the development and progression of cancer (Chauhan et al., 2021 (link)). Numerous studies have shown that targeting USPs might be a promising therapeutic approach for cancer treatment (Dai et al., 2020 (link); Du et al., 2021 (link); Li et al., 2020 (link); Ma et al., 2019 (link); Nininahazwe et al., 2021 (link); Zhu et al., 2020 (link)).