Deubiquitylating Enzymes

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Background

Ubiquitin-proteasome pathway is an important protein degradation regulatory system in cells. Through the polyubiquitination of substrate proteins and proteasome degradation, a variety of cellular activities can be affected or regulated, including gene transcription, cell cycle regulation, immune response, cell receptor function, tumor growth, inflammatory process and so on. This pathway is also a dynamic protein bidirectional modification regulation system, in which the substrate is modified by ubiquitin ligase system (E1-E2-E3) in vivo. The DUB family is responsible for deubiquitination by hydrolyzing the ester bond, peptide bond or isopeptide bond at the carboxyl end of ubiquitin to hydrolyze ubiquitin molecules specifically from proteins or precursor proteins linked to ubiquitin. Reverse regulation of protein degradation, thus affecting the function of protein.

Introduction

Deubiquitylating enzymes are a large family of proteases. The human genome encodes about 100 Deubiquitylating enzymes, which are mainly divided into five families: ubiquitin carboxyl terminal hydrolase (UCH) family, ubiquitin specific protease (USP/UBP) family, Otubaim (OTU) family, Josephin domain protein family and JAMM family.

• Ubiquitin C-terminal hydrolase family (UCHs)

UCHs belongs to cysteine protease. They are usually small molecular proteins, and their substrates are usually peptides with small molecular weights. UCHs can release ubiquitin molecules from small polypeptide substrates by cleavage C-terminal 76 glycine. To some extent, the narrow cracks and the diameter limitation of ring structure on the active site of UCHs can specifically recognize the substrate and prevent it from binding and catalysing some macromolecular ubiquitinated proteins.

• Ubiquitin specific processing enzyme family (UBPs or USPs)

This family is known to have the largest number of members and the most diverse structure of ubiquitin enzymes, and it also belongs to cysteine proteases, including Ubp-M, UBP41, UBP4, HAUSP, ISOT1 and so on. These enzyme molecules contain two short and conserved fragments, lysine box and histidine box, with catalytic triple residues, cysteine, histidine, aspartic acid/asparagine, which can remove ubiquitin molecules from large proteins.

• Ovarian tumor associated protease (OTU)

Through crystal structure analysis, it is found that although this kind of protease is different from other families of deubiquitin enzymes in amino acid sequence, it also has a core domain composed of triple catalytic active site (Cys, His, Asp), which is very similar to UBP family proteins, and has been proved to play a role in deubiquitination.

• MJD deubiquitylating enzymes family

The Machado-Joseph disease-related protein Ataxin-3, which is associated with neurodegenerative disorders, has been clearly studied. There are four human Josephin family proteins, their structures are similar to the UCH deubiquitinase family, they are Ataxin-3, Ataxin-3L, Josephin-1, and Josephin2. Ataxin-3 is a cysteine protease, which can bind to the ubiquitin chain connected by K48 and K63, but is more specific to the ubiquitin chain connected by K63. Ataxin-3 and Ataxin3L are 85% homologous in amino acid sequence and fold in a similar way, but bind Ub in a very different way.

• JAMM protease family

This type of deubiquitinase is represented by a homologue in POH1, yeast cells called Rpn 11. This is a class of metalloproteinases that bind ubiquitin molecules on ubiquitin proteins and have MPN sequences, or JAMM (Jab1/MPN domain associated metalloisopeptidase, Jab1/MPN domain related metal isopeptidases) sequences. This sequence contains two conserved fluoric acid residues and one aspartic chloric acid residue, which together with divalent zinc ions from the catalytic center.

Application

Deubiquitylating enzymes is an important mechanism involved in protein regulation, which regulates intracellular protein function at transcriptional level, post-translational modification, protein localization, and protein interaction, signal transduction, chromatin remodeling, and so on. Deubiquitinating enzymes inhibitors act on cysteine proteases and metalloproteinases. At present, the main deubiquitylating enzymes related to 19s proteasome are UCHL5 (or UCH37), USP14, USP7, PSMD14 (POH1), and so on. P5091 belongs to thiophene small molecule inhibitor, which mainly acts on USP7 with P22077. Studies have found that the use of P5091 in multiple myeloma patients who are resistant to Bortezomib therapy can induce tumor cell death. Both WP-1130 and b-AP15 can act on multiple deubiquitinases. The accumulation of polyubiquitin-modified proteins blocks the cell cycle, thus effectively inhibiting the development of colon cancer and other tumors.

Conclusion

Deubiquitinating enzymes participate in the process of tumors and other diseases, are important target for the treatment of tumors and other diseases. a number of small molecule inhibitors have been used in the research and development of anti-tumor and other diseases. Providing new therapeutic targets and diagnostic indicators for clinical treatment of related diseases has become an important direction in the research and development of therapeutic drugs for tumors and other diseases.

References:

1. Singhal, S., Taylor, M. C., & Baker, R. T. (2008). Deubiquitylating enzymes and disease. BMC biochemistry, 9(1), 1-8.
2. Amer-Sarsour, F., Kordonsky, A., Berdichevsky, Y., Prag, G., & Ashkenazi, A. (2021). Deubiquitylating enzymes in neuronal health and disease. Cell death & disease, 12(1), 1-11.
3. Baker, R. T., Catanzariti, A. M., Karunasekara, Y., Soboleva, T. A., Sharwood, R., Whitney, S., & Board, P. G. (2005). Using deubiquitylating enzymes as research tools. Methods in enzymology, 398, 540-554.

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