The ubiquitin-proteasome pathway is an essential protein degradation and regulatory system within cells. By polyubiquitinating substrate proteins and targeting them for degradation in the proteasome, it can influence or regulate various cellular activities, including gene transcription, cell cycle regulation, immune responses, cell receptor function, tumor growth, and inflammatory processes. This pathway is also a dynamic, bidirectional protein modification and regulatory system. Inside the body, substrate proteins undergo ubiquitination modifications by the ubiquitin ligase system (E1-E2-E3), and the deubiquitinating enzyme (DUB) family is responsible for selectively removing ubiquitin molecules from ubiquitin-conjugated proteins or precursor proteins by hydrolyzing the carboxyl-terminal ester bonds, peptide bonds, or isopeptide bonds of ubiquitin molecules. This deubiquitination process acts in opposition to ubiquitination, regulating protein degradation and thereby impacting protein function.
Deubiquitinating Enzyme Family
Deubiquitinating enzymes (DUBs) constitute a large protein enzyme family, with approximately 100 DUBs encoded in the human genome. They are mainly classified into five families: ubiquitin C-terminal hydrolases (UCHs) family, ubiquitin-specific proteases (USP/UBP) family, otubains (OTU) family, Josephin domain protein family, and JAMM family.
1. Ubiquitin C-terminal Hydrolases Family (UCHs)
UCHs are part of the cysteine protease enzyme family. Typically, they are small-molecule proteins, including molecules like UCH-L1, UCH-L2, UCH-L3, UCH-L4, UCH-L5, and others. Their substrates usually consist of small peptide molecules. UCHs catalyze the release of ubiquitin molecules from these smaller peptide substrates by cleaving the carboxyl-terminal glycine at position 76. The narrow cleft at the active site of UCHs and the restricted diameter of the ring structure play a role in specific substrate recognition, preventing them from binding to and catalyzing large-molecule ubiquitinated proteins to some extent.
2. Ubiquitin-Specific Processing Enzyme Family (USPs)
This family is currently known as the largest and structurally most diverse group among deubiquitinating enzymes. It also belongs to the cysteine protease class and includes members like Ubp-M, UBP41, UBP4, HAUSP, ISOT1, and others. These enzyme molecules all contain two short yet conserved segments known as the lysine box and histidine box. Within their sequences, there are three crucial amino acid residues responsible for catalytic activity, namely cysteine, histidine, and aspartic acid/asparagine. These residues have the ability to remove ubiquitin molecules from larger proteins.
3. Ovarian Tumor-Related Proteases (OTU)
OTU has been shown to have deubiquitinating activity and shares significant similarity with the UBP family proteins. Through crystal structure analysis, it has been discovered that although these proteases have amino acid sequences that differ from other families of deubiquitinating enzymes, they also possess a core structural domain consisting of a triad catalytic active site (Cys, His, Asp).
4. MJD Deubiquitinase Family
The human Josephin family proteins consist of four members, and their structures resemble those of the UCH deubiquitinase family. These members are Ataxin-3, Ataxin-3L, Josephin-1, and Josephin-2. Among them, Ataxin-3 is a cysteine protease capable of binding to ubiquitin chains linked through both K48 and K63, but it exhibits greater specificity towards K63-linked ubiquitin chains. Ataxin-3 and Ataxin-3L share 85% homology in their amino acid sequences and fold similarly, but they have distinct modes of binding to ubiquitin.
5. JAMM Protease Family
Representatives of this deubiquitinase family include POH1, and its homologue in yeast cells is called Rpn 11. These are a class of metalloproteases capable of binding to ubiquitin molecules on ubiquitinated proteins. They possess an MPN sequence, also known as the JAMM sequence. This sequence contains two relatively conserved cysteine residues and one aspartic acid residue, which together form the catalytic center in coordination with divalent zinc ions.
Functions of Deubiquitinating Enzymes
In cells, deubiquitinating enzymes serve various functions, which can be broadly categorized into the following aspects:
Processing ubiquitin precursors: Deubiquitinating enzymes can process ubiquitin precursors, generating free ubiquitin molecules.
Removal of ubiquitin chains from proteins: This helps prevent proteins from being targeted for proteasomal degradation, thereby maintaining protein stability.
Removal of non-degradative ubiquitin signals on proteins: Deubiquitinating enzymes can detach ubiquitin marks that do not lead to protein degradation.
Preserving the homeostasis of cellular ubiquitin molecules: They ensure the stability of ubiquitin molecules within the cell by preventing ubiquitin molecules from being degraded along with substrate proteins.
Handling free ubiquitin chains: Deubiquitinating enzymes are involved in dismantling free ubiquitin chains.
Editing the types of ubiquitin chains: They can also change the specific type of ubiquitin chain by cleaving ubiquitin chains.
These functions make deubiquitinating enzymes play a crucial role within cells, helping to maintain the balance of protein modifications, ensuring protein stability, and normal cellular function.
References
- Lecker S. H.; et al. Protein degradation by the ubiquitin–proteasome pathway in normal and disease states. Journal of the American Society of Nephrology. 2006, 17(7):1807-19.
- Evans P. C.; et al. A novel type of deubiquitinating enzyme. Journal of Biological Chemistry. 2003, 278(25):23180-6.
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