[3][4][5] DUBs can reverse these effects by cleaving the peptide or isopeptide bond between ubiquitin and its substrate protein.

In humans there are nearly 100 DUB genes, which can be classified into two main classes: cysteine proteases and metalloproteases.

[3][4][5] DUBs play the antagonistic role in this axis by removing these modifications, therefore reversing the fate of the proteins.

[2] DUBs also cleave single ubiquitin proteins that may have had their C-terminal tails accidentally bound to small cellular nucleophiles.

[6][17] The catalytic domain of DUBs is what classifies them into particular groups; USPs, OTUs, MJDs, UCHs and MPN+/JAMMs.

They use either catalytic dyads or triads (either two or three amino acids) to catalyse the hydrolysis of the amide bonds between ubiquitin and the substrate.

This polarised residue lowers the pKa of the cysteine, allowing it to perform a nucleophilic attack on the isopeptide bond between the ubiquitin C-terminus and the substrate lysine.

Metalloproteases coordinate zinc ions with histidine, aspartate and serine residues, which activate water molecules and allows them to attack the isopeptide bond.

[18][19] Ubiquitin-like (UBL) domains have a similar structure (fold) to ubiquitin, except they lack the terminal glycine residues.

[22][23] Single or multiple tandem DUSP domains of approximately 120 residues are found in six USPs.

The function of the DUSP domain is currently unknown but it may play a role in protein-protein interaction, in particular to DUBs substrate recognition.

The DUSP domain displays a novel tripod-like fold comprising three helices and an anti-parallel beta-sheet made of three strands.

Within most DUSP domains in USPs there is a conserved sequence of amino acids known as the PGPI motif.

[29] The deubiquitinating enzymes UCH-L3 and YUH1 are able to hydrolyse mutant ubiquitin UBB+1 despite the fact that the glycine at position 76 is mutated.

Ubiquitin-specific-processing protease (USP) is a family of deubiquitinating enzymes that play a crucial role in cell cycle regulation.

One of the key regulators of this pathways is Ras, a GTPase that, upon activation, binds GTP to "turn on" the subsequent signaling cascade.

[34] Such stabilization of RCE1 allows for proper localization of Ras, thus promoting proliferation upon activation of early receptors in the ERK Pathway.

USP17 also regulates cell cycle progression by acting on SETD8 to downregulate transcription of cyclin-dependent kinase inhibitor 1 (CDKN1A), also known as p21.

SETD8, a methyltransferase, uses S-Adenosyl methionine to methylate the Lys20 residue of histone 4, resulting in the condensation of chromosomes.

[40] Such a mechanism is crucial, as errors in chromosomal separation have been implicated in cancer, birth defects, and antibiotic resistance in pathogens.

[42] The resulting destruction of securing release separase,[40] which hydrolyzes cohesion – the protein that binds sister chromatids together.

New research from Stegmeier and colleagues[35] published in the journal Nature demonstrates a crucial role for USP44 in regulating the spindle checkpoint.

Using an shRNA screen, USP44 was identified to stabilize the inhibition of APC/C[35] The binding of CDC20 to APC/C is required for the ubiquitination of securin.

[44] It is important to note that ubiquitination of CDC20 does not serve to mark it for degradation, but rather promote dissociation of hMAD2 from the hMAD2-CDC-APC complex.

Upon DNA damage, cell cycle progression is halted to prevent propagation of the mutation.