<p>Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, <db_xref db="INTERPRO" dbkey="IPR000011"/>), a ubiquitin-conjugating enzyme (E2, <db_xref db="INTERPRO" dbkey="IPR000608"/>), and a ubiquitin ligase (E3, <db_xref db="INTERPRO" dbkey="IPR000569"/>, <db_xref db="INTERPRO" dbkey="IPR003613"/>), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process [<cite idref="PUB00015623"/>]. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (<db_xref db="INTERPRO" dbkey="IPR005375"/>), SUMO1 (<db_xref db="INTERPRO" dbkey="IPR003653"/>), NEDD8, Rad23 (<db_xref db="INTERPRO" dbkey="IPR004806"/>), Elongin B and Parkin (<db_xref db="INTERPRO" dbkey="IPR003977"/>), the latter being involved in Parkinson's disease [<cite idref="PUB00015624"/>].</p><p>Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome [<cite idref="PUB00015619"/>]. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking [<cite idref="PUB00015620"/>]. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation [<cite idref="PUB00015621"/>]. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [<cite idref="PUB00015622"/>].</p> Ubiquitin