The Protein Ubiquitylation Unit

What is Protein Ubiquitylation?

Protein ubiquitylation is an extremely versatile control mechanism that regulates almost all aspects of cell life.  In this process, the C-terminal carboxylate residue of a small (76 amino acid residue) protein called ubiquitin becomes attached covalently to lysine residues in proteins.  A lysine residue on the first ubiquitin can then attach covalently to the C-terminal carboxylate of a second ubiquitin and so-on to create polyubiquitinated proteins. There are seven lysine residues in ubiquitin at positions 6, 11, 27, 29, 33, 48 and 63, so that many types of polyubiquitylated proteins can be formed in cells which have different topologies, can vary in length and have different functional consequences. For example, Lys48-linked polyubiquitination primes proteins for proteolytic destruction by the proteasome, while Lys63-linked polyubquitylation plays a key role in regulating processes such as the innate immune system, the response to DNA damage and endocytosis. 

The ubiquitylation process requires a ubiquitin-activating E1 enzyme, an E2 conjugating enzyme and an E3 ubiquitin ligase.  The first step involves the activation of ubiquitin, which is achieved by the formation of a thioester bond with the E1, while in the second step, ubiquitin is transferred to the E2.  From there, ubiquitin is either passed on to a substrate-associated HECT-type E3 ubiquitin ligase or it cooperates with RING or U-box-E3 ligases to achieve attachment of ubiquitin to a lysine residue of the substrate protein.

The polyubiquitylation process is reversible and removal of the ubiquitin moieties on proteins (deubiquitylation) is catalysed by deubiquitylases (DUBs), which are proteinases that can be subdivided into four subfamilies.  Finally, there are a number of other ubiquitin-like modifiers in cells that can become attached covalently to lysine residues in proteins by a mechanism analogous to ubiquitylation.  Thus the covalent attachment to proteins of SUMO (sumoylation) or NEDD (NEDDylation) also requires E1, E2 and E3 enzymes. 

The number and diversity of ubiquitin and ubiquitin-like modifications of proteins is huge and, to deal with this complexity, the human genome encodes three E1 enzymes, about 50 E2 conjugating complexes, over 600 ubiquitin ligases and about 100 DUBs.   Moreover, there is increasing evidence that abnormal levels of ubiquitylation may be a cause or consequence of many diseases, such as cancer and chronic inflammatory diseases.  For these reasons there is growing interest in targeting components of the ubiquitin system to develop novel drugs to treat disease.  Indeed, the first drug that targets a component of the ubiquitin system, Velcade, was approved for clinical use in 2007.  This compound, developed by Millenium Pharmaceuticals, inhibits the proteasome and is being used to treat haematological tumours, such as multiple myeloma and relapsed mantle cell lymphoma.