Structural Biochemistry/Ubiquitin

Ubiquitin
Ubiquitin is a highly conserved, heat-stable protein found only in eukaryotic cells. It is made up of 76 amino acids and is involved in many cellular processes. It plays a big role in regulating the cell cycle, including DNA repair, embryogenesis, the regulation of transcription, and apoptosis. The Ub genes exist in two states:

These fusion proteins can be cleaved by protein Ub-C-term hydrolase that can detach an individual UB and ribosomal protein (cleave Ub-ribosomal fusion proteins) or a set of Ub monomers (cleave polyubiquitin molecule).
 * The ubiquitin and ribosomal protein gene that are fused together to make translation products called Ub-ribosomal fusion proteins.
 * A polyubiquitin molecule: Ub molecules can fused together to make a linear chain of repeated Ub-molecules.



Ubiquitin Structure
Ubiquitin’s protein structure is a compact β-grasp fold featuring a flexible C-terminal tail with six residues, and a core with rigid residues as seen in Figure 2a. Despite these rigid core residues, the flexible β1/ β2 loop that contains Leu8 (as seen in Figure 2b) plays a crucial role in allowing the recognition of ubiquitin by ubiquitin-binding proteins. The fact that only three conservative changes are observed from yeast to man indicates the importance of conserving ubiquitin’s structure as preserved by evolutionary pressure to resist change. This is important in facilitating the consistency of recognition of ubiquitin by ubiquitin-binding domains, also known as UBDs.

A hydrophobic surface comprised of the residues Ile44, Leu8, Val70, and His68 (as seen in Figures 2a-c) facilitates the recognition of ubiquitin by other proteins. The different residues built into the ubiquitin structure uniquely contribute to the interactions of ubiquitin with other proteins and to ubiquitin’s many different functions. One example is Ile44 which plays an important role in cell division because it binds proteasomes and most ubiquitin-binding domains. Another example is Ile36 which serves as a mediator for interactions between ubiquitin molecules conformed as chains. This residue is recognized by and specifically interacts with ubiquitin-binding domains (UBDs), deubiquitinating enzymes (DUBs), and HECT (Homologous to E6AP C terminus) E3s which is a type of ubiquitin ligase. Residues can also work together to perform particular functions of ubiquitin. For example, Gln2, Phe4, and Thr12 work together to facilitate cell division in yeast (as shown in Figure 2c). Also, ubiquitin’s TEK-box in higher eukaryotes which features Thr12, Thr14, Glu34, Lys6, and Lys11 plays an important role in mitotic degradation (also shown in Figure 2c). These are only few of the many structural features of ubiquitin and their roles in the many different functions of ubiquitin.

The most essential parts of the ubiquitin structure can be found in the N terminus with its seven lysine residues. These residues serves as chain assembly attachment sites in the process of ubiquitylation, a regulatory mechanism of the cell in which polymeric chains of ubiquitin are used to modify proteins and ultimately decide their fate in the cell. As in Figure 2d, these lysine residues are positioned in the three-dimensional structure in such a way that they face different directions and cover all of ubiquitin’s surfaces. The most dynamic area of ubiquitin’s structure features two particular lysine residues: Lys6 and Lys11. These regions are subject to conformational changes once ubiquitin associates with UBDs or while ubiquitin is in a chain conformation.

Ubiquitin (Ub) Function
Ub primarily exists to regulate protein turnover by regulating degradation of specific proteins. This is a very important process in the cell. By quickly eliminating a particular regulating protein, a turn on of a gene expression can be prevented. Proteins that are to be degraded are tagged by Ub and are then recognized by another protein called 26S proteosome to be degraded. Ub depends on ATP to mark specific proteins to be degraded. The Ub itself does not degrade proteins but slows down the rate of dissociation between proteasomes and substrate proteins.

The Ubiquitin- Proteasome Pathway:
There are three types of enzymes that participate in the process: E1- Ub-activating enzymes (turn Ub into reactive state), E2- Ub conjugating enzymes (aid the linking process between Ub and substrate protein), E3- Ub ligases (work together with E2, role mainly on recognizing the substrate protein). The general reaction pathway starts when Ub is activated by E1 in the present of ATP. After that, E2 and E3 work collaboratively to recognize the substrate protein and conjugate Ub to the substrate. From then the ubiquinated protein is ready for degradation.



These three enzymes can catalyze the binding of a substrate lysine and the C terminus of ubiquitin. This leads to monoubiquitylation. When multiple lysine residues be bound, multimonoubiquitylation will occur. Ubiquitin also can form polymeric chains when the N terminus or one of the lysine residues attached to a substrate. If the chains are elongated by the same residue, this will be called homogeneous ubiquitin chain. If the chains are elongated by the mixed residues, this will be called mixed ubiquitin chain. However, only monoubiquitylation and four homogenous chain types have found that have outcomes in the cell.

Degradation Signals
Though not fully understood, there are a few theories to help understand what determines a protein will be marked by Ub
 * 1) N-degron: In 1986, Alexander Varshavsky observed that there is a correlation between the half life of a protein and its N-terminal residue. This suggested that one could predict the lifespan of the protein by its N-terminal amino acid.
 * 2) Certain amino acid sequences such as PEST signal protein degradation. The PEST sequence is rich in proline, glutamic acid, serine, and threonine. It has been seen that removal of the PEST sequence in the protein increases protein half life.
 * 3) Mutant proteins revealing degradation signals are more prone to degradation than a normal protein. Usually the signals would be hidden away in the hydrophobic core, but sometimes mutation causes a partial folding that exposes the signal to Ub.

Reference
http://homepages.bw.edu/~mbumbuli/cell/ublec/

Komander, David and Rape, Michael. “The Ubiquitin Code” Annual Reviews Biochem.