Ubiquitin

Summary

This transcript explores the process of ubiquitination, where a small protein called ubiquitin is attached to lysine residues on target proteins. This modification, facilitated by enzymes E1, E2, and E3, plays a crucial role in regulating protein degradation, DNA damage response, and inflammation. The process involves the attachment of ubiquitin through an isopeptide bond, forming polyubiquitin chains with distinct functions. Ubiquitination can target proteins for degradation via the proteasome or modulate protein activities. The diversity of E3 ligases and E2 enzymes ensures the specific targeting of substrates for various biological functions.

Takeaways

• 😀 Ubiquitination is a post-translational modification involving the attachment of ubiquitin to lysine side chains of target proteins.
• 😀 Ubiquitin is a small 76 amino acid protein found in all eukaryotes and is covalently attached to target proteins via an isopeptide linkage.
• 😀 The attachment of ubiquitin adds significant molecular weight to a protein, more than 100 times the weight of a single phosphate group.
• 😀 Ubiquitin can form polyubiquitin chains, with different types of chains formed depending on which lysine residue is involved in the linkage.
• 😀 There are eight types of polyubiquitin chains, each defined by the lysine residue through which one ubiquitin attaches to the next.
• 😀 The most well-understood function of polyubiquitin chains is targeting proteins for degradation via the proteasome, especially with a K48-linked polyubiquitin chain.
• 😀 K63-linked polyubiquitin chains play a critical role in regulating DNA damage response and inflammatory response.
• 😀 Ubiquitination involves a cascade of reactions catalyzed by three enzymes: E1 (activating enzyme), E2 (conjugating enzyme), and E3 (ligase).
• 😀 The process begins with the activation of ubiquitin by E1, which is then transferred to E2, and finally conjugated to a lysine residue on the target protein by E3.
• 😀 E3 ligases are diverse and can be classified into types like RING ligases, which stimulate direct transfer of ubiquitin, or HECT ligases, which intermediate the transfer to an active site cysteine before attaching ubiquitin.

Q & A

What is ubiquitination and how does it occur?

Ubiquitination is the process where ubiquitin, a small 76-amino acid protein, is covalently attached to lysine side chains on a target protein. This occurs through a process involving three enzymes: E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3 (ubiquitin ligase). The C-terminus of ubiquitin is linked to a lysine residue on the target protein through an isopeptide bond.

What is the role of ubiquitin in post-translational modifications?

Ubiquitin plays a crucial role in post-translational modifications by being covalently attached to proteins. It often marks proteins for degradation, especially through polyubiquitin chains, but can also affect protein activity and localization in the cell. Its attachment adds substantial mass to the protein and influences its function.

How many types of polyubiquitin chains are there and what is their significance?

There are eight different types of polyubiquitin chains, each distinguished by the lysine residue through which one ubiquitin molecule is attached to the next. These chains have distinct biological functions, such as marking proteins for degradation (e.g., K48-linked chains) or regulating DNA damage and inflammatory responses (e.g., K63-linked chains).

What is the biological function of K48-linked polyubiquitin chains?

K48-linked polyubiquitin chains are primarily involved in targeting proteins for degradation by the proteasome. The proteasome recognizes these chains and processes the substrate protein into short peptides for further degradation.

What is the role of E1, E2, and E3 enzymes in ubiquitination?

E1 is the ubiquitin-activating enzyme that attaches ubiquitin to itself. E2 is the ubiquitin-conjugating enzyme that receives the ubiquitin from E1. E3 is the ubiquitin ligase that facilitates the transfer of ubiquitin from E2 to the target protein's lysine residue, completing the ubiquitination process.

How does the transfer of ubiquitin occur in the ubiquitination process?

In the ubiquitination process, the C-terminus of ubiquitin is first transferred to the E1 enzyme via a thioester bond. Then, the ubiquitin is transferred to the E2 enzyme. Finally, the ubiquitin is transferred from E2 to the target protein's lysine residue via the action of E3 ligase, forming a covalent isopeptide bond.

What distinguishes the different types of E3 ligases?

The different types of E3 ligases are distinguished by their structural domains. The most common type is the RING E3 ligase, which directly facilitates the transfer of ubiquitin to the target protein. Other types, like HECT E3 ligases, temporarily transfer ubiquitin to the E3 enzyme's active site before transferring it to the substrate.

Why are there so many different E2 and E3 enzymes in cells?

The large number of E2 and E3 enzymes (e.g., 30 E2 enzymes and over 500 E3 enzymes in humans) allows for specific targeting of proteins for ubiquitination. This diversity enables cells to finely regulate protein function and degradation by choosing which proteins to modify and by what type of ubiquitin chain.

What is the role of polyubiquitin chains in the regulation of protein activity?

Polyubiquitin chains, particularly those linked through K63, are involved in regulating protein activities that do not necessarily lead to degradation. For instance, K63-linked polyubiquitin chains are important in controlling DNA damage responses and inflammatory signaling, rather than targeting proteins for degradation.

How does ubiquitination influence the proteasome's ability to degrade proteins?

Ubiquitination, particularly with K48-linked polyubiquitin chains, marks proteins for degradation by the proteasome. The proteasome recognizes these polyubiquitin chains and processes the substrate protein into short peptides, which are then further degraded, thereby regulating protein levels in the cell.