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Structure, Functions, and Enzymes in Protein Ubiquitination

Ubiquitination, also referred to as ubiquitylation, constitutes a post-translational modification process wherein a small protein known as ubiquitin is covalently attached to a target protein. This modification plays a critical role in regulating diverse cellular processes. The covalent attachment of ubiquitin to a target protein is achieved through the sequential action of three types of enzymes: E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3 (ubiquitin ligase).

Ubiquitination operates as a molecular tag capable of modifying the target protein's function, localization, or fate. This process is pivotal in cellular regulation, protein degradation, signal transduction, and other fundamental biological processes. The type and pattern of ubiquitin attachment, such as mono-ubiquitination, multi-ubiquitination, or polyubiquitination, determine the specific impact on the target protein, influencing its interactions and activities within the cell.

The Ubiquitin Molecule

Ubiquitin Structure: Ubiquitin is a small protein composed of 76 amino acids with a highly conserved structure across species. Its three-dimensional structure is crucial for its function and its role in protein ubiquitination.

Functional Domains:

β-grasp Fold: The ubiquitin molecule adopts a β-grasp fold, which consists of a four-stranded beta-sheet and one alpha-helix. This fold creates a compact globular structure.
Glycine 76 (G76): At the C-terminus of ubiquitin, there is a critical Glycine (G76) residue. It is at this G76 that ubiquitin forms an isopeptide bond with the ε-amino group of a Lysine (K) residue on the target protein during the ubiquitination process. This covalent attachment is the key to the regulation of target proteins.
Seven Lysine Residues: Ubiquitin contains seven internal Lysine (K) residues: K6, K11, K27, K29, K33, K48, and K63. These Lysine residues are crucial for the formation of different types of ubiquitin chains (e.g., K48-linked and K63-linked chains) when multiple ubiquitin molecules are attached to a target protein. The type of ubiquitin linkage determines the fate and function of the target protein.

Polyubiquitin Chains: Ubiquitin can form polyubiquitin chains by linking multiple ubiquitin molecules together through one of the seven internal Lysine residues. The most well-known and extensively studied polyubiquitin chains are K48-linked and K63-linked chains:

K48-Linked Chains: K48-linked chains are involved in targeting proteins for proteasomal degradation. When proteins are tagged with K48-linked polyubiquitin chains, they are recognized and subsequently degraded by the proteasome.
K63-Linked Chains: K63-linked chains play a role in various cellular processes, such as DNA repair, endocytosis, and signal transduction. They do not typically lead to proteasomal degradation but instead serve as signals for protein interactions and cellular responses.

The structure of ubiquitin and its ability to form various ubiquitin chains make it a versatile regulator of cellular processes. Understanding the structure and functions of ubiquitin is essential for comprehending how it modulates protein activities, influences cellular regulation, and determines the fate of proteins in the cell.

Ubiquitin and overview of the process of ubiquitination (Dougherty et al., 2020).

The Ubiquitination Enzymes

E1 Enzymes

E1 enzymes, also termed ubiquitin-activating enzymes, initiate the ubiquitination process by activating ubiquitin and subsequently transferring it to E2 enzymes. The significance of E1 enzymes lies in their pivotal role, as they determine the specificity of the ubiquitination process.

E2 Enzymes

E2 enzymes, known as ubiquitin-conjugating enzymes, collaborate with E3 enzymes to facilitate the transfer of ubiquitin from E1 enzymes to the target protein. They play a vital role in selecting appropriate target proteins and aiding in the transfer of ubiquitin to specific lysine residues.

E3 Enzymes

E3 enzymes, ubiquitin ligases, stand as central figures in protein ubiquitination. They contribute specificity to the process by recognizing target proteins and catalyzing the transfer of ubiquitin from E2 enzymes to the target protein. E3 enzymes exist in various forms, each fulfilling distinct roles in the ubiquitination process.

Types of Protein Ubiquitination

Protein ubiquitination can manifest in various forms, including:

Mono-ubiquitination: In this form, a single ubiquitin molecule is attached to a specific lysine residue on the target protein. Mono-ubiquitination regulates various cellular processes, including endocytosis and DNA repair.
Multi-ubiquitination: Multiple ubiquitin molecules are attached to the target protein, modulating its activity and localization. Multi-ubiquitination can have diverse effects on protein function.
Polyubiquitination: In polyubiquitination, ubiquitin molecules form a chain on the target protein, with each ubiquitin molecule attached to the previous one. Different types of ubiquitin linkages (K48, K63, etc.) in polyubiquitin chains determine the fate of the target protein.

Functions of Protein Ubiquitination

Cellular Regulation

Protein ubiquitination is central to the regulation of various cellular processes, including the cell cycle, DNA repair, and transcription. It acts as a molecular switch, controlling the activation or inactivation of proteins involved in these processes.

Protein Degradation

Ubiquitination plays a critical role in the targeted degradation of proteins by the proteasome. Proteins marked with K48-linked polyubiquitin chains are recognized and degraded by the proteasome, ensuring the maintenance of protein homeostasis.

Signal Transduction

Ubiquitination is involved in signal transduction pathways, enabling the regulation of cellular responses to extracellular stimuli. The attachment of ubiquitin chains to signaling molecules influences their activation, localization, and degradation.

A Proteomics Approach to Understanding Protein Ubiquitination

Proteomics is a scientific approach aimed at the comprehensive study of proteins within a biological system. In the context of protein ubiquitination, this involves several sequential steps:

Sample Preparation: Researchers start by enriching samples to specifically capture ubiquitinated proteins. Common methods include affinity purification using antibodies designed to recognize ubiquitin.
Mass Spectrometry: Mass spectrometry is the primary analytical technique employed to identify, quantify, and characterize proteins by measuring the mass-to-charge ratios of molecules. In ubiquitination studies, it assists in identifying ubiquitinated proteins and pinpointing their sites of modification.
Tandem Mass Spectrometry (MS/MS): MS/MS is utilized to fragment peptides derived from ubiquitinated proteins, generating spectra that reveal the amino acid sequence of these peptides.
Database Searches: The MS/MS data is then compared to protein databases, and search algorithms match observed spectra to known proteins, aiding in the identification of ubiquitinated proteins.
Quantification: Proteomics allows for the quantification of ubiquitinated proteins, offering insights into alterations in ubiquitination levels in response to various conditions or stimuli.
Functional Insights: Beyond identification and quantification, proteomics provides valuable insights into the functions and pathways associated with ubiquitinated proteins. This aids researchers in understanding how ubiquitination influences cellular processes.

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Ubiquitin Binding and Targeting for Degradation

Ubiquitin binding and targeting for degradation are fundamental aspects of protein ubiquitination:

E3 Ligases: E3 ligases, also known as ubiquitin ligases, recognize specific target proteins. They form a complex with both the target protein and the E2-ubiquitin complex.
Ubiquitin Transfer: E3 ligases catalyze the transfer of ubiquitin from the E2-ubiquitin complex to the target protein. This results in the formation of an isopeptide bond between the C-terminus of ubiquitin and a lysine residue on the target protein.
Ubiquitin Linkage Types: The type of ubiquitin linkage formed (e.g., K48-linked or K63-linked) determines the fate of the target protein. K48-linked chains target proteins for degradation by the proteasome, while K63-linked chains have other regulatory roles.
Proteasomal Degradation: Proteins marked with K48-linked polyubiquitin chains are recognized by the proteasome, a cellular complex responsible for protein degradation. This process maintains protein balance and cellular functions.

Reference

Dougherty, Shannon E., et al. "Expanding role of ubiquitin in translational control." International journal of molecular sciences 21.3 (2020): 1151.

* For Research Use Only. Not for use in diagnostic procedures.

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