Ubiquitin D is a protein that in humans is encoded by the UBD gene, also known as FAT10. [5] [6] [7] UBD acts like ubiquitin, by covalently modifying proteins and tagging them for destruction in the proteasome.
Ubiquitin D is a protein that in humans is encoded by the UBD gene, also known as FAT10. [5] [6] [7] UBD acts like ubiquitin, by covalently modifying proteins and tagging them for destruction in the proteasome.
Ubiquitin is a protein composed of 76 amino acids. In order for ubiquitin to bind to other proteins, it must go through an activation process by E1, an ATP-dependent ubiquitin activating enzyme. The carboxyl terminal (C-terminus) of ubiquitin is linked to the cysteine residue of the E1 protein by a high energy thioester linkage and activated. This reaction requires ATP and proceeds through a covalent AMP-ubiquitin intermediate.
Proteolysis in cells is an essential process to prevent the production of unwanted or abnormal proteins. During protein degradation, the process in which proteolytic enzymes act in an ATP-dependent manner mainly occurs in the degradation of substrate proteins with short half-lives. In particular, in eukaryotic cells, the proteolysis process by the binding of ubiquitin composed of 76 amino acids plays an important role in regulating the half-life and function of proteins. [8]
E1, E2 proteins and E3 enzymes are essential for attaching ubiquitin to matrix proteins. Among them, only one type of E1 protein exists in an individual, and it is known that the number is the highest.
About a dozen E2 proteins are known to exist in yeast as transfer proteins that transfer ubiquitin from E1 to E3 or substrates, and it has been confirmed that more types exist in higher eukaryotes than yeast. E3 enzyme, also called E3 ligase, is an enzyme that acts in the final step of attaching ubiquitin to a substrate protein. The specificity of the substrate protein to be ubiquitinated is determined by the E3 enzyme.
In particular, E3 enzymes can be divided into four types such as HECT, RING-finger, U-box, and PHD-finger according to the method of determining the specificity of the substrate protein. Among them, the RING-finger E3 enzyme is known to follow the amino terminal rule the best. The amino-terminal rule means that the degradation rate of a protein, that is, the half-life of a protein, varies depending on what the amino-terminal amino acid residue is. In the amino-terminal rule of yeast, it is known that the half-life of proteins varies depending on the presence of 12 unstable amino acid residues (arginine, lysine, histidine, tyrosine, tryptophan, isoleucine, aspartic acid, glutamic acid, asparagine, glutamine) out of 20 amino acids. When methionine, glycine, serine, valine, or proline is located at the amino-terminus, it has a half-life of more than 20 hours, whereas when residues such as tyrosine, glutamine, leucine, phenylalanine, aspartate, lysine, or arginine are located, the half-life is reduced to less than 10 minutes. [9]
Activated ubiquitin bound to E1 is transferred to the cysteine residue of the E2 molecule (ubiquitin conjugating enzyme). E2 molecules form complexes with E3 protein molecules, which are accessory proteins. In the E2-E3 complex, called ubiquitin ligase, the E3 component binds to a specific degradation signal in the substrate protein, and then the E2 enzyme helps to form a multi-ubiquitin chain at the lysine residue of the substrate protein. In order to form a multi-ubiquitin chain, the C-terminal region of the next ubiquitin molecule is linked to the lysine residue of the preceding ubiquitin.
About 30 different E2s exist in mammalian cells, and more than 300 specific E2-E3 complexes have been found. Thanks to the function of the E3 component, they can recognize specific degradation signals of target proteins. In general, E2 is called ubiquitin-linking enzyme, and E3 is traditionally called ubiquitin-linking enzyme. Functionally, however, it is more accurate to call the E2-E3 complex a ubiquitin ligase. Multi-ubiquitin chains on target proteins are recognized by specific receptors on the proteasome.
In general, the proteasome is responsible for removing structurally abnormal proteins, but also contributes to regulating the lifespan of specific proteins according to the intracellular environment. For example, mitotic cyclins required for the induction of mitosis (or mitosis) remain long-lived throughout the cell cycle, but are destined for abrupt degradation at the end of mitosis.
Then, how does this regulation of protein degradation occur? Activation of E3, a ubiquitin linking enzyme, can be achieved by phosphorylation or allosteric transition following ligand or subunit binding. For example, the anaphase-promoting complex (APC) is a multiubiquitin-linking enzyme that is activated during mitosis by the addition of subunits along the cell cycle. Activated APC promotes proteolysis of mitotic cyclins and metaphase-late transition regulators. [10]
UBD was first discovered in reticuloendothelial tissues and mucosal-associated lymphoid immunological systems as one of the genes at the human major histocompatibility complex class I locus on chromosome 6. The UBD gene encodes an 18 kDa protein containing an N- and C-terminus with 29 and 36% identity with ubiquitin, respectively. Of the ubiquitin-like proteins that have been identified, UBD is the only one of that conjugate to target proteins by a free diglycine motif at the C-terminus and directly guides noncovalently bound proteins to proteasomal degradation.
UBD also has important roles in cell mitosis, chromosome instability, apoptosis and immune response. UBD deregulation may induce abnormal alterations in apoptosis, cell division or chromosome instability, which are associated with neoplastic change. Tumor UBD expression shows some tissue specificity, with transcriptional upregulation observed in liver, uterine cervix, ovarian, pancreatic, gastric and small intestine adenocarcinomas, but not in thyroid, prostate or kidney cancers. In hepatic cancer cells, increased expression of UBD was associated with Proliferating Cell Nuclear Antigen, a cell proliferation marker, and reported to provide a growth advantage over cells without UBD expression. High UBD expression also promoted hepatocellular carcinoma development in a mouse model and formation of Mallory–Denk bodies, which are preneoplastic changes in chronic liver disease. Overexpression of UBD in gastric cancer has been correlated with metastasis and tumor staging, and both UBD mRNA and protein levels were identified as independent prognostic factors for this disease. Increased UBD has also been positively correlated with mutant p53 expression, which may activate UBD expression and indirectly facilitate gastric cancer progression. Interferon-γ and tumor necrosis factor-α act synergistically to induce the UBD promoter through an interferon sequence resposive element. Collectively, these data indicate that UBD may be a marker for precancerous lesions and may promote cancer progression. [11]
UBD has been shown to interact with NUB1 [12] and MAD2L1. [13]
Proteasomes are protein complexes which degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that help such reactions are called proteases.
Ubiquitin is a small regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ubiquitously. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Four genes in the human genome code for ubiquitin: UBB, UBC, UBA52 and RPS27A.
Anaphase-promoting complex is an E3 ubiquitin ligase that marks target cell cycle proteins for degradation by the 26S proteasome. The APC/C is a large complex of 11–13 subunit proteins, including a cullin (Apc2) and RING (Apc11) subunit much like SCF. Other parts of the APC/C have unknown functions but are highly conserved.
A ubiquitin ligase is a protein that recruits an E2 ubiquitin-conjugating enzyme that has been loaded with ubiquitin, recognizes a protein substrate, and assists or directly catalyzes the transfer of ubiquitin from the E2 to the protein substrate. In simple and more general terms, the ligase enables movement of ubiquitin from a ubiquitin carrier to another thing by some mechanism. The ubiquitin, once it reaches its destination, ends up being attached by an isopeptide bond to a lysine residue, which is part of the target protein. E3 ligases interact with both the target protein and the E2 enzyme, and so impart substrate specificity to the E2. Commonly, E3s polyubiquitinate their substrate with Lys48-linked chains of ubiquitin, targeting the substrate for destruction by the proteasome. However, many other types of linkages are possible and alter a protein's activity, interactions, or localization. Ubiquitination by E3 ligases regulates diverse areas such as cell trafficking, DNA repair, and signaling and is of profound importance in cell biology. E3 ligases are also key players in cell cycle control, mediating the degradation of cyclins, as well as cyclin dependent kinase inhibitor proteins. The human genome encodes over 600 putative E3 ligases, allowing for tremendous diversity in substrates.
Ubiquitin-like modifier activating enzyme 1 (UBA1) is an enzyme which in humans is encoded by the UBA1 gene. UBA1 participates in ubiquitination and the NEDD8 pathway for protein folding and degradation, among many other biological processes. This protein has been linked to X-linked spinal muscular atrophy type 2, neurodegenerative diseases, and cancers.
Deubiquitinating enzymes (DUBs), also known as deubiquitinating peptidases, deubiquitinating isopeptidases, deubiquitinases, ubiquitin proteases, ubiquitin hydrolases, or ubiquitin isopeptidases, are a large group of proteases that cleave ubiquitin from proteins. Ubiquitin is attached to proteins in order to regulate the degradation of proteins via the proteasome and lysosome; coordinate the cellular localisation of proteins; activate and inactivate proteins; and modulate protein-protein interactions. DUBs can reverse these effects by cleaving the peptide or isopeptide bond between ubiquitin and its substrate protein. In humans there are nearly 100 DUB genes, which can be classified into two main classes: cysteine proteases and metalloproteases. The cysteine proteases comprise ubiquitin-specific proteases (USPs), ubiquitin C-terminal hydrolases (UCHs), Machado-Josephin domain proteases (MJDs) and ovarian tumour proteases (OTU). The metalloprotease group contains only the Jab1/Mov34/Mpr1 Pad1 N-terminal+ (MPN+) (JAMM) domain proteases.
In molecular biology, SUMOproteins are a family of small proteins that are covalently attached to and detached from other proteins in cells to modify their function. This process is called SUMOylation. SUMOylation is a post-translational modification involved in various cellular processes, such as nuclear-cytosolic transport, transcriptional regulation, apoptosis, protein stability, response to stress, and progression through the cell cycle.
Chemical modification refers to a number of various processes involving the alteration of the chemical constitution or structure of molecules.
Endoplasmic-reticulum-associated protein degradation (ERAD) designates a cellular pathway which targets misfolded proteins of the endoplasmic reticulum for ubiquitination and subsequent degradation by a protein-degrading complex, called the proteasome.
An isopeptide bond is a type of amide bond formed between a carboxyl group of one amino acid and an amino group of another. An isopeptide bond is the linkage between the side chain amino or carboxyl group of one amino acid to the α-carboxyl, α-amino group, or the side chain of another amino acid. In a typical peptide bond, also known as eupeptide bond, the amide bond always forms between the α-carboxyl group of one amino acid and the α-amino group of the second amino acid. Isopeptide bonds are rarer than regular peptide bonds. Isopeptide bonds lead to branching in the primary sequence of a protein. Proteins formed from normal peptide bonds typically have a linear primary sequence.
Ubiquitin-activating enzymes, also known as E1 enzymes, catalyze the first step in the ubiquitination reaction, which can target a protein for degradation via a proteasome. This covalent bond of ubiquitin or ubiquitin-like proteins to targeted proteins is a major mechanism for regulating protein function in eukaryotic organisms. Many processes such as cell division, immune responses and embryonic development are also regulated by post-translational modification by ubiquitin and ubiquitin-like proteins.
Ubiquitin-conjugating enzymes, also known as E2 enzymes and more rarely as ubiquitin-carrier enzymes, perform the second step in the ubiquitination reaction that targets a protein for degradation via the proteasome. The ubiquitination process covalently attaches ubiquitin, a short protein of 76 amino acids, to a lysine residue on the target protein. Once a protein has been tagged with one ubiquitin molecule, additional rounds of ubiquitination form a polyubiquitin chain that is recognized by the proteasome's 19S regulatory particle, triggering the ATP-dependent unfolding of the target protein that allows passage into the proteasome's 20S core particle, where proteases degrade the target into short peptide fragments for recycling by the cell.
NEDD8 is a protein that in humans is encoded by the NEDD8 gene. This ubiquitin-like (UBL) protein becomes covalently conjugated to a limited number of cellular proteins, in a process called NEDDylation similar to ubiquitination. Human NEDD8 shares 60% amino acid sequence identity to ubiquitin. The primary known substrates of NEDD8 modification are the cullin subunits of cullin-based E3 ubiquitin ligases, which are active only when NEDDylated. Their NEDDylation is critical for the recruitment of E2 to the ligase complex, thus facilitating ubiquitin conjugation. NEDD8 modification has therefore been implicated in cell cycle progression and cytoskeletal regulation.
Autophagy related 7 is a protein in humans encoded by ATG7 gene. Related to GSA7; APG7L; APG7-LIKE.
Cdc4 is a substrate recognition component of the SCF ubiquitin ligase complex, which acts as a mediator of ubiquitin transfer to target proteins, leading to their subsequent degradation via the ubiquitin-proteasome pathway. Cdc4 targets primarily cell cycle regulators for proteolysis. It serves the function of an adaptor that brings target molecules to the core SCF complex. Cdc4 was originally identified in the model organism Saccharomyces cerevisiae. CDC4 gene function is required at G1/S and G2/M transitions during mitosis and at various stages during meiosis.
Cdh1 is one of the substrate adaptor proteins of the anaphase-promoting complex (APC) in the budding yeast Saccharomyces cerevisiae. Functioning as an activator of the APC/C, Cdh1 regulates the activity and substrate specificity of this ubiquitin E3-ligase. The human homolog is encoded by the FZR1 gene, which is not to be confused with the CDH1 gene.
Ubiquitin-like 1-activating enzyme E1B (UBLE1B) also known as SUMO-activating enzyme subunit 2 (SAE2) is an enzyme that in humans is encoded by the UBA2 gene.
Ubiquitin conjugating enzyme E2 Z (UBE2Z), also known as UBA6-specific E2 enzyme 1 (USE1), is an enzyme that in humans is encoded by the UBE2Z gene on chromosome 17. It is ubiquitously expressed in many tissues and cell types. UBE2Z is an E2 ubiquitin conjugating enzyme and participates in the second step of protein ubiquitination during proteolysis. A genome-wide association study (GWAS) revealed the UBE2Z gene to be associated with chronic kidney disease. The UBE2Z gene also contains one of 27 SNPs associated with increased risk of coronary artery disease.
Ubiquitin-like proteins (UBLs) are a family of small proteins involved in post-translational modification of other proteins in a cell, usually with a regulatory function. The UBL protein family derives its name from the first member of the class to be discovered, ubiquitin (Ub), best known for its role in regulating protein degradation through covalent modification of other proteins. Following the discovery of ubiquitin, many additional evolutionarily related members of the group were described, involving parallel regulatory processes and similar chemistry. UBLs are involved in a widely varying array of cellular functions including autophagy, protein trafficking, inflammation and immune responses, transcription, DNA repair, RNA splicing, and cellular differentiation.
Arabidopsis SUMO-conjugation enzyme (AtSCE1) is an enzyme that is a member of the small ubiquitin-like modifier (SUMO) post-translational modification pathway. This process, and the SCE1 enzyme with it, is highly conserved across eukaryotes yet absent in prokaryotes. In short, this pathway results in the attachment of a small polypeptide through an isopeptide bond between modifying enzyme and the ε-amino group of a lysine residue in the substrate. In plants, the 160 amino acid SCE1 enzyme was first characterized in 2003. One functional gene copy, SCE1a, was found on chromosomes 3.