Ubiquitination (also known as ubiquitylation) is an enzymatic, post-translational modification (PTM) process in which a ubiquitin protein is attached to a substrate protein. This process most commonly binds the last amino acid of ubiquitin (glycine 76) to a lysine residue on the substrate. An isopeptide bond is formed between the carboxylic acid group of the ubiquitin's glycine and the epsilon amino group of the substrate's lysine. Cases are known in which the amine group of a protein's N-terminus is used for ubiquitination, rather than a lysine residue. In a few rare cases nonlysine residues have been identified as ubiquitination targets, such as cysteine, threonine and serine. The end result of this process is the addition of one ubiquitin molecule (monoubiquitination) or a chain of ubiquitin molecules (polyubiquitination) to the substrate protein.

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Wiki: Ubiquitination

    Tyrosine phosphorylation is the addition of a phosphate (PO43?) group to the amino acid tyrosine on a protein. It is one of the main types of protein phosphorylation. This transfer is made possible through enzymes called tyrosine kinases. Tyrosine phosphorylation is a key step in signal transduction and the regulation of enzymatic activity.

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Wiki: Tyrosine phosphorylation

    In particular, dimethylation and trimethylation of lysine side chains in proteins increase both hydrophobicity and steric bulk and can affect protein¨Cprotein interactions if they are in an interacting surface.

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Wiki: Trimethylation

    Protein phosphorylation is a post-translational modification of proteins in which a serine, a threonine or a tyrosine residue is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Regulation of proteins by phosphorylation is one of the most common modes of regulation of protein function, and is often termed "phosphoregulation". In almost all cases of phosphoregulation, the protein switches between a phosphorylated and an unphosphorylated form, and one of these two is an active form, while the other one is an inactive form. A serine/threonine protein kinase is a kinase enzyme that phosphorylates the OH group of serine or threonine (which have similar sidechains). At least 125 of the 500+ human protein kinases are serine/threonine kinases (STK). Serine/Threonine Kinase receptors play a role in the regulation of cell proliferation, programmed cell death (apoptosis), cell differentiation, and embryonic development.

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Wiki: Threonine phosphorylation

    SUMO proteins are similar to ubiquitin, and SUMOylation is directed by an enzymatic cascade analogous to that involved in ubiquitination. In contrast to ubiquitin, SUMO is not used to tag proteins for degradation. Mature SUMO is produced when the last four amino acids of the C-terminus have been cleaved off to allow formation of an isopeptide bond between the C-terminal glycine residue of SUMO and an acceptor lysine on the target protein.

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Wiki: SUMOylation

    Protein phosphorylation is a reversible post-translational modification of proteins in which an amino acid residue is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Phosphorylation alters the structural conformation of a protein, causing it to become activated, deactivated, or otherwise modifying its function.[1] Approximately 13,000 human proteins have sites that are phosphorylated.

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Wiki: Serine phosphorylation

    Propionylation is a post-translational modification of proteins, in which a propionyl-group is added to a lysine amino acid of a protein. Propionylation participates in crucial biological processes, including metabolic processes and cellular stress response. Lysine propionylation was first identified on histone proteins, and since has also been identified on other proteins. Histone propionylation is a mark of active chromatin. The substrate for protein propionylation is propionyl-CoA. Propionyl-CoA in the cell is metabolised by the enzyme propionyl-CoA carboxylase. Accumulation of propionyl-CoA leads to increased protein propionylation. In patients with propionic acidemia, a rare autosomal recessive metabolic disorder, propionyl-CoA levels elevated and increased propionylation, which might contribute to the pathology in these patients.

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Wiki: Propionylation

    Polyubiquitination is the formation of a ubiquitin chain on a single lysine residue on the substrate protein. Following addition of a single ubiquitin moiety to a protein substrate, further ubiquitin molecules can be added to the first, yielding a polyubiquitin chain. These chains are made by linking the glycine residue of a ubiquitin molecule to a lysine of ubiquitin bound to a substrate. Ubiquitin has seven lysine residues and an N-terminus that may serve as points of ubiquitination; they are K6, K11, K27, K29, K33, K48, and K63. Lysine 48-linked chains were the first identified and are the best-characterised type of ubiquitin chain. K63 chains have also been well-characterised, whereas the function of other lysine chains, mixed chains, branched chains, N-terminal linear chains, and heterologous chains (mixtures of ubiquitin and other ubiquitin-like proteins) remains more unclear.

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Wiki: Polyubiquitination

    In biochemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology. Protein phosphorylation often activates (or deactivates) many enzymes.

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Wiki: Phosphorylation

    Palmitoylation is the covalent attachment of fatty acids, such as palmitic acid, to cysteine (S-palmitoylation) and less frequently to serine and threonine (O-palmitoylation) residues of proteins, which are typically membrane proteins. The precise function of palmitoylation depends on the particular protein being considered. Palmitoylation enhances the hydrophobicity of proteins and contributes to their membrane association. Palmitoylation also appears to play a significant role in subcellular trafficking of proteins between membrane compartments, as well as in modulating protein¨Cprotein interactions. In contrast to prenylation and myristoylation, palmitoylation is usually reversible (because the bond between palmitic acid and protein is often a thioester bond). The reverse reaction in mammalian cells is catalyzed by acyl-protein thioesterases (APTs) in the cytosol and palmitoyl protein thioesterases in lysosomes. Because palmitoylation is a dynamic, post-translational process, it is believed to be employed by the cell to alter the subcellular localization, protein¨Cprotein interactions, or binding capacities of a protein.

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Wiki: Palmitoylation

    Palmitoleoylation is type of protein lipidation where the monounsaturated fatty acid palmitoleic acid is covalently attached to serine or threonine residues of proteins. Palmitoleoylation appears to play a significant role in trafficking and targeting and function of Wnt proteins. O-Palmitoleoylation of Wnt proteins is catalysed by PORCN. The inverse reaction is done by NOTUM.

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Wiki: O-Palmitoleoylation

    In organic chemistry, nitration is a general class of chemical processes for the introduction of a nitro group (?NO2) into an organic compound. The term also is applied incorrectly to the different process of forming nitrate esters (?ONO2) between alcohols and nitric acid (as occurs in the synthesis of nitroglycerin). The difference between the resulting molecular structures of nitro compounds and nitrates (NO?3) is that the nitrogen atom in nitro compounds is directly bonded to a non-oxygen atom (typically carbon or another nitrogen atom), whereas in nitrate esters (also called organic nitrates), the nitrogen is bonded to an oxygen atom that in turn usually is bonded to a carbon atom (nitrito group).

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Wiki: Nitration

    Neddylation (also NEDDylation) is the process by which the ubiquitin-like protein NEDD8 is conjugated to its target proteins. This process is analogous to ubiquitination, although it relies on its own E1 and E2 enzymes. No NEDD8-specific E3 has yet been identified and it is possible that the Neddylation system relies on E3 ligases with dual specificity.

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Wiki: Neddylation

    Protein N-myristoylation is an important fatty acylation catalyzed by N-myristoyltransferases (NMTs), which are ubiquitous enzymes in eukaryotes. Specifically, attachment of a myristoyl group is vital for proteins participating in various biological functions, including signal transduction, cellular localization, and oncogenesis. Recent studies have revealed unexpected mechanisms indicating that protein N-myristoylation is involved in host defense against microbial and viral infections.

Reference
Pubmed: Wang B, Dai T, Sun W, Wei Y, Ren J, Zhang L, Zhang M, Zhou F. Protein N-myristoylation: functions and mechanisms in control of innate immunity. Cell Mol Immunol. 2021 Apr;18(4):878-888. doi: 10.1038/s41423-021-00663-2.

    N-linked glycosylation, is the attachment of an oligosaccharide, a carbohydrate consisting of several sugar molecules, sometimes also referred to as glycan, to a nitrogen atom (the amide nitrogen of an asparagine (Asn) residue of a protein), in a process called N-glycosylation, studied in biochemistry. The resulting protein is called an N-linked glycan, or simply an N-glycan.

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Wiki: N-linked glycosylation

    Monoubiquitination is the addition of one ubiquitin molecule to one substrate protein residue. Multi-monoubiquitination is the addition of one ubiquitin molecule to multiple substrate residues. The monoubiquitination of a protein can have different effects to the polyubiquitination of the same protein. The addition of a single ubiquitin molecule is thought to be required prior to the formation of polyubiquitin chains. Monoubiquitination affects cellular processes such as membrane trafficking, endocytosis and viral budding.

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Wiki: Monoubiquitination

    Methylation, in the chemical sciences, is the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These terms are commonly used in chemistry, biochemistry, soil science, and biology. In biological systems, methylation is catalyzed by enzymes; such methylation can be involved in modification of heavy metals, regulation of gene expression, regulation of protein function, and RNA processing. In vitro methylation of tissue samples is also a way to reduce some histological staining artifacts. The reverse of methylation is demethylation.

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Wiki: Methylation

    Protein lysine methylation, is a PTM involving the transfer of one, two or three methyl groups to the epsilon - amine of a lysine side chain. Lysine methylation represents a complex and often elusive PTM that has nonetheless the potential to alter the function of the modified protein. lysine methylation has been observed in both nuclear and cytoplasmic proteins and is now considered a prevalent modification in eukaryotes, prokaryotes and archaea. Two groups of enzymes, both using S - adenosyl - L - methionine (SAM) as a methyl donor, catalyze the addition of a methyl group to the epsilon - amine group of a lysine side chain. The first type of protein lysine methyltransferase regroups the enzymes containing a catalytic SET domain and the second class of PKMTs, the seven beta - strand methyltransferases (class I methyltransferases), belongs to an extended superfamily of methyltransferases found throughout eukaryotes, prokaryotes and archaea.

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Wiki: Lysine methylation

    Protein hydroxylation is a post-translational modification catalyzed by 2-oxoglutarate-dependent dioxygenases. The hydroxylation modification can take place on various amino acids, including but not limited to proline, lysine, asparagine, aspartate and histidine.

Reference
Pubmed: Zurlo G, Guo J, Takada M, Wei W, Zhang Q. New Insights into Protein Hydroxylation and Its Important Role in Human Diseases. Biochim Biophys Acta. 2016 Dec;1866(2):208-220. doi: 10.1016/j.bbcan.2016.09.004.

    Glycosylphosphatidylinositol or glycophosphatidylinositol (GPI) is a phosphoglyceride that can be attached to the C-terminus of a protein during posttranslational modification. The resulting GPI-anchored proteins play key roles in a wide variety of biological processes. GPI is composed of a phosphatidylinositol group linked through a carbohydrate-containing linker (glucosamine and mannose glycosidically bound to the inositol residue) and via an ethanolamine phosphate (EtNP) bridge to the C-terminal amino acid of a mature protein. The two fatty acids within the hydrophobic phosphatidyl-inositol group anchor the protein to the cell membrane.

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Wiki: GPI-anchor

    Glycosylation is the reaction in which a carbohydrate (or 'glycan'), i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule (a glycosyl acceptor) in order to form a glycoconjugate. In biology (but not always in chemistry), glycosylation usually refers to an enzyme-catalysed reaction, whereas glycation (also 'non-enzymatic glycation' and 'non-enzymatic glycosylation') may refer to a non-enzymatic reaction.

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Wiki: Glycosylation

    Deubiquitinating enzymes (deubiquitinases; DUBs) oppose the role of ubiquitylation by removing ubiquitin from substrate proteins. They are cysteine proteases that cleave the amide bond between the two proteins. They are highly specific, as are the E3 ligases that attach the ubiquitin, with only a few substrates per enzyme. They can cleave both isopeptide (between ubiquitin and lysine) and peptide bonds (between ubiquitin and the N-terminus). In addition to removing ubiquitin from substrate proteins, DUBs have many other roles within the cell. Ubiquitin is either expressed as multiple copies joined in a chain (polyubiquitin) or attached to ribosomal subunits. DUBs cleave these proteins to produce active ubiquitin. They also recycle ubiquitin that has been bound to small nucleophilic molecules during the ubiquitylation process. Monoubiquitin is formed by DUBs that cleave ubiquitin from free polyubiquitin chains that have been previously removed from proteins.

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Wiki: Deubiquitination

    In biochemistry, dephosphorylation is the removal of a phosphate (PO43?) group from an organic compound by hydrolysis. It is a reversible post-translational modification. Dephosphorylation and its counterpart, phosphorylation, activate and deactivate enzymes by detaching or attaching phosphoric esters and anhydrides. A notable occurrence of dephosphorylation is the conversion of ATP to ADP and inorganic phosphate. Dephosphorylation employs a type of hydrolytic enzyme, or hydrolase, which cleaves ester bonds. The prominent hydrolase subclass used in dephosphorylation is phosphatase, which removes phosphate groups by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl (-OH) group. The reversible phosphorylation-dephosphorylation reaction occurs in every physiological process, making proper function of protein phosphatases necessary for organism viability. Because protein dephosphorylation is a key process involved in cell signalling, protein phosphatases are implicated in conditions such as cardiac disease, diabetes, and Alzheimer's disease.

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Wiki: Dephosphorylation

    Neddylation (also NEDDylation) is the process by which the ubiquitin-like protein NEDD8 is conjugated to its target proteins. This process is analogous to ubiquitination, although it relies on its own E1 and E2 enzymes. No NEDD8-specific E3 has yet been identified and it is possible that the Neddylation system relies on E3 ligases with dual specificity.

Reference
Wiki: Deneddylation

    Demethylation is the chemical process resulting in the removal of a methyl group (CH3) from a molecule. A common way of demethylation is the replacement of a methyl group by a hydrogen atom, resulting in a net loss of one carbon and two hydrogen atoms. The counterpart of demethylation is methylation.

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Wiki: Demethylation

    In chemistry, acetylation is an organic esterification reaction with acetic acid. It introduces an acetyl group into a chemical compound. Such compounds are termed acetate esters or simply acetates. Deacetylation is the opposite reaction, the removal of an acetyl group from a chemical compound.

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Wiki: Deacetylation

    Cholesterol, the most abundant sterol in mammalian cells, plays critical roles in Hh signaling. On one hand, the linkage of cholesterol to the carboxyl terminus of the mature Hh protein facilitates its secretion. On the other hand, the Hh-receiving cells require cholesterol to activate SMO to transduce the signal. Recent structural studies have revealed multiple sterol binding sites in the SMO protein.

Reference
Pubmed: Hu A, Zhang JZ, Wang J, Li CC, Yuan M, Deng G, Lin ZC, Qiu ZP, Liu HY, Wang XW, Wei PC, He X, Zhao X, Qiu WW, Song BL. Cholesterylation of Smoothened is a calcium-accelerated autoreaction involving an intramolecular ester intermediate. Cell Res. 2022 Mar;32(3):288-301. doi: 10.1038/s41422-022-00622-0.

    Arginine methylation is a prevalent post-translational modification found on both nuclear and cytoplasmic proteins. The methylation of arginine residues is catalyzed by the protein arginine Nmethyltransferase (PRMT) family of enzymes. Proteins that are arginine methylated are involved in a number of different cellular processes, including transcriptional regulation, RNA metabolism and DNA damage repair (Bedford and Richard, 2005). Most PRMTs methylate glycine- and arginine-rich patches (GAR motifs) within their substrates.

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Wiki: Arginine methylation

    In chemistry, acetylation is an organic esterification reaction with acetic acid. It introduces an acetyl group into a chemical compound. Such compounds are termed acetate esters or simply acetates. Deacetylation is the opposite reaction, the removal of an acetyl group from a chemical compound.

Reference
Wiki: Acetylation