Isopeptide bond

An isopeptide bond is an amide bond that can form for example between the carboxyl group of one amino acid and the amino group of another. At least one of these joining groups is part of the side chain of one of these amino acids. This is unlike in a peptide bond which is sometimes called an eupeptide bond, especially when discussing about both of these bond types in the same context to make a distinction between the two. An isopeptide bond is an amide bond that can form for example between the carboxyl group of one amino acid and the amino group of another. At least one of these joining groups is part of the side chain of one of these amino acids. This is unlike in a peptide bond which is sometimes called an eupeptide bond, especially when discussing about both of these bond types in the same context to make a distinction between the two. Lysine for example has an amino group on its side chain and glutamic acid has a carboxy group on its side chain. These amino acids among other similar amino acids may join together or with some other amino acids to form an isopeptide bond. Isopeptide bond may also form between a γ-carboxamide group ( -(C=O)NH2 ) of glutamine and primary amine ( RNH2 ) of some amino acid as follows Bond formation can be either enzyme catalyzed, as in the case for the isopeptide bond formed between lysine and glutamine catalyzed by transglutaminases (their reaction is similar to the reaction above), or it can form spontaneously as observed in HK97 bacteriophage capsid formation and Gram-positive bacterial pili. Spontaneous isopeptide bond formation requires the presence of another residue, glutamic acid, which catalyzes bond formation in a proximity induced manner. An example of a small peptide containing an isopeptide bond is glutathione, which has a bond between the side chain of a glutamate residue and the amino group of a cysteine residue. An example of a protein involved in isopeptide bonding is ubiquitin, which gets attached to other proteins with a bond between the C-terminal glycine residue of ubiquitin and a lysine side chain of the substrate protein. The function of enzyme generated isopeptide bonds can be roughly divided into two separate categories; signaling and structure. In the case of the former these can be a wide range of functions, influencing protein function, chromatin condensation, or protein half-life. With regard to the latter category, isopeptides can play a role in a variety of structural aspects, from helping to form the clots in wound healing, roles in extra cellular matrix upkeep & apoptosis pathway, roles in the formation of pathogenic pilin, restructuring of the actin skeleton of a host cell to help in the pathogenecity of V. cholerae, and modifying the properties micro-tubilin to influence its role in the structure of a cell. The chemistry involved in the formation of these isopeptide bonds also tend to fall into these two categories. In the case of ubiquitin and ubiquitin-like proteins, tend to have a structured pathway of continuously passing along the peptide with a series of reactions, using multiple intermediate enzymes to reach the target protein for the conjugation reaction. The structural enzymes while varying from bacterial and eukaryotic domains, tend to be single enzymes that generally in a single step, fuse the two substrates together for a larger repetitive process of linking and inter-linking the said substrates to form and influence large macromolecular structures. The chemistries of isopeptide bond formation are divided in the same manner as their biological roles. In the case of isopeptides used for conjugating one protein to another for the purpose of signal transduction, the literature is generally dominated by the very well-studied Ubiquitin protein and related proteins. While there are many related proteins to Ubiquitin, such as SUMO, Atg8, Atg12, and so on, they all tend to follow relatively the same protein ligation pathway. Therefore, the best example is to look at Ubiquitin, as while there can be certain differences, Ubiquitin is essentially the model followed in all these cases. The process essentially has three tiers, in the initial step, the activating protein generally denominated as E1 activates the Ubiquitin protein by adenylating it with ATP. Then the adenylated Ubiquitin is essentially activated and can be transferred to a conserved cysteine using a thioester bond which is between the carboxyl group of the c-terminal glycine of the ubiquitin and the sulfur of the E1 cysteine. The activating E1 enzyme then binds with and transfers the Ubiquitin to the next tier, the E2 enzyme which accepts the protein and once again forms a thioester with a conserved bond. The E2 acts to certain degree as an intermediary which then binds to E3 enzyme ligase for the final tier, which leads to the eventual transfer of the ubiquitin or ubiquitin related protein to a lysine site on the targeted protein, or more commonly for ubiquitin, onto ubiquitin itself to form chains of said protein.