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This covalent acyl-enzyme intermediate is then hydrolyzed by activated water to complete catalysis by releasing the second half of the product and regenerating the free enzyme That residue performs a nucleophilic attack to covalently link the protease to the substrate protein, releasing the first half of the product. Serine, threonine, and cysteine proteases use a nucleophilic residue (usually in a catalytic triad).Aspartic, glutamic, and metallo-proteases activate a water molecule, which performs a nucleophilic attack on the peptide bond to hydrolyze it.Some detach the terminal amino acids from the protein chain ( exopeptidases, such as aminopeptidases, carboxypeptidase A) others attack internal peptide bonds of a protein ( endopeptidases, such as trypsin, chymotrypsin, pepsin, papain, elastase).Ĭatalysis is achieved by one of two mechanisms: Proteases are involved in digesting long protein chains into shorter fragments by splitting the peptide bonds that link amino acid residues. Basic proteases (or alkaline proteases)Įnzymatic function and mechanism.Here, it is released by mast cells and causes activation of complement and kinins. Neutral proteases involved in type 1 hypersensitivity.Classification based on optimal pH Īlternatively, proteases may be classified by the optimal pH in which they are active: trypsin, elastase, thrombin and streptogrisin within the S1 family).Ĭurrently more than 50 clans are known, each indicating an independent evolutionary origin of proteolysis. Each family may contain many hundreds of related proteases (e.g. the S1 and C3 families within the PA clan). Within each 'clan', proteases are classified into families based on sequence similarity (e.g. the PA clan where P indicates a mixture of nucleophile families). In this database, proteases are classified firstly by 'clan' ( superfamily) based on structure, mechanism and catalytic residue order (e.g. Evolutionary phylogeny Īn up-to-date classification of protease evolutionary superfamilies is found in the MEROPS database. Given its fundamentally different mechanism, its inclusion as a peptidase may be debatable. During this reaction, the catalytic asparagine forms a cyclic chemical structure that cleaves itself at asparagine residues in proteins under the right conditions. Its proteolytic mechanism is unusual since, rather than hydrolysis, it performs an elimination reaction. This is not an evolutionary grouping, however, as the nucleophile types have evolved convergently in different superfamilies, and some superfamilies show divergent evolution to multiple different nucleophiles.Ī seventh catalytic type of proteolytic enzymes, asparagine peptide lyase, was described in 2011. One way to make a nucleophile is by a catalytic triad, where a histidine residue is used to activate serine, cysteine, or threonine as a nucleophile. The mechanism used to cleave a peptide bond involves making an amino acid residue that has the cysteine and threonine (proteases) or a water molecule ( aspartic acid, metallo- and acid proteases) nucleophilic so that it can attack the peptide carboxyl group. The threonine and glutamic-acid proteases were not described until 19 respectively. Proteases were first grouped into 84 families according to their evolutionary relationship in 1993, and classified under four catalytic types: serine, cysteine, aspartic, and metallo proteases. Asparagine peptide lyases - using an asparagine to perform an elimination reaction (not requiring water).Metalloproteases - using a metal, usually zinc.Glutamic proteases - using a glutamate carboxylic acid.Aspartic proteases - using an aspartate carboxylic acid.Threonine proteases - using a threonine secondary alcohol.Cysteine proteases - using a cysteine thiol.Serine proteases - using a serine alcohol.Proteases can be classified into seven broad groups: Hierarchy of proteases Based on catalytic residue
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