Peptidase classification

Page MJ, Di Cera E. Serine peptidases classification, structure and function. Cell. Mol. Life Sci. In press. 

Table 12.5-1. Principles of peptidase classification according to the Enzyme Commission (E.C.) of the International Union of Biochemistry and Molecular Biology 16 ...

Peptidase classification. Mechanism of catalysis catalytic site reaction catalyzed cleavage site and molecular structure and homology amino acid sequences and three-dimensional structures... 

Peptidases have been classified by the MEROPS system since 1993 [2], which has been available viatheMEROPS database since 1996 [3]. The classification is based on sequence and structural similarities. Because peptidases are often multidomain proteins, only the domain directly involved in catalysis, and which beais the active site residues, is used in comparisons. This domain is known as the peptidase unit. Peptidases with statistically significant peptidase unit sequence similarities are included in the same family. To date 186 families of peptidase have been detected. Examples from 86 of these families are known in humans. A family is named from a letter representing the catalytic type ( A for aspartic, G for glutamic, M for metallo, C for cysteine, S for serine and T for threonine) plus a number. Examples of family names are shown in Table 1. There are 53 families of metallopeptidases (24 in human), 14 of aspartic peptidases (three of which are found in human), 62 of cysteine peptidases (19 in human), 42 of serine peptidases (17 in human), four of threonine peptidases (three in human), one of ghitamicpeptidases and nine families for which the catalytic type is unknown (one in human). It should be noted that within a family not all of the members will be peptidases. Usually non-peptidase homologues are a minority and can be easily detected because not all of the active site residues are conserved. 

Merops (http //merops.sanger.ac.uk), database of peptidases and their proteinaceous inhibitors. Includes enzyme classification and nomenclature, external links to literature, and the structure of proteins of interest (if known). Enables one to find the gene coding for a given peptidase or to find the best enzyme to digest a chosen substrate. 

Enzymes that act on peptide bonds (i.e., peptidases and proteases) hydrolyze peptide bonds in peptides and proteins. We examine first their classification before outlining their localizations and some physiological roles. 

The classification adopted by the Nomenclature Committee (NC) of the International Union of Biochemistry and Molecular Biology (IUBMB) divides peptidases into classes and subclasses according to the positional specificity in the cleavage of the peptide link of the substrate. The last publication of the complete printed version of the Enzyme Nomenclature was in 1992 [1][2], but a constantly updated version with supplements is available on the World Wide Web at http //www.chem.qmul.ac.uk/iubmb/enzyme/. Similarly, all available Protein Data Bank (PDB) entries classified as recommended by the NC-IUBMB can be found on the WWW at http //www.bio-chem.ucl.ac.uk/bsm/enzymes/. 

Fig. 2.1. Classification of peptidases according to the site along the polypeptide chain cleaved...

One of the general principles of the Nomenclature Committee is that enzymes should be classified and named according to the reaction they catalyze. However, the overlapping specificities of and great similarities in the action of different peptidases render naming solely on the basis of function impossible [10]. For example, some enzymes can act as both endo- and exopeptidases. Thus, cathepsin H (EC 3.4.22.16) is not only an endopeptidase but also acts as an aminopeptidase (EC 3.4.11), and cathepsin B (EC 3.4.22.1) acts as an endopeptidase as well as a peptidyl-dipeptidase (EC 3.4.15). The actual classification of peptidases is, therefore, a compromise based not only on the reaction catalyzed but also on the chemical nature of the catalytic site, on physiological function, and on historical priority. 

The peptidases were separated into catalytic types according to the chemical nature of the group responsible for catalysis. The major catalytic types are, thus, Serine (and the related Threonine), Cysteine, Aspartic, Metallo, and As-Yet-Unclassified. An in-depth presentation of catalytic sites and mechanisms, based on this classification, is the subject of Chapt. 3. 

Thus, more than 500 peptidases are listed in the Handbook of Proteolytic Enzymes [7a], this classification being summarized in part in Table 2.1. 

The evolutionary classification has a rational basis, since, to date, the catalytic mechanisms for most peptidases have been established, and the elucidation of their amino acid sequences is progressing rapidly. This classification has the major advantage of fitting well with the catalytic types, but allows no prediction about the types of reaction being catalyzed. For example, some families contain endo- and exopeptidases, e.g., SB-S8, SC-S9 and CA-Cl. Other families exhibit a single type of specificity, e.g., all families in clan MB are endopeptidases, family MC-M14 is almost exclusively composed of carboxypeptidases, and family MF-M17 is composed of aminopeptidases. Furthermore, the same enzyme specificity can sometimes be found in more than one family, e.g., D-Ala-D-Ala carboxypeptidases are found in four different families (SE-S11, SE-S12, SE-S13, and MD-M15). 

The previous chapter offered a broad overview of peptidases and esterases in terms of their classification, localization, and some physiological roles. Mention was made of the classification of hydrolases based on a characteristic functionality in their catalytic site, namely serine hydrolases, cysteine hydrolases, aspartic hydrolases, and metallopeptidases. What was left for the present chapter, however, is a detailed presentation of their catalytic site and mechanisms. As such, this chapter serves as a logical link between the preceding overview and the following chapters, whose focus is on metabolic reactions. 

Two isoenzymes, peptidase A and glutathione reductase, have been reported to have polymorphic forms in negro populations and little or no variants in Caucasians (13, 14, 15). Thus, should the rare variant be demonstrated in a stain, there would be a high probability concerning the ethnic origin of the blood. In addition, research has been initiated into the use of Gm and Inv typing to assist in the anthropological classification of bloodstains (2, 17). For example, the combination of Gm factors 1,... 

Referring to a mechanistic classification of organocatalysts (Seayad and List 2005), currently the two most prominent classes are Brpnsted acid catalysts and Lewis base catalysts. Within the latter class chiral secondary amines (enamine, iminium, dienamine activation for a short review please refer to List 2006) play an important role and can be considered as—by now—already widely extended mimetics of type I aldolases, whereas acylation catalysts, for example, refer to hydrolases or peptidases (Spivey and McDaid 2007). Thiamine-dependent enzymes, a versatile class of C-C bond forming and destructing biocatalysts (Pohl et al. 2002) with their common catalytically active coenzyme thiamine (vitamin Bi), are understood to be the biomimetic roots ofcar-bene catalysis, a further class of nucleophilic, Lewis base catalysis with increasing importance in the last 5 years. 

In addition to the above mentioned databases that try to cover the entire world of enzymes, there are a number of more topical databases focusing on particular enzyme families. The MEROPS database, maintained at the Babraham Institute in Cambridge, provides a catalog and a structure-based classification scheme for all proteolytic enzymes 58. In addition to the classification, the database also provides a digest of published information on the peptidases as well as dadograms and multiple sequence alignments of the peptidase families. 

Starting with the earlier work of Rawlings and Barret1171 and improved in the handbook141 another level of sophistification to the classification of peptidases has been developed. Evolutionary considerations can be taken into account due to the relative ease by which cDNA-derived sequences can now be obtained. According to this principle of classification a family of peptidases is defined as a group in which... 

Table 12.5-2. Evolutionary classification of peptidases into families and clans based on primary and teriary structure.

The definition of the scope of the specificity of proteolytic enzymes with regard to the chemical configurations in the vicinity of the hydrolyzable peptide bond has necessarily been restricted to their peptidase activity in order that substrates of known chemical structure can be used. The familiar classification of proteinases on the basis of specificity towards peptides as model substrates, ss, 84, 85 meet rigorous testing on those rare... 

Peptidases including keratinases are hydrolases able to hydrolyze peptide bonds in proteins and peptides. They are classified using three different approaches (1) the chemical mechanism of catalysis (based on the catalytic amino acid or metal ion at then-active site, represented by serine, cysteine, threonine, aspartic, asparagine, glutamic and metallocatalytic type), (2) the catalytic reaction (this type of classification depends on the selectivity for the bonds that the peptidases will hydrolyze), and (3) the molecular structure and homology. In this latter approach, amino acid... 

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