Enzyme nomenclatures

The systematic name of an enzyme consists of two parts, the first originating from the equation, the second from the type of reaction catalyzed. In addition, according to the recommendations of the International Union of Pure and Applied Chemistry and the International Union of Biochemistry (1973), each enzyme bears a number from the international EC (Enzyme Classification) system, which reflects the main class, the subclass, and the subgroup. The number is completed by a special enzyme number. Thus, for example the EC number 1.1.3.4 of the enzyme with the trivial name glucose oxidase results from the following  

For practical reasons, the trivial name is usually used. 

This section begins with a discussion of enzyme nomenclature and is followed with discussions of enzymes as proteins and catalysts. 

Historically, individual enzymes were identified using the name of the substrate or group upon which the enzyme acts and then adding the suffix -ase. For example, the enzyme hydrolyzing urea was urease. Later, the type of reaction involved was also identified, as in carbonic anhydrase, D-amino acid oxidase, and succinate dehydrogenase. In addition, some enzymes had been given empirical names such as trypsin, diastase, ptyalin, pepsin, and emulsin. 

Because this combination of trivial common names and semisystematic names was found to be inadequate, the International Union of Biochemistry (lUB) appointed an Enzyme 

Commission (EC) in 1955 to study the problem of enzyme nomenclature. Its subsequent recommendations, with periodic updating, provide a rational and practical basis for identifying all enzymes now known and enzymes that wfil be discovered in the future (http //www.chem.qmw.ac.uk/ iubmb/enzyme/) 

To illustrate how this system is used to name an enzyme, consider the enzyme creatine kinase that catalyzes the reaction  

The prosthetic group accepts electrons from the substrate species to generate reduced flavin from the oxidized form in the active site the primary product diffuses away from the active site, and a secondary substrate, an electron acceptor such as molecular oxygen, then regenerates the oxidized form of the flavin in the active site to complete the catalytic cycle. This is represented by Eqs. 2.3-2.5  

This cycle is typical of many enzymatic reactions, in that the initial substrate conversion is followed by an enzyme regeneration step. 

Enzyme names apply to a single catalytic entity, rather than to a series of individually catalyzed reactions. Names are related to the function of the enzyme, in particular, to the type of reaction catalyzed. This convention implies that one name may, in fact, designate a family of enzymes that are slightly different from each other yet still catalyze the same reaction. For example, lactate dehydrogenase (LDH) has five such isoenzymes in humans. LDH catalyzes the oxidation of L-lactic acid by 

While each of the five LDH isoenzymes catalyzes the conversion of lactic acid to pyruvic acid, the isoenzymes are produced in different organs. Because of this, the polypeptide moieties and the rates at which lactate can be converted to pyruvate are slightly different for each isoenzyme. Similarly, different species often possess identical metabolic pathways, and have equivalent but slightly different enzymes that catalyze identical reactions. The differences that occur within such a family of enzymes usually occur in noncritical regions of the polypeptide moiety, by the substitution of one amino acid residue for another, or by the deletion of amino acid residues. 

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Enzymes are classified in terms of the reactions which they catalyse and were formerly named by adding the suffix ase to the substrate or to the process of the reaction. In order to clarify the confusing nomenclature a system has been developed by the International Union of Biochemistry and the International Union of Pure and Applied Chemistry (see Enzyme Nomenclature , Elsevier, 1973). The enzymes are classified into divisions based on the type of reaction catalysed and the particular substrate. The suffix ase is retained and recommended trivial names and systematic names for classification are usually given when quoting a particular enzyme. Any one particular enzyme has a specific code number based upon the new classification. 

Enzyme Nomenclature. The number of enzymes known exceeds two thousand. A system of classification and nomenclature is required to identify them unambiguously. During the nineteenth century, it was the practice to identify enzymes by adding the suffix -in to the name of their source. Names such as papain, ftcin, trypsin, pepsin, etc, are still in use. However, this system does not give any indication of the nature of the reaction catalyzed by the enzyme or the type of substrate involved. 

International Union of Biochemistry and Molecular Biology Nomenclature Committee, 1992. Enzyme Nomenclature. New York Academic Press. A reference volume and glossary on die official classification and nomenclature of enzymes. 

An exopeptidase that sequentially releases an amino from the C-terminus of a protein or peptide. Carbox-ypeptidases are classified in Enzyme Nomenclature according to catalytic type and are included in subsubclasses 3.4.16-3.4.18. 

An exopeptidase that can only degrade a dipeptide. Examples are carnosine dipeptidase I (MEROPS M20.006), which degrades carnosine (beta-Ala-His), and membrane dipeptidase (MEROPS Ml9.001), which is important in the catabolism of glutathione, degrading the dipeptides Cys-Gly. Dipeptidases are included in Enzyme Nomenclature sub-subclass 3.4.13. 

An exopeptidase that sequentially releases a dipeptide from the N-terminus of a protein or peptide. Dipeptidy 1-peptidases are included in Enzyme Nomenclature subsubclass 3.4.14 along with tripeptidyl-peptidases. 

Peptidases are enzymes that catalyse the hydrolysis of peptide bonds - the bonds between amino acids that are found in peptides and proteins. The terms protease , proteinase and proteolytic enzyme are synonymous, but strictly speaking can only be applied to peptidases that hydrolase bonds in proteins. Because there are many peptidases that act only on peptides, the term peptidase is recommended. Peptidases are included in subclass 3.4 of enzyme nomenclature [1,5]. 

An exopeptidase that does not cleave standard peptide bonds. An example is pyroglutamyl-peptidase I (MEROPS C15.010), which releases an N-terminal pyroglutamyl from hormones such as thyrotropinreleasing hormone and luteinizing hormone. Omega peptidases are included in Enzyme Nomenclature subsubclass 3.4.19. 

S. Aiba, A. E. Humphrey u. N.F. Millis, Biochemical Engineering, 2. Aufl., Academic Press, New York 1973. Enzyme Nomenclature. Recommendations (1972) of the International Union of Pure and Applied Chemistry and... 

Note. In Enzyme Nomenclature [23] dehydro names are used in the context of enzymic reactions. The substrate is regarded as the parent compound, but the name of the product is chosen according to the priority given in 2-Carb-2.2. 

IUB Nomenclature Committee, Enzyme Nomenclature , Academic Press, Orlando, Florida (1992). 

International Union of Biochemistry Enzyme Nomenclature. Elsevier, Amsterdam. 1965, p.7. 

M Florkin, EH Stotz, eds. Enzyme Nomenclature. New York Elsevier, 1972. 

The responsibility for enzyme nomenclature is supported by the Nomenclature Committee of the International Union of Biochemistry (IUB now the International Union of Biochemistry and Molecular Biology, IUBMB) and the International Union of Pure and Applied Chemistry (IUPAC). These committees collect information about changes and additions to enzyme nomenclature13"15. 

According to the IUPAC-IUB Enzyme Nomenclature,11 pectinesterase belongs to the carboxyl ester hydrolases (EC 3.1.1.11) and has the systematic name pectin pectyl-hydrolase. The literature also contains the expressions pectin methylesterase, pectin demethoxylase, and pectin methoxylase for the same enzyme. The old name pectase,... 

All enzymes already mentioned, except oligo-D-galactosiduronate hydrolase, are included in the Enzyme Nomenclature of the IUPAC-IUB Enzyme Commission,11 and their code numbers and suitably modified, systematic names are used herein. 

Enzyme modification, performance improvement, 3 671 Enzyme multiplied immunological technique (EMIT), 12 97 Enzyme Nomenclature, 17 402 Enzyme-product (EP) complex, 10 318 Enzyme production, Bacillus and, 12 477 Enzymes. See also Restriction enzymes Enzymes, 5 201... 

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/. 

The classification system of the Enzyme Nomenclature Committee divides esterases into classes according to the type of ester bond they cleave (Table 2.4 see also Sect. 2.2.1) [1], The enzymes within these classes are further divided according to the nature of their preferred substrate(s). 

A selection of carboxylic ester hydrolases (EC 3.1.1) of major or more-modest significance in xenobiotic metabolism is given in Table 2.5. The recommendations of the Enzyme Nomenclature Committee on the classification of esterases cannot be considered completely satisfactory, but, even after decades of debate, a more satisfactory classification system remains to be proposed [56] [57], The main difficulties with esterase classification have been summarized as follows [58],... 

First, the true physiological substrates of most esterases are unknown. It is, therefore, hardly practicable to systematically name esterases according to the recommendations of the Enzyme Nomenclature Committee [1], i.e., based on the definite (physiological) role of the enzyme. The difficulty is that the use of nonphysiological substrates during purification and in characterization assays does not contribute to discovering the physiological role of an enzyme. 

NAD(P)+ as Anode Mediator. A majority of redox enzymes require the cation nicotinamide adenine dinucleotide, possibly phosphorylated (NAD(P)+) as a cofactor. Of the oxidoreductases listed in Enzyme Nomenclature, over 60% have NAD(P)+ as a reactant or product.For example, methanol can be oxidized to form formaldehyde by methanol dehydrogenase (MDH, EC 1.1.1.244) according to... 

Table 3.1 Major classes in the Enzyme Commission system for enzyme nomenclature...

Enzyme Nomenclature, International Union of Biochemistry, Academic Press, 1982. 

Only the enzymes mentioned in this atlas are listed here, from among the more than 2000 enzymes known. The enzyme names are based on the iUBlVlB s of dal Enzyme nomenclature 1992. The additions shown in round brackets belong to the enzyme name, while prosthetic groups and other cofactors are enclosed in square brackets. Common names of enzyme groups are given in italics, and trivial names are shown in quotation marks. 

Webb EC, editor. Enzyme nomenclature 1992. San Diego International Union of Biochemistry and Molecular Biology/Academic Press, 1992. 

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