Nomenclature of enzymes

Some enzymes were named in the early days of the study of enzymes and have non-systematic names for example, the digestive enzymes pepsin, trypsin and ptyalin. 

Reaction Recommended name Systematic name Code number 

Hydrolysis of terminal non-reducing 1,4-Unked alpha-D-glucose residues of alpha glucose (e.g. maltose to glucose) Alpha-glucosidase Alpha-D-glucoside glucohydrolase 3.2.1.20 

Enzymes are organic cataiysts. They are ciassi-fied into six major groups according to the functions they perform  

The majority of enzymes are based on complex high-molecular-weight proteins, many of which need organic cofactors (coenzymes) if they are to work efficiently. Others need metallic cofactors, either bound to the enzyme by covalent bonds or forming an integral part of the molecule. Others do not bind to the molecule but bind to the primary substrate. 

Originally enzymes were given nondescriptive names such as rennin curding of milk to start cheese-making processcr pepsin hydrolyzes proteins at acidic pH trypsin hydrolyzes proteins at mild alkaline pH 

The nomenclature was later improved by adding the suffix -ase to the name of the substrate with which the enzyme functions, or to the reaction that is catalyzed.myfootnote1 For example  

According to the first report of the Enzyme Commission from 1961, all enzymes are classified in six enzyme classes, depending on the reaction being catalyzed. Within the scheme of identification, each enzyme has a number ( E.C. stands for 

The number of known enzymes has risen significantly, from 712 in the first edition of Enzyme Nomenclature of 1961 through 2477 in 1984 to 3196 in 1992, the year of the third edition. It is important to note that this classification scheme does not organize enzymes according to amino acid sequence or type of three-dimensional structure, and in principle not even according to chemical mechanism. 

The question is often posed of whether biocatalysts operate by different scientific principles from organic catalysts. Careful analysis reveals that they do not (Knowles, 1991 Menger, 1993). Enzymes are not different, just better (Knowles, 1991). The multitude of enzyme models including oligopeptidic or polypeptidic catalysts (Chapter 18) proves that all enzyme action can be explained by rational chemical and physical principles. However, enzymes can create unusual and superior reaction conditions, such as extremely low pKa values for a lysine residue (Westheimer, 1995) or a high positive potential for a redox metal ion (Wittung-Stafshede, 1998). 

Enzymes increasingly have been found to catalyze almost any reaction of organic chemistry. Table 1.4 provides examples for a series of reactions. 

The principles of how and why enzymes work are discussed in the next chapter. 

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A system based partly on historical names, partly on the substrate, and partly on the type of reaction catalyzed is far from satisfactory. In 1956, the International Union of Biochemistry set up a Commission on Enzymes to consider the classification and nomenclature of enzymes. The Commission presented a report in 1961 whose recommendations for naming and classifying enzymes were subsequently adopted (12). Enzymes are classified on the basis of the reactions they catalyze. Despite its apparent complexities, the system is precise and very descriptive, accommodating existing enzymes and serving as a systematic basis for the naming of new enzymes. AH enzymes are placed in one of the six principal classes. 

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. 

Let us consider an enzymatic reaction in which two substrates are utilized to from two products (in the nomenclature of enzyme reaction mechanisms this situation is referred to as a bi-bi mechanism). A reaction in which one substrate yields two products is referred to as a uni-bi mechanism, and one in which two substrates combine to form a single product is referred to as a bi-uni mechanism (see Copeland, 2000, for further details). For the purposes of illustration let us use the example of a group transfer reaction, in which a chemical species, X, is transferred from one substrate to the other in forming the products of the reaction ... 

In accordance with the recommendation of the Commission of the International Union of Biochemistry [R. H. S. Thompson, Classification and nomenclature of enzymes and coenzymes, Nature 193, 1227 (1902)] the terms NAD and NADP have been used instead of DPN and TPN, except in Fig. 4. The generic term nicotinamide nucleotides is used with the same significance as pyridine nucleotides. 

As will be seen below, the nomenclature of enzymes acting on pectic substances is even less satisfactory. 

Enzymes are usually named with reference to the reaction they catalyze. It is customary to add the suffix -ase to the name of its major substrate. The Enzyme Commission (EC) has recommended nomenclature of enzymes based on the six major types of enzyme-catalyzed reactions (http //www.chem.qmw.ac.uk/iubmb/ enzyme/) ... 

This is a repository relative to the nomenclature of enzymes. It accepts EC numbers. It provides connections with BRENDA, EMR, KEGG, IUBMB, and BioCarti. 

Nitriles, a-amino, mutarotation of, 13 Nitrogen compounds, of cyclic monosaccharides, 115 — 232 Nojirimycin, 116,132,133 Nomenclature, of enzymes, 306 Nuclear magnetic resonance anomer determination by, 43 characterization of anhydrodeoxyaldi-tolsby, 74,77,79... 

Preliminary consultations must be on a broad scale, so that the commission may account for all existing tendencies. Nomenclature of enzymes is an example of this preparatory survey. At Lucerne in 1936 (8), the commission drew up a preliminary report which was submitted to almost all recognized enzymologists. Although this work was interrupted by the war, the following details were obtained from the records of the commission. 

In 1936, the commission started to elaborate the precise terms for the nomenclature of enzymes. World War II prevented the commission from finishing its work. A great number of answers received by the commission have been compiled by its former secretary, Ren6 Fabre, who kindly put his files at the author s disposal. 

The recommendations (1978) of the Nomenclature Committee of the International Union of Biochemistry on the nomenclature of enzymes has been published. This publication is a revision of the 1972 Recommendations of the International Union of Pure and Applied Chemistry and the International Union... 

Fig. 2. Prechorismate portion of the shikimic acid pathway involved in the synthesis of aromatic amino acid precursors. Nomenclature of enzymes and substrates are described in Table I and cross-referenced to each numbered reaction.

The nomenclature of reciprocal plots in the foregoing chapters on enzyme inhibition is based on the usual (or common) nomenclature of enzyme inhibitors. Thus, the term competitive describes the systems yielding reciprocal plots that... 

Biochemical nomenclature of enzymes [28] usually follotvs historical classifications that are different from the needs of synthetic organic chemists today. Whereas the common EC numbers are valuable for reference, in this overview an enzyme designation w ill be used that utilizes a three-letter code as reference to the natural substrate (from w hich usually stereochemistry is immediately obvious), follow ed by a single capital letter that indicates the conversion type (e.g., aldolases (A), synthases (S), isomerases (I), dehydrogenases (D), oxidases (O), kinases (K), (glycosyl)transferases (T), epimerases (E)etc.) [25]. 

Accordii to the International Classification and Nomenclature of enzymes adopted by the Commission of the International Biochemical Union, with the participation of Soviet biochemists, in the abbreviation of the English name of these enzymes and its Russian translation, transfer RNA is given with the symbol (sRNA) from soluble RNA, and not with the symbol t, frequently used in scientific papers. In future, therefore, we shall use the abbreviation sRNA. 

Hoffmannd)stenhof, O., Suggestions for a More Rational Classification and Nomenclature of Enzymes. XIV 219... 

Until very recently the naming of the individual enzymes has been entrusted largely to the discoverers. This resulted often in such descriptive names as zwisch-enferment or pH 5 enzyme. An international commission meanwhile has drafted specific rules for the classification and nomenclature of enzymes. The commission has established six main classes, which are further subdivided into sub-classes and sub-sub-classes, according to the nature of the reaction catalyzed and to the type of bond formed or severed. In Table IX several examples of each main class are listed to illustrate the system. 

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