Enzyme systematic classification

Systematic Classification of Enzymes According to the Enzyme Commission ... 

Classification of Enzymes. A systematic classification and nomenclature has been established by the Commission on Enzymes of the International Union of Biochemistry (6), which divides enzymes into six general groups ... 

In addition, at each step the four-figure EC number (see p. 88) for the enzyme responsible for a reaction is given in italics. The enzyme name and its systematic classification in the system used by the Enzyme Catalogue are available in the following annotated enzyme list (pp. 420-430), in which all of the enzymes mentioned in this book are listed according to their EC number. The book s index is helpful when looking for a specific enzyme in the text. 

Table 2.1 Partial Outline of the Systematic Classification of Enzymes...

All enzymes are named according to a classification system designed by the Enzyme Commission (EC) of the International Union of Pure and Applied Chemistry (IUPAC) and based on the type of reaction they catalyze. Each enzyme type has a specific, four-integer EC number and a complex, but unambiguous, name that obviates confusion about enzymes catalyzing similar but not identical reactions. In practice, many enzymes are known by a common name, which is usually derived from the name of its principal, specific reactant, with the suffix -ase added. Some common names do not even have -ase appended, but these tend to be enzymes studied and named before systematic classification of enzymes was undertaken. 

The International Union of Biochemistry (lUB) established a commission on enzyme nomenclature to adopt a systematic classification and nomenclature of all the existing and yet to be discovered enzymes. This system is based on the substrate and reaction specificity. Although, this International Union of Biochemistry system is complex, it is precise, descriptive and informative. 

Enzyme names. Most enzyme names end in ase. Enzymes usually have both a common name and a systematic classification that includes a name and an Enzyme Commission (EC) number. 

The Nomenclature Commitee of the International Union of Biochemistry and Molecular Biology (lUBMB) adopted rules last amended in 1992 for the systematic classification and designation of enzymes based on reaction specificity. All enzymes are classified into six major classes according to the nature of the chemical reaction catalyzed ... 

Table 2.4. Systematic classification of some enzymes of importance to food chemistry...

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. 

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. 

The International Union of Biochemistry has recommended that enzymes have three names, namely a systematic name, which shows the reaction being catalysed and the type of reaction based on the classification in Table A7.1, a recommended trivial name and a four figure Enzyme Commission code (EC code). Nearly all systematic and trivial enzyme names have the suffix -ase. Systematic names show, often in semi-chemical equation form, the conversion the enzyme promotes and the class of the enzyme. Trivial names are usually based on the function of the enzyme but may also include or be based on the name of the substrate. However, some trivial names in current use are historical and bear no relationship to the action of the enzyme or its substrate, for example, pepsin and trypsin are the names commonly used for two enzymes that catalyse the breakdown of proteins during digestion. The Enzyme Commission s code is unique for each enzyme. It is based on the classification in Table A7.1 but further subdivides each class of enzyme according to how it functions. The full code is... 

In the second place, the enzyme can make distinctions between isomers. In fact, nowhere is the selection ability of enzymes so manifest as in the ability to distinguish between isomeric structures. The various possibilities for a given number of atoms may be examined systematically. Thus, we can imagine the enzyme confronted with two materially identical molecules, making yes/no decisions in accordance with a defined classification chart. The enzyme asks Can the two molecules be superposed Arrows from the left sides of the diamonds indicate a yes answer from the right sides the arrows represent no (see Scheme 1). The possibility of superposition is... 

Again each class is divided into subclasses according to the type of reaction catalysed. Each enzyme is assigned a recommended name usually a short one for everyday use, a systematic name which identify the reaction it catalyses and a classification number which is used where accurate and unambiguous identification of an enzyme is required (Table 6.1). 

A-17 According to lUB system enz)mies are grouped in six major classes. Each with sub classes based on the t) e of reaction catalyzed. Systemic classification of enzymes based on numbering system is used. Each enzyme is assigned a code number or EC (enzyme commission number) four-digit classification number and a systematic name, which identifies the reaction catalyzed. 

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 ... 

In the early days of biochemistry, enzymes were named at the whim of their discoverers. Often enzyme names provided no clue to their function (e.g., trypsin), or several names were used for the same enzyme. Enzymes were often named by adding the suffix -ase to the name of the substrate. For example, urease catalyzes the hydrolysis of urea. To eliminate confusion, the International Union of Biochemistry (IUB) instituted a systematic naming scheme for enzymes. Each enzyme is now classified and named according to the type of chemical reaction it catalyzes. In this scheme an enzyme is assigned a four-number classification and a two-part name called a systematic name. In addition, a shorter version of... 

The ENZYME database1501, maintained by the Swiss Institute for Bioinformatics (SIB), provides a comprehensive list of all IUBMB classifications, together with associated information such as systematic and alternative enzyme names, cofactor requirements, and pointers to the corresponding entry in the SWISS-PROT database of protein sequences1511. In addition, there is a concise free-text description of the reaction catalyzed, together with a description of preferential substrates and products. Currently, the ENZYME database holds entries for approximately 3700 enzymes. 

A much more ambitious database that builds on the IUBMB classification is BRENDA, maintained by the Institute of Biochemistry at the University of Cologne. In addition to the data provided by the ENZYME database, the BRENDA curators have extracted a large body of information from the enzyme literature and incorporated it into the database. The database format strives to be readable by both humans and machines. The categories of data stored in BRENDA comprise the EC-number, systematic and recommended names, synonyms, CAS-registry numbers, the reaction catalyzed, a list of known substrates and products, the natural substrates, specific activities, KM values, pH and temperature optima, cofactor and ion requirements, inhibitors, sources, localization, purification schemes, molecular weight, subunit structure, posttranslational modifications, enzyme stability, database links, and last but not least an extensive bibliography. Currently, BRENDA holds entries for approximately 3500 different enzymes. 

A large number of different enzymes has been described. Their nomenclature has been rather haphazard, although many enzymes are named by placing -ase after their substrate others are called product synthetase. Enzymes that transfer phosphate from ATP to a substrate are called substrate kinase. An international enzyme commission (EC) has developed a classification number, a systematic name, and a recommended name. Recommended names are widely used, but the EC numbers and systematic names are increasingly used to avoid confusion, often in a footnote. 

It is noteworthy that almost all fermentation reactions refer to the doublet and triplet types and systematic consideration shows that a classification widely known in enzymic chemistrj (357) coincides with the classification made according to the indexes of the multiplet theory (see Table X). This circumstance, as well as the fact that enzymes are colloidal, i.e., heteorogeneous catalysts, permits an attempt at application of the multiplet theory to them, namely, its principles of structural and energetic correspondence. The reactions carried on by chemical enzymic models also fit into the doublet classification (35S, 359). 

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