Enzyme Commission system

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

The first Enzyme Commission, in its 1961 report, devised a system for classification of enzymes that also serves as a basis for assigning code numbers to them. Every enzyme has got a 4-digit number EC A.B.C.D. where EC stands for Enzyme Commission with the following properties encoded ... 

EC - Enzyme Commission number system W - indicates the reaction catalysed (1—6)... 

More than 2000 different enzymes are currently known. A system of classification has been developed that takes into account both their reaction specificity and their substrate specificity. Each enzyme is entered in the Enzyme Catalogue with a four-digit Enzyme Commission number (EC number). The first digit indicates membership of one of the six major classes. The next two indicate subclasses and subsubclasses. The last digit indicates where the enzyme belongs in the subsubclass. For example, lactate dehydrogenase (see pp. 98-101) has the EC number 1.1.1.27 (class 1, oxidoreductases subclass 1.1, CH-OH group as electron donor sub-subclass 1.1.1, NAD(P) " as electron acceptor). 

In this section, enzymes in the EC 2.4. class are presented that catalyze valuable and interesting reactions in the field of polymer chemistry. The Enzyme Commission (EC) classification scheme organizes enzymes according to their biochemical function in living systems. Enzymes can, however, also catalyze the reverse reaction, which is very often used in biocatalytic synthesis. Therefore, newer classification systems were developed based on the three-dimensional structure and function of the enzyme, the property of the enzyme, the biotransformation the enzyme catalyzes etc. [88-93]. The Carbohydrate-Active enZYmes Database (CAZy), which is currently the best database/classification system for carbohydrate-active enzymes uses an amino-acid-sequence-based classification and would classify some of the enzymes presented in the following as hydrolases rather than transferases (e.g. branching enzyme, sucrases, and amylomaltase) [91]. Nevertheless, we present these enzymes here because they are transferases according to the EC classification. 

Many categorization systems exist for enzymes, and the most commonly encountered method is international Enzyme Commission (EC) numbers (Table 4.2). The first number defines the main type of reaction and ranges from one to six. The later numbers further... 

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. 

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. 

According to the Enzyme Commission (EC) system, enzymes are classified according to their function and substrates. The code numbers contain four elements, with the first number indicating one of six main divisions (classes) and the following numbers indicating subclasses. The six main divisions are ... 

Enzyme activity is expressed in units of activity. The Enzyme Commission of the International Union of Biochemistry recommends to express it in international units (lU), defining 1 lU as the amount of an enzyme that catalyzes the transformation of 1 pmol of substrate per minute under standard conditions of temperature, optimal pH, and optimal substrate concentration (International Union of Biochemistry). Later on, in 1972, the Commission on Biochemical Nomenclature recommended that, in order to adhere to SI units, reaction rates should be expressed in moles per second and the katal was proposed as the new unit of enzyme activity, defining it as the catalytic activity that will raise the rate of reaction by 1 mol/second in a specified assay system (Anonymous 1979). This latter definition, although recommended, has some practical drawbacks. The magnitude of the katal is so big that usual enzyme activities expressed in katals are extremely small numbers that are hard to appreciate the definition, on the other hand, is rather vague with respect to the conditions in which the assay should be performed. In practice, even though in some journals the use of the katal is mandatory, there is reluctance to use it and the former lU is still more widely used. 

The large number of enzymes now known has made it desirable to adopt a systematic nomenclature system known as the Enzyme Commission (EC) system. Enzymes are grouped into six major classes on the basis of the reaction catalyzed (see I Table 10.1). 

Table 4.1 The Enzyme Commission s system of classification of enzymes and assigning code numbers (Palmer, 2001)...

Though various methods for the determination of enzyme activity are used routinely in clinical laboratories, many of them are covered by patents, and the components of their test kits are not commercially available. In clinical chemistry, reference methods and certified enzyme reference materials (enzyme calibrators) for determination of activities of enzymes in human blood serum are recommended by international commissions (ISOTC/212, International Federation of Clinical Chemistry IFCC, Institute for Reference Materials and Measurements EU, etc.) at present for improved accuracy and establishment of traceability chains of the enzyme measurement system. By using these reference materials, the inaccuracy (imprecision between laboratories) has been minimized to within several per cent in several enzymes, such as lactate dehydrogenase (LDH) (EC 1.1.1.27), y-glutamyltrans-peptidase (y-GT) (EC 2.3.2.2), alanine aminotransferase (ALT) (EC 2.6.1.2), creatine kinase (CK) (EC 2.7.3.2), alkaline phosphatase (ALP) (EC 3.1.3.1), acid phosphatase (EC 3.1.3.2), and a-amylase (AMY)... 

When making use of the chapter on enzymes, readers must take into account the fact that, whereas the Enzyme Commission numbering system suggests that there is only one enzyme per number, it is becoming increasingly realized that there are many variants of each enzyme. Such a situation will only be fully clarified when full structural and substrate specificity data are available. 

Enzymes are conunonly classified, via a system of Enzyme Commission (EC) numbers, into six divisions oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases (34). In this work, we are concerned with three types of polymer reactions polymer syntheses, polymer modifications, and polymer degradation and hydrolyses. For these reactions, only hydrolases, oxidoreductases, and transferases are being used extensively in polymers and biomaterials. A summary is given in Table 1. 

Tissue was homogenised with an equal volume of buffer (2 ml Tris-HCl (pH 8.0), 0.1 ml mercaptoethanol, 10 g sucrose, and 25 mg NADP per 100 ml H2O - adjusted to pH 7.2 with HCl). Electrophoresis was performed on cellulose acetate plates (Titan III Helena Laboratories). A preliminary survey of 42 enzymes detected four enzyme loci, coding for four different enzyme systems that were polymorphic and consistently resolvable. These enzymes were used for the analysis and were as follows (abbreviation and enzyme commission number in parentheses) hexokinase (HK, E.C. 2.7.1.1), mannose-6-phosphate isomerase (MPI, E.C. 5.3.1.8), 6-phosphogluconate dehydrogenase (6PGD, E.C. 1.1.1.44), and phosphoglucose isomerase (PGI, E.C. 5.3.1.9). 

A comprehensive list of all annotated transport proteins is freely available online on the TCDB website (http //www.tcdb.org). This Transporter Classification Database uses an International Union of Biochemistry and Molecular Biology (lUBMB) approved system of nomenclature for transport protein classification. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information (Saier et al., 2006 Saier et al., 2009). 

By the late 1950s, enzyme nomenclature was in confusion. Without any guiding authority, the increase in known enzymes had led to the assignment of misleading or inappropriate names, and in many cases the same enzyme became known by several names while some catalytically different enzymes were identically named. In 1961, the first Enzyme Commission reported a system for enzyme classification and the assignment of code numbers. 

Another field in which nomenclature has grown up haphazardly is that of the enzymes of lipid metabolism. This has now been formalized to some extent under the Enzyme Commission (EC) nomenclature. The system is incomplete and not all lipid enzymes have EC names and numbers. Moreover, the system is very cumbersome for routine use and we have decided not to use it here. You will find a reference to this nomenclature in the reading list should you wish to learn about it. Enzymes that catalyse the biosynthesis of certain molecules are sometimes called synthetases or alternatively synthases. We shall standardize on the term synthetase in this book. 

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. 

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