Molecular Biology: Protein Structure and Functions - Stepanov V.M. 2005

Enzymes
Enzyme Systematics

Each of the roughly 2–3 thousand metabolic reactions in a Cell is catalyzed by its own specific enzyme; consequently, even without taking species diversity into account, there are at least 2–3 thousand Enzymes. This number increases significantly when considering that Reactions of the same type can be catalyzed by enzymes of different origins, as well as enzymes involved in signal Transduction and processes characteristic of Multicellular Organisms (for example, Blood clotting enzymes). The total number of enzyme types likely approaches ten thousand.

There is currently insufficient data for a strictly rigorous Classification of such a vast number of enzymes. A rational Taxonomy would be one based on evolutionary relationships among enzymes and a profound understanding of their Structural and functional characteristics. This would make it possible to group enzymes that evolved from a common ancestor into taxa of appropriate ranks. Such a classification is currently being developed for certain groups of enzymes, notably proteinases.

However, the Structure/182.html">Practical Application of an evolutionary-based classification requires not only prior study of numerous related enzymes, but also a large body of data regarding the properties and, above all, The structure of the enzyme being classified—something that is difficult to achieve in the Cytology/cytology/16.html">Early stages of research.

Therefore, the officially adopted Enzyme Classification uses substrate Specificity and The Nature of the catalyzed reaction as its primary distinguishing features—precisely those properties that are identified first upon the discovery and isolation of an enzyme. While this approach is practically convenient, one must keep in mind that it can group together enzymes of diverse origin, structure, and even MECHANISM OF ACTION.

The International Enzyme Commission (EC) classification divides enzymes into the following six classes based on the type of reaction they catalyze.

Oxidoreductases. This Class comprises all enzymes catalyzing oxidation-reduction reactions. The substrate undergoing oxidation is considered a hydrogen donor; hence, the term dehydrogenase is frequently applied to enzymes of this class, although this name reflects only one of two possible reaction directions. The term oxidase is used exclusively when O₂ acts as the direct hydrogen acceptor.

Transferases. Enzymes of this class transfer a specific chemical group from one molecule to another. Examples include Kinases—enzymes that transfer a phosphoryl group from ATP to various substrates—and aminotransferases (transaminases), which transfer an amino group from an amino acid to a keto acid.

Hydrolases. These Enzymes can be regarded as transferases that transfer a specific group to a Water molecule. Their classification into a separate group is justified by the extremely widespread occurrence of hydrolases, which are involved, in particular, in the degradation of Biopolymers. Hydrolases are known to catalyze the Hydrolysis of C—O, C—N, C—C, O—P, and various other bonds. Sometimes the same enzyme is capable of hydrolyzing bonds of different natures. For example, certain proteinases that cleave peptide bonds in Proteins can hydrolyze esters with even greater efficiency, thus acting as esterases. The choice of the term proteinase in such cases is based on The Physiological Role of the enzyme and, consequently, the nature of its natural substrate.

Lyases. These include enzymes that cleave C—C, C—O, C—N, and certain other bonds by means of the elimination of a corresponding molecule, accompanied by The formation of a double bond. In the reverse reaction, lyases catalyze The addition of water, ammonia, etc., across a double bond. A case in point is Histidine ammonia-lyase, an enzyme that eliminates ammonia from histidine to yield unsaturated urocanic acid:

Isomerases. This type of enzyme catalyzes geometric or structural rearrangements—isomerizations—within a single molecule. These notably include racemases, tautomerases, and cycloisomerases. Examples include Lysine lactate racemase, which catalyzes the mutual interconversion of the L- and D-isomers of this compound (see Chapter 1), and Triosephosphate isomerase, which catalyzes the interconversion of phosphoglyceraldehyde and dihydroxyacetone phosphate.

Ligases (synthetases). This class comprises enzymes that catalyze the joining of two molecules coupled with the hydrolysis of ATP. They play a pivotal role in biosynthetic processes by utilizing the energy of ATP hydrolysis to drive reactions that would otherwise be thermodynamically unfavorable. Aminoacyl-tRNA synthetases serve as a classic example.

Each of the six listed enzyme classes is further divided (again based on specificity) into subclasses and sub-subclasses, which are assigned sequential numbers in accordance with the International Classification. For example, hydrolases acting on carboxylic ester bonds belong to class 3 (hydrolases), subclass 3.1 (enzymes acting on ester bonds), and sub-subclass 3.1.1 (carboxylic ester hydrolases). A specific enzyme within a sub-subclass is assigned its own serial number; for instance, lipase, which hydrolyzes triacylglycerols, is designated as 3.1.1.3.