BIOCHEMISTRY: A TEXTBOOK FOR UNIVERSITIES - E. S. Severin - 2004

SECTION 2. ENZYMOLOGY

II. Classification and Nomenclature of Enzymes

Each enzyme has two names. The first is a short, so-called working (or trivial) name, convenient for everyday use. The second, more complete name is the systematic name, used for the unambiguous identification of the enzyme.

A. Working Name

The names of most Enzymes contain the suffix "-ase" attached to the name of the reaction substrate—for example, urease, sucrase, lipase, and nuclease—or to the type of chemical Transformation of a specific substrate, such as Lactate dehydrogenase, adenylate cyclase, phosphoglucomutase, and Pyruvate carboxylase. According to the Russian Classification of Enzymes (EC), enzyme names are written as a single compound word. However, usage has preserved A number of trivial, historically established enzyme names that provide no indication of either the substrate or the type of chemical transformation, such as Trypsin, Pepsin, renin, and Thrombin.

B. Enzyme Classes

In 1961, the International Union of Biochemistry and Molecular Biology developed a systematic nomenclature according to which all enzymes are divided into 6 main classes based on the type of chemical reaction catalyzed. Each Class consists of numerous subclasses and sub-subclasses, taking into account the chemical group of the substrate being modified, the donor and acceptor of the transferred groups, the presence of additional molecules, and so forth. Each of the 6 classes has its own strictly assigned serial number.

1. Oxidoreductases

Catalyze various oxidation-reduction reactions involving 2 substrates (transfer of e^- or hydrogen atoms from one substrate to another).

The systematic name of these enzymes is formed according to the formula "donor: acceptor oxidoreductase", and the working name follows the format "substrate oxidoreductase subclass".

Dehydrogenases. This subclass includes enzymes that catalyze dehydrogenation reactions (removal of hydrogen). The Coenzymes NAD⁺, NADP⁺, FAD, and FMN (see below) serve as electron acceptors. All enzymes in this group exhibit high substrate Specificity. Example of a reaction:

Oxidases. Molecular oxygen serves as the electron acceptor. Example of a reaction catalyzed by cytochrome c oxidase:

Oxygenases (hydroxylases) — an oxygen atom from an oxygen molecule is incorporated into the substrate. Example of a reaction:

2. Transferases

Catalyze The transfer of functional groups from one compound to another. They are subdivided according to the group being transferred.

The names of these enzymes are formed according to the formula "donor: acceptor transferred-group transferase". The class of transferases includes aminotransferases, Acyltransferases, methyltransferases, Glycosyltransferases, and Kinases (phosphotransferases). Examples of reactions (see Scheme A).

3. Hydrolases

Catalyze Hydrolysis reactions (Cleavage of a covalent bond with The addition of a Water molecule at the site of the break). They are subdivided according to the bond being cleaved.

Enzyme names are formed using the formula "substrate hydrolase" or by directly appending the suffix "-ase" to the substrate name—for example, protease, lipase, phospholipase, and Ribonuclease. Example of a reaction (see Scheme B).

For certain classes of hydrolases, special terms are used that characterize the hydrolysis of a specific chemical bond: esterases, Phosphatases, etc.

4. Lyases

Lyases are enzymes that catalyze the non-hydrolytic removal of a specific group from substrates (often eliminating СО₂, Н₂О, NН₂, SН₂, etc.) or, conversely, add a group across a double bond, most commonly a water molecule.

Enzyme names are typically formulated according to the "substrate—removed or added group" pattern. For reaction examples, see Scheme B.

5. Isomerases

These enzymes catalyze various intramolecular rearrangements. They are further classified depending on the type of isomerization reaction.

"Isomerases" is used as the general name for enzymes in this class (for example, see Scheme A).

Isomerases can catalyze intramolecular redox reactions, facilitating the interconversion of aldoses and ketoses, ketone and enol groups, as well as the shifting of double bonds within the molecule (see Scheme B).

When isomerization involves the intramolecular transfer of a group, the enzyme is referred to as a "mutase" (for example, see Scheme C).

6. Ligases (Synthetases)

These enzymes catalyze the joining of two molecules together, forming a covalent bond. This process is coupled with the cleavage of a phosphoester bond in ATP (or other nucleoside triphosphates) or high-energy bonds in Other Compounds. In the first case (utilizing the energy of ATP hydrolysis), such enzymes are called ligases or synthetases (see Scheme D).

When the energy source is any other high-energy compound (other than ATP), the enzymes are called synthases (see scheme on p. 83).

Scheme

C. Systematic Name

In accordance with the classification system, each enzyme is assigned a systematic name that uniquely describes the chemical reaction it catalyzes. For example, D-glyceraldehyde-3-phosphate: NAD oxidoreductase (commonly known as glyceraldehyde-3-phosphate dehydrogenase). The enzyme's name indicates that its substrate is D-glyceraldehyde-3-phosphate and that it catalyzes an oxidation-reduction reaction in the presence of the NAD⁺ coenzyme.

In 1972, the Nomenclature Commission of the International Union of Pure and Applied Chemistry (IUPAC) proposed the "Rules of Enzyme Nomenclature," featuring a four-digit code designation. In this code, the first digit represents the enzyme class, the second digit (subclass) specifies the group being transformed, the third digit (sub-subclass) identifies additional reaction participants (such as the donor and acceptor), and the fourth digit is the serial number of the enzyme within that sub-subgroup. For instance, malate dehydrogenase has the systematic name L-malate: NAD oxidoreductase and the code number 1.1.1.38. This code indicates that the enzyme belongs to the first class of enzymes (oxidoreductases), acts on a hydroxyl group as the oxidized group (1) in the presence of the NAD⁺ coenzyme (1), and has the serial number 38 in this subgroup. Code nomenclature for enzymes is primarily used in scientific literature.