Nomenclature of enzymes: description, classification, structure and principles of construction

The rapid discovery of a huge number of enzymes (today more than 3 thousand are known) made it necessary to systematize them, but for a long time there was no single approach to this issue. The modern nomenclature and classification of enzymes was developed by the Commission on Enzymes of the International Biochemical Union and approved at the Fifth World Biochemical Congress in 1961.

General characteristics of enzymes

Enzymes (aka enzymes) are unique biological catalysts that provide a huge amount of biochemical reactions that take place in the cell. Moreover, the latter proceed millions of times faster than could happen without the participation of enzymes. Each enzyme has an active site for binding to a substrate.

The nomenclature and classification of enzymes in biochemistry are closely related, since the name of each enzyme is based on its group, type of substrate and type of catalyzed chemical reaction. The exception is the trivial nomenclature, which is based on historical names and covers a relatively small part of the enzymes.

Enzyme classification

The modern classification of enzymes is based on the characterization of catalyzed chemical reactions. On this basis, 6 main groups (classes) of enzymes were identified:

1. Oxidoreductases carry out redox reactions that are responsible for the transfer of protons and electrons. The reactions proceed according to Scheme A reduced + B oxidized = A oxidized + B reduced, where the starting materials A and B are substrates of the enzyme.
2. Transferases catalyze the intermolecular transfer of chemical groups (except for the hydrogen atom) from one substrate to another (AX + B = A + BX).
3. Hydrolases are responsible for the cleavage (hydrolysis) of intramolecular chemical bonds formed with the participation of water.
4. Lyases cleave chemical groups from the substrate by a non-hydrolytic mechanism (without the participation of water) with the formation of double bonds.
5. Isomerases carry out interisomeric transformations.
6. Ligases catalyze the connection of two molecules, which is associated with the destruction of macroergic bonds (for example, ATP).

In turn, each of these groups is further divided into subclasses (from 4 to 13) and subclasses, more specifically describing different types of chemical transformations carried out by enzymes. A lot of parameters are taken into account here, including:

• donor and acceptor of convertible chemical groups;
• chemical nature of the substrate;
• participation in the catalytic reaction of additional molecules.

Each class corresponds to a serial number assigned to it, which is used in the digital code of enzymes.

Oxidoreductases

The division of oxidoreductases into subclasses occurs according to the donor of the redox reaction, and into subclasses according to the acceptor. The main groups of this class include:

• Dehydrogenases (aka reductases or anaerobic dehydrogenases) are the most common type of oskidoreductases. These enzymes accelerate the dehydrogenation reaction (removal of the hydrogen atom). Various compounds (NAD +, FMN, etc.) can act as an acceptor.
• oxidases (aerobic dehydrogenases) - oxygen acts as an acceptor;
• oxygenases (hydroxylases) - attach one of the atoms of an oxygen molecule to a substrate.

Coenzyme of more than half of oxidoreductases is the compound NAD +.

Transferase

This class has about five hundred enzymes, which are divided according to the type of tolerated groups. On this basis, subclasses such as phosphotransferases (transfer of phosphoric acid residues), acyltransferases (acyl transfer), aminotransferase (transamination reactions), glycosyl transferase (transfer of glycosyl residues), methyltransferase (transportation of monocarbon residues), etc.

Hydrolases

Hydrolases are subclassed by the nature of the substrate. The most important of them are:

• esterases - responsible for the breakdown of esters;
• glycosidases - hydrolyze glycosides (including carbohydrates);
• peptide hydrolases - destroy peptide bonds;
• non-peptide CN-binding enzymes

The hydrolase group includes about 500 enzymes.

Lyases

Many groups can undergo non-hydrolytic cleavage under the influence of lyases, including CO ₂ , NH ₂ , H ₂ O, SH _2, and others. In this case, the molecules decompose along the -, -, CN bonds, etc. One of the most important subclasses of this group are carbon-carbon-lyase.

Some cleavage reactions are reversible. In such cases, under certain conditions, lyases can catalyze not only decay, but also synthesis.

Ligase

All ligases are divided into two groups depending on which compound provides energy for the formation of a covalent bond. Enzymes using nucleoside triphosphates (ATP, GTP, etc.) are called synthetases. Ligases, the action of which is associated with other macroergic compounds, are called synthases.

Isomerase

This class is relatively small and includes about 90 enzymes that cause geometric or structural rearrangements in the substrate molecule. The most important enzymes of this group include triosophosphatisomerase, phosphoglycerate phosphomutase, aldosomutarotase and isopentenyl pyrophosphatisomerase.

Enzyme classification number

The introduction into the biochemistry of enzymes of a nomenclature of a code character was carried out in 1972. According to this innovation, each enzyme received a classification code.

The individual enzyme number consists of 4 digits, the first of which indicates the class, the second and third are the subclass and subclass. The final digit corresponds to the sequence number of the specific enzyme in the subclass according to the alphabetical order. Cipher numbers are separated by numbers. In the international list of enzymes, the classification number is indicated in the first column of the table.

Principles of Enzyme Nomenclature

Currently, there are three approaches to the formation of enzyme names. In accordance with them, the following types of nomenclature are distinguished:

• trivial (oldest system);
• working - convenient to use, very often used in educational literature;
• systematic (or scientific) - the most detailed and accurate characterizes the mechanism of action of the enzyme, but is too complicated for everyday use.

The systematic and working nomenclature of enzymes have a common feature, which is to attach to the end of any name the suffix "aza". The latter is a kind of "calling card" of enzymes that distinguishes them from a number of other groups of biological compounds.

There is another system for compiling names based on the structure of the enzyme. The nomenclature in this case does not focus on the type of chemical reaction, but on the spatial structure of the molecule.

In addition to the name itself, part of the nomenclature of enzymes is their indexation, according to which each enzyme has its own classification number. In the databases of enzymes, their code, working and scientific names, as well as the chemical reaction scheme are usually indicated.

Modern principles for constructing the nomenclature of enzymes are based on three characteristics:

• features of the chemical reaction carried out by the enzyme;
• enzyme class;
• substrate to which catalytic activity is applied.

The features of the disclosure of these items depend on the type of nomenclature (working or systematic) and the subclass of the enzyme to which they are applied.

Trivial nomenclature

The trivial nomenclature of enzymes appeared at the very beginning of the development of enzymology. At that time, the discoverers gave names to the enzymes. Therefore, this nomenclature is otherwise called historical.

The trivial names are based on arbitrary signs associated with the specific action of the enzyme, but they do not contain information about the substrate and the type of chemical reactions. Such names are much shorter than workers and systematic.

Trivial names usually reflect some feature of the action of the enzyme. For example, the name of the enzyme "lysozyme" reflects the ability of a given protein to lyse bacterial cells.

Classical examples of the trivial nomenclature are pepsin, trypsin, renin, chemotrypsin, thrombin and others.

Rational nomenclature

The rational nomenclature of enzymes was the first step towards the development of a single principle for the formation of enzyme names. It was developed in 1898 by E. Duclos and was based on a combination of the name of the substrate with the suffix "aza".

So, the enzyme that catalyzes the hydrolysis of urea was called urease, and the fat-breaking enzyme was called lipase, etc.

The names of holoenzymes (molecular complexes of the protein part of complex enzymes with a cofactor) were based on the nature of the coenzyme.

Working nomenclature

It received such a name for convenience in everyday use, as it contains basic information about the mechanism of action of the enzyme while maintaining the relative brevity of the names.

The working nomenclature of enzymes is based on a combination of the chemical nature of the substrate with the type of catalyzed reaction (DNA ligase, lactate dehydrogenase, phosphoglucomutase, adenylate cyclase, RNA polymerase).

Sometimes rational names (urease, nuclease) or abbreviated systematic are used as working names. For example, the complex compound name "peptidyl-prolyl-cis-trans-isomerase" is replaced by the simplified "peptidyl-prolyl isomerase" with a shorter and more uniform spelling.

Systematic Nomenclature of Enzymes

Like the working one, it is based on the characteristics of the substrate and the chemical reaction, however, these parameters are disclosed much more accurately and in more detail, indicating such things as:

• a substance acting as a substrate;
• nature of the donor and acceptor;
• name of the enzyme subclass;
• description of the essence of the chemical reaction.

The last paragraph implies clarifying information (the nature of the transferred group, the type of isomerization, etc.).

Not all enzymes indicate a complete set of the above characteristics. Each class of enzymes has its own formula for compiling systematic names.

Sometimes in the systematic name of the enzyme contains clarifying information, which is enclosed in brackets. For example, the enzyme catalyzing the redox reaction L-malate + NAD ⁺ = pyruvate + CO ₂ + NADH corresponds to the name L-malate: NAD ⁺ -oxidoreductase (decarboxylating).