Human Biochemistry, Volume 1 - Murray R. 1993

Structure and Functions of Proteins and Enzymes
Enzymes: General Properties
Enzyme Classification and Nomenclature

Originally, Enzymes were named by adding the suffix -ase to the name of the substrate upon which the enzyme acts. For example, enzymes hydrolyzing starch (amylon) were named amylases; enzymes hydrolyzing fats (lipos) were called lipases; and enzymes hydrolyzing Proteins were designated as proteinases. Later, enzymes catalyzing similar types of reactions began to be named after the type of reaction involved, such as dehydrogenases, oxidases, Decarboxylases, acylases, and so on. Many of these names are still in use today.

The nomenclature introduced by the International Union of Biochemistry (IUB) may seem complex and cumbersome at first glance, but it has the advantage of being unambiguous. Its core principle is that enzymes are named and classified According to the type of chemical reaction catalyzed and its mechanism, which significantly facilitates the systematization of data related to various aspects of METABOLISM. The Main Features of the system introduced by the IUB are as follows.

1. Reactions and the enzymes catalyzing them are divided into six classes, each containing several subclasses (ranging from four to 13).

2. An enzyme name consists of two parts: the first part indicates the substrate (or substrates), while the second specifies the type of reaction catalyzed and ends in -ase.

3. Additional information, when necessary for clarification, is enclosed in parentheses. For example, The enzyme catalyzing the reaction L-malate + NAD⁺ = Pyruvate + CO₂ + NADH + H⁺ has the code number 1.1.1.37 and is named L-malate: NAD⁺ oxidoreductase (decarboxylating).

4. Each enzyme is assigned an Enzyme Commission (EC) code number; the first digit designates the reaction Class, the second the subclass, and the third the sub-subclass. The fourth digit indicates the serial number of the enzyme within its sub-subclass. Thus, EC 2.7.1.1 means that the enzyme belongs to class 2 (transferases), subclass 7 (transfer of phosphorus-containing groups), and sub-subclass 1 (where the phosphate acceptor is an alcohol). The final digit denotes the enzyme hexokinase, or ATP: D-hexose-6-phosphotransferase, i.e., the enzyme catalyzing The transfer of a phosphate group from ATP to the hydroxyl group at the sixth carbon position of glucose.

Below are all six enzyme classes along with specific Examples. The recommended name is indicated in parentheses.

1. Oxidoreductases. Enzymes catalyzing oxidation-reduction Reactions Involving Two substrates, S and S':

They catalyze reactions involving groups such as CH—OH, CH—CH, C = O, CH—NH₂, and —CH—NH—. Some subclasses include:

1.1. Enzymes acting on the CH—OH group of Donors. For example:

1.1.1.1. Alcohol: NAD⁺ oxidoreductase [Alcohol dehydrogenase]

Alcohol + NAD⁺ = Aldehyde or ketone + NADH + H⁺.

1.4. Enzymes acting on the CH—NH₂ group of donors. For example:

1.4.1.3. L-Glutamate: NAD(P)⁺ oxidoreductase (deaminating) [animal Liver Glutamate dehydrogenase]. The designation NAD(P)⁺ indicates that either NAD⁺ or NADP⁺ can serve as the electron acceptor.

L-Glutamate + H₂O + NAD(P)⁺ =

= a-Ketoglutarate + NH⁺₄ + NAD(P)H + H⁺.

2. Transferases. Enzymes catalyzing the transfer of a group G (other than a hydrogen atom) from a substrate S to a substrate S':

S—G + S' = S'—G + S.

They catalyze the transfer of single-carbon groups, aldehyde or ketone residues, as well as acyl, alkyl, glycosyl groups, and groups containing phosphorus and sulfur. Some subclasses include:

2.3. Acyltransferases. For example:

2.3.1.6. Acetyl-CoA:Choline O-acetyltransferase [choline acetyltransferase]

Acetyl-CoA + Choline = CoA + O-Acetylcholine.

2.7. Enzymes catalyzing the transfer of phosphorus-containing groups. For example:

2.7.1.1. ATP: D-hexose 6-phosphotransferase [hexokinase]

ATP + D-Hexose = ADP + D-Hexose-6-phosphate.

3. Hydrolases. Enzymes that catalyze the Hydrolysis of ether, ester, peptide, and glycosidic bonds, acid anhydrides, C—C, C-halide, and P—N bonds. For example:

3.1. Enzymes acting on ester bonds. For example:

3.1.1.8. Acylcholine acylhydrolase [pseudocholinesterase]

Acylcholine + Н₂О = Choline + Acid.

3.2. Enzymes acting on glycosyl compounds. For example:

3.2.1.23. ß-D-Galactoside galactohydrolase [ß-galactosidase]

ß-D-Galactoside + Н₂О = Alcohol + D-Galactose.

3.4. Enzymes acting on peptide bonds.

The Classification (divided into 11 subclasses) takes into account the differences between peptidases and proteases, distinguishes enzymes that hydrolyze dipeptides or larger Peptides, cleave off one or more Amino Acids, and attack the bond at the C- or N-terminus. According to their catalytic mechanism, proteinases are subdivided into Serine, thiol, and metallo-dependent. For example:

3.4.21. Serine proteinases. For example: Chymotrypsin, Trypsin, plasmin, Blood Coagulation factors IXa and XIa.

3.4.23. Carboxyl (acid) proteinases. For example: pepsins A, B, and C.

4. Lyases. Enzymes that cleave groups from substrates by non-hydrolytic mechanisms, resulting in The formation of double bonds.

Enzymes acting on C—C, C—O, C—N, C—S, and C-halide bonds. Some subgroups:

4.1.2. Aldehyde-lyases. For example:

4.1.2.7. Ketose-1-phosphate aldehyde-lyase [aldolase]

Ketose-1-phosphate = Dihydroxyacetone phosphate + Aldehyde.

4.2. Carbon-oxygen lyases. For example:

4.2.1.2. L-malate hydro-lyase [fumarase]

L-malate = Fumarate + Н₂O.

5. Isomerases. This class includes all enzymes that catalyze the interconversion of optical, geometric, and positional isomers. Some subclasses:

5.2. Cis-trans-isomerases. For example:

5.2.1.3. all-trans-Retinal 11-cis-trans-isomerase [retinal isomerase]

all-trans-Retinal = 11-cis-Retinal.

5.3. Enzymes catalysing the interconversion of aldoses and ketoses. For example:

5.3.1.1. D-Glyceraldehyde-3-phosphate ketol-isomerase [Triosephosphate isomerase]

D-Glyceraldehyde 3-phosphate = Dihydroxyacetone phosphate.

6. Ligases (from Lat. ligare meaning to bind). Enzymes catalysing the joining of two molecules coupled with the hydrolysis of a pyrophosphate bond in ATP or a similar triphosphate. This class includes enzymes that catalyse reactions forming C—O, C—S, C—N, and C—C bonds. Some subclasses include:

6.3. Enzymes catalysing the formation of C—N bonds. For example:

6.3.1.2. L-Glutamate:ammonia ligase (ADP-forming) [Glutamine Synthetase]

ATP + L-Glutamate + NH⁺₄ = ADP + Orthophosphate + L-Glutamine.

6.4. Enzymes catalysing the formation of C—C bonds. For example:

6.4.1.2. Acetyl-CoA:CO₂ ligase (ADP-forming) [acetyl-CoA carboxylase]

АТР + Ацетил-СоА + СО₂ = ADP + Рі + Малонил-СоА.