Structural Biochemistry, Catalytic Strategies, Enzyme Classification

Since many enzymes have common names that do not refer to their function or what kind of reaction they catalyze, an enzyme classification system was established. There were six classes of enzymes that were created so that enzymes could easily be named. These classes are Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, and Ligases. This is the international​ classification used for enzymes. Enzymes are normally used for catalyzing the transfer of functional groups, electrons, or atoms. Since this is the case, they are assigned names by the type of reaction they catalyze. The enzymes were numbered 1-6 and from here, they were divided into subdivisions. This allowed for the addition of a four-digit number that would precede EC(Enzyme Commission) and each enzyme could be identified. The reaction that an enzyme catalyzes must be known before it can be classified.[1]

Oxidoreductases catalyze oxidation-reduction reactions where electrons are transferred. These electrons are usually in the form of hydride ions or hydrogen atoms. When a substrate is being oxidized it is the hydrogen donor. The most common name used is a dehydrogenase and sometimes reductase will be used. An oxidase is referred to when the oxygen atom is the acceptor.

Glutathione S-transferase (Image: Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute, Public domain)

Transferases catalyze group transfer reactions. The transfer occurs from one molecule that will be the donor to another molecule that will be the acceptor. Most of the time, the donor is a cofactor that is charged with the group about to be transferred. Example: Hexokinase is used in glycolysis.

Hydrolases catalyze reactions that involve hydrolysis. This case usually involves the transfer of functional groups to water. When the hydrolase acts on amide, glycosyl, peptide, ester, or other bonds, they not only catalyze the hydrolytic removal of a group from the substrate but also a transfer of the group to an acceptor compound. These enzymes could also be classified under transferases since hydrolysis can be viewed as a transfer of a functional group to water as an acceptor. However, as the acceptor's reaction with water was discovered very early, it's considered the main function of the enzyme which allows it to fall under this classification. For example Chymotrypsin.

Lyases catalyze reactions where functional groups are added to break double bonds in molecules or the reverse where double bonds are formed by the removal of functional groups. For example, Fructose bisphosphate aldolase used in converting fructose 1,6-bisphosphate to G3P and DHAP by cutting the C-C bond.

Isomerases catalyze reactions that transfer functional groups within a molecule so that isomeric forms are produced. These enzymes allow for structural or geometric changes within a compound. Sometimes the interconversion is carried out by an intramolecular oxidoreduction. In this case, one molecule is both the hydrogen acceptor and donor, so there's no oxidized product. The lack of an oxidized product is the reason this enzyme falls under this classification. The subclasses are created under this category by the type of isomerism. For example phosphoglucose isomerase for converting glucose 6-phosphate to fructose 6-phosphate. Moving chemical group inside the same substrate.

Ligases are used in catalysis where two substrates are ligated and the formation of carbon-carbon, carbon-sulfide, carbon-nitrogen, and carbon-oxygen bonds due to condensation reactions. These reactions are coupled to the cleavage of ATP.

Translocase are enzymes that catalyze the movement of ions or molecules across membranes or their separation within membranes. It is a general term for a protein that assists in moving another molecule, usually across a cell membrane. The reaction is designated as a transfer from “side 1” to “side 2” because the designations “in” and “out”, which had previously been used, can be ambiguous. Translocases are the most common secretion system in Gram-positive bacteria.

Subcategories

Each of the seven main categories holds the following subcategories[2].

Oxidoreductases

• EC 1.1 includes oxidoreductases that act on the CH-OH group of donors (alcohol oxidoreductases)
• EC 1.2 includes oxidoreductases that act on the aldehyde or oxo group of donors
• EC 1.3 includes oxidoreductases that act on the CH-CH group of donors (CH-CH oxidoreductases)
• EC 1.4 includes oxidoreductases that act on the CH-NH2 group of donors (Amino acid oxidoreductases, Monoamine oxidase)
• EC 1.5 includes oxidoreductases that act on CH-NH group of donors
• EC 1.6 includes oxidoreductases that act on NADH or NADPH
• EC 1.7 includes oxidoreductases that act on other nitrogenous compounds as donors
• EC 1.8 includes oxidoreductases that act on a sulfur group of donors
• EC 1.9 includes oxidoreductases that act on a heme group of donors
• EC 1.10 includes oxidoreductases that act on diphenols and related substances as donors
• EC 1.11 includes oxidoreductases that act on peroxide as an acceptor (peroxidases)
• EC 1.12 includes oxidoreductases that act on hydrogen as donors
• EC 1.13 includes oxidoreductases that act on single donors with incorporation of molecular oxygen (oxygenases)
• EC 1.14 includes oxidoreductases that act on paired donors with incorporation of molecular oxygen
• EC 1.15 includes oxidoreductases that act on superoxide radicals as acceptors
• EC 1.16 includes oxidoreductases that oxidize metal ions
• EC 1.17 includes oxidoreductases that act on CH or CH2 groups
• EC 1.18 includes oxidoreductases that act on iron-sulfur proteins as donors
• EC 1.19 includes oxidoreductases that act on reduced flavodoxin as a donor
• EC 1.20 includes oxidoreductases that act on phosphorus or arsenic in donors
• EC 1.21 includes oxidoreductases that act on X-H and Y-H to form an X-Y bond
• EC 1.97 includes other oxidoreductases

Transferases

• EC 2.1 includes enzymes that transfer one-carbon groups (methyltransferase)
• EC 2.2 includes enzymes that transfer aldehyde or ketone groups
• EC 2.3 includes acyltransferases
• EC 2.4 includes glycosyltransferases
• EC 2.5 includes enzymes that transfer alkyl or aryl groups, other than methyl groups
• EC 2.6 includes enzymes that transfer nitrogenous groups (transaminase)
• EC 2.7 includes enzymes that transfer phosphorus-containing groups (phosphotransferase, including polymerase and kinase)
• EC 2.8 includes enzymes that transfer sulfur-containing groups (sulfurtransferase and sulfotransferase)
• EC 2.9 includes enzymes that transfer selenium-containing groups

Hydrolases

• EC 3.1: ester bonds (esterases: nucleases, phosphodiesterases, lipase, phosphatase)
• EC 3.2: sugars (DNA glycosylases, glycoside hydrolase)
• EC 3.3: ether bonds
• EC 3.4: peptide bonds (Proteases/peptidases)
• EC 3.5: carbon-nitrogen bonds, other than peptide bonds
• EC 3.6 acid anhydrides (acid anhydride hydrolases, including helicases and GTPase)
• EC 3.7 carbon-carbon bonds
• EC 3.8 halide bonds
• EC 3.9: phosphorus-nitrogen bonds
• EC 3.10: sulfur-nitrogen bonds
• EC 3.11: carbon-phosphorus bonds
• EC 3.12: sulfur-sulfur bonds
• EC 3.13: carbon-sulfur bonds

Lyases

• EC 4.1 includes lyases that cleave carbon-carbon bonds, such as decarboxylases (EC 4.1.1), aldehyde lyases (EC 4.1.2), oxo acid lyases(EC 4.1.3) and others (EC 4.1.99)
• EC 4.2 includes lyases that cleave carbon-oxygen bonds, such as dehydratases
• EC 4.3 includes lyases that cleave carbon-nitrogen bonds
• EC 4.4 includes lyases that cleave carbon-sulfur bonds
• EC 4.5 includes lyases that cleave carbon-halide bonds
• EC 4.6 includes lyases that cleave phosphorus-oxygen bonds, such as adenylate cyclase and guanylate cyclase
• EC 4.99 includes other lyases, such as ferrochelatase

Isomerases

• EC 5.1 includes enzymes that catalyze racemization (racemases) and epimerization (epimerases)
• EC 5.2 includes enzymes that catalyze the isomerization of geometric isomers (cis-trans isomerases)
• EC 5.3 includes intramolecular oxidoreductases
• EC 5.4 includes intramolecular transferases (mutases)
• EC 5.5 includes intramolecular lyases
• EC 5.99 includes other isomerases (including topoisomerases)

Ligases

• EC 6.1 includes ligases used to form carbon-oxygen bonds
• EC 6.2 includes ligases used to form carbon-sulfur bonds
• EC 6.3 includes ligases used to form carbon-nitrogen bonds (including argininosuccinate synthetase)
• EC 6.4 includes ligases used to form carbon-carbon bonds
• EC 6.5 includes ligases used to form phosphoric ester bonds
• EC 6.6 includes ligases used to form nitrogen-metal bonds

Translocases

• EC 7.1 includes enzymes catalyzing the translocation of hydrons
• EC 7.2 includes those catalyzing the translocation of inorganic cations and their chelates
• EC 7.3 includes those catalyzing the translocation of inorganic anions
• EC 7.4 includes those catalyzing the translocation of amino acids and peptides
• EC 7.5 includes those catalyzing the translocation of carbohydrates and their derivatives
• EC 7.6 includes those catalyzing the translocation of other compounds.

References

• ↑ Berg, Jeremy M., John L. Tymoczko, and Lubert Stryer. BIOCHEMISTRY. 6th ed. New York: W. H. FREEMAN AND COMPANY, 2007.
• ↑ Webb, Edwin C. (1992). Enzyme nomenclature 1992: recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes. San Diego: Published for the International Union of Biochemistry and Molecular Biology by Academic Press. ISBN 0-12-227164-5.

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