Prepared by Er.

Abuzer Amir

Er. Abuzer Amir

NAMING OF ENZYMES

Enzymes are classified and named according to the nature of the chemical reactions they catalyze.
Enzymes are assigned two names and a classification number.

1. Recommended name: The most commonly used name for the enzyme is usually used, provided that it
is unambiguous appending –ase to either the:

 Name of a substrate
 Type of catalytic reaction

A number of generic words indicating reaction types may be used in recommended names, but not in the
systematic names, e.g. dehydrogenase, reductase, oxidase, peroxidase, kinase, tautomerase, deaminase,
dehydratase, etc. Where additional information is needed to make the reaction clear, a phrase indicating
the reaction or a product may be added in parentheses after the second part of the name, e.g. (ADP-
forming), (dimerizing).

2. Systematic name: This attempt to describe in unambiguous terms what the enzyme actually catalyzes.
Systematic names consist of two parts. The first contains the name of the substrate or, in the case of a
bimolecular reaction, of the two substrates separated by a colon. The second part, ending in -ase, indicates
the nature of the reaction. A number of generic words indicating a type of reaction may be used in either
recommended or systematic names: oxidoreductase, oxygenase, transferase (with a prefix indicating the
nature of the group transferred), hydrolase, lyase, racemase, epimerase, isomerase, mutase, and ligase.
Where additional information is needed to make the reaction clear, a phrase indicating the reaction or a
product should be added in parentheses after the second part of the name, e.g. (ADP-forming),
(dimerizing).

3. EC number: In 1961, according to the report of the first Enzyme Commission (EC) of International
Union of Pure and Applied Chemistry (IUPAC), Enzymes are classified in to six types on the basis of
reaction they catalyze. They were assigned code numbers, prefixed by E.C., which contain four elements
separated by points and have the following meaning as shown in fig. 1.2.
 Prepared by Er. Abuzer Amir

Figure.2: Naming of enzyme according to ‘International Union of Biochemistry’ formed a

ENZYME CLASSES AND DEFINITIONS

According to the type of reactions that the enzymes catalyze, enzymes are classified into seven categories,
which are oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases, and translocases.
Oxidoreductases, transferases and hydrolases are the most abundant forms of enzymes. Individual enzyme
classes are further classified systematically based on the chemical name of the substrate and its reaction
mechanism.

According to the unified classification principle of enzymes published by the International Society of
Biochemistry, each group of enzymes in the above seven categories can be further divided into several
subgroups according to the characteristics of the functional groups or bonds in the substrates. In order to
show the properties of substrates or reactants more accurately, each subclass is further divided into
subclasses and directly contains a quantity of enzymes. In this part we will study each class in detail.

1. Class 1 Oxidoreductases

This class contains the enzymes catalyzing oxidation reactions. Since the oxidation of one group must be
accompanied by the reduction of another, they are grouped together as oxidoreductases. The systematic
enzyme name is in the form donor:acceptor oxidoreductase. The substrate that is being oxidized is
regarded as being the hydrogen donor. The recommended name is commonly donor dehydrogenase,
 Prepared by Er. Abuzer Amir
although the term reductase is sometimes used as an alternative. The term donor oxidase is used only
when O2 is the acceptor.

The second figure in the code number of the oxidoreductases denotes the type of group in the hydrogen-
donor substrate that is oxidized or reduced. The third number denotes the hydrogen acceptor: 1 denotes
NAD(P), 2 a cytochrome, 3 molecular oxygen, 4 a disulfide, 5 a quinone or similar compound, 6 a
nitrogenous group, 7 an iron– sulfur protein and 8 a flavin. The number 99 is used for all other acceptors.
This group contains a number of enzymes that have been shown to work with synthetic acceptors, such as
2,6-dichloroindophenol or phenazine methosulfate, but where the physiological acceptor is unknown. It is
intended that they should be transferred to more descriptive sub-subclasses when the natural acceptor is
identified.

Example

EC 1.1.1.14

Recommended name: L-iditol 2-dehydrogenase

Reaction: L-iditol + NAD = L-sorbose + NADH2

Other name(s): polyol dehydrogenase; sorbitol dehydrogenase

Systematic name: l-iditol:NAD 2-oxidoreductase

2. Class 2 Transferases

These enzymes transfer a group from one substrate (the donor) to another (the acceptor) according to the
general reaction:

X–Y + Z = X + Y–Z

The systematic name is in the form donor:acceptor grouptransferase. The recommended names are
normally formed according to acceptor grouptransferase or donor grouptransferase. Sometimes
transferase reactions can be considered in different ways; for example, the general reaction shown above
may be regarded as a transfer of the group Y from X to Z and would therefore be termed a Y-transferase.
However, it could also be considered as a breaking of the X–Y bond by the introduction of Z. For
example, where Z represents phosphate, the process is often referred to as phosphorolysis and the enzyme
catalyzing the reaction as a phosphorylase. For systematic purposes, these enzymes are classified as
phosphotransferases.

The second figure in the code number of the transferases denotes the general nature of the group
transferred (a one carbon group, 2.1; aldehydic or ketonic group, 2.2; acyl group, 2.3, etc.) and the third
number further specifies that group (methyltransferase, 2.1.1; formyltransferase, 2.1.2, etc.). The
exception is the case of the enzymes transferring phosphorus-containing groups (subclass 2.7), where the
third number specifies the nature of the acceptor group.

Example

EC 2.1.1.114
 Prepared by Er. Abuzer Amir
Recommended name: hexaprenyl dihydroxybenzoate methyltransferase

Reaction:

S-adenosyl-L-methionine + 3-hexaprenyl 4,5-dihydroxybenzoate = S-adenosyl-L-homocysteine + 3-

Other name(s): 3,4-dihydroxy-5-hexaprenyl benzoate methyltransferase; dihydroxy hexaprenyl benzoate

Systematic name: S-adenosyl-L-methionine:3-hexaprenyl-4,5-dihydroxylate O-methyltransferase

3. Class 3 Hydrolases

These enzymes catalyze the hydrolytic cleavage of bonds such as C–O, C–N, C–C and some other bonds,
including phosphoric anhydride bonds. The overlapping specificities of many of these enzymes make it
difficult to formulate general rules that are applicable to all members of this class. The systematic name
usually takes the form substrate X-hydrolase, where X is the group removed by hydrolysis. The
recommended name is, in many cases, formed by the name of the substrate with the suffix -ase. It is
understood that the name of the substrate with this suffix means a hydrolytic enzyme.

The second number indicates the nature of the bond hydrolyzed, and the third normally specifies the
nature of the substrate, e.g. in the esterases the carboxylic ester hydrolases (3.1.1), thiolester hydrolases
(3.1.2), phosphoric monoester hydrolases (3.1.3); in the glycosidases, the O-glycosidases (3.2.1), N-
glycosidases (3.2.2), and so on.

Examples

EC 3.1.2.23

Recommended name: 4-hydroxybenzoyl-CoA thioesterase

Reaction: 4-hydroxybenzoyl-CoA + H2O = 4-hydroxybenzoate + CoA

Systematic name: 4-hydroxybenzoyl-CoA hydrolase

4. Class 4 Lyases

These enzymes cleave C–C, C–O, C–N and other bonds by means other than hydrolysis or oxidation.
They differ from other enzymes in that two substrates are involved in one reaction direction but only one
in the other. When acting on the single substrate, a molecule is eliminated leaving double bonds or rings.
The systematic name is formed according to the pattern substrate group-lyase. The hyphen is an important
part of the name and, to avoid confusion, should not be omitted, e.g. hydro-lyase not ‘hydrolyase’. In the
recommended names, expressions like decarboxylase or aldolase (in case of elimination of CO2 or
aldehyde, respectively) are used. Dehydratase is used for those enzymes catalyzing the elimination of
water. In cases where the reverse reaction is much more important, or the only one demonstrated,
synthase (not synthetase) may be used in the name. Although, the term synthetase has sometimes been
used in the names of enzymes from this class, that use is discouraged in order to prevent confusion with
enzymes from Class 6.
 Prepared by Er. Abuzer Amir
The second figure in the code number indicates the bond broken: 4.1 are carbon–carbon lyases, 4.2 are
carbon–oxygen lyases, and so on. The third figure gives further information on the group eliminated (e.g.
CO2 in 4.1.1 and H2O in 4.2.1).

Example

EC 4.1.2.39

Recommended name: hydroxynitrilase

Reaction: 2-hydroxyisobutyronitrile = cyanide + acetone

Other name(s): hydroxynitrile lyase; oxynitrilase

Systematic name: 2-hydroxyisobutyronitrile acetonelyase

5. Class 5 Isomerases

These enzymes catalyze geometric or structural changes within one molecule. According to the type of
isomerism involved they may be called racemases, epimerases, cis– trans-isomerases, isomerases,
tautomerases, mutases or cycloisomerases. The second number denotes the type of isomerism involved,
and the third number the type of substrate. In some cases, the reaction involves an intermolecular
oxidoreduction, but since the donor and acceptor groups are in the same molecule they are classified as
isomerases rather than oxidoreductases, even though they may contain firmly bound NAD or NADP.

Example:

EC 5.1.99.4

Recommended name: α-methylacyl-CoA racemase

Reaction: (2S)-2-methylacyl-CoA = (2R)-2-methylacyl-CoA

Systematic name: 2-methylacyl-CoA 2-epimerase

6. Class 6 Ligases

These enzymes catalyse the joining together (ligating) of two molecules with the concomitant hydrolysis
of a diphosphate bond in ATP or a similar triphosphate. The systematic enzyme name takes the form A:B
ligase (XDP or XMP-forming). The recommended name often takes the form A–B ligase. Sometimes the
name synthase is used for the recommended name to emphasize the synthetic nature of the reaction,
which can also be helpful if the reaction is complex. The name synthetase is also sometimes used instead
of synthase in the names of enzymes in this class. The second figure in the code number indicates the
bond formed: 6.1 for C–O bonds (enzymes acylating tRNA), 6.2 for C–S bonds (acyl-CoA derivatives),
etc. Sub-subclasses are only in use in the C–N ligases (6.3), which include the amide synthases (6.3.1),
the peptide synthases (6.3.2), enzymes forming heterocyclic rings (6.3.3), etc.

Example

EC 6.2.1.33
 Prepared by Er. Abuzer Amir
Recommended name: 4-chlorobenzoate-CoA ligase

Reaction: 4-chlorobenzoate + CoA + ATP = 4- chlorobenzoyl-CoA + AMP + diphosphate

Systematic name: 4-chlorobenzoate:CoA ligase

References

1. https://www.amu.ac.in/emp/studym/100018287.pdf
2. https://www.yumpu.com/en/document/view/37971187/a0000710-enzyme-classification-and-
nomenctaturepdf-koissk
3. https://iubmb.org/wp-content/uploads/sites/10116/2018/11/A-Brief-Guide-to-Enzyme-
Classification-and-Nomenclature-rev.pdf
4. https://infinitabiotech.com/blog/classification-and-evolution-of-enzymes/
5. http://dhingcollegeonline.co.in/attendence/classnotes/files/1602609230.pdf
6. https://www.researchgate.net/publication/227572283_Enzyme_Classification_and_Nomenclature
7. https://docplayer.net/amp/204043676-Enzyme-classification-and-nomenclature.html