IUB System of Nomenclature and Classification of Enzymes (Biochemistry Lecture Notes)

Learning Objectives: How Enzymes are Named? What is IUB System, Components of Enzyme Nomenclature, Seven Major Classes of Enzymes with Examples, What is Enzyme Commission Number?

How enzymes are named?

Ø  Enzymes are classified based on the reaction they catalyze.
Ø  Usually, the enzymes are named by adding the suffix “-ase” to the name of their substrate or to a word describing their activity.
Ø  Example:

$.   Urease:- Catalyzes the hydrolysis of urea.

$.   DNA Polymerase:– Catalyzes the polymerization of DNA.

Ø  Many enzymes have common names that provide little information about the reactions that they catalyze.

Ø  Example: Trypsin – a proteolytic enzyme secreted by the pancreas.

Rules for the Nomenclature and Classification of Enzymes

Ø  Biochemists follow systematic rules for the Nomenclature (naming) and Classification of enzymes.

Ø  Rules for the Nomenclature and Classification of enzymes were prepared by the International Union of Biochemistry (IUB*) in 1964.

Ø  *IUB is now IUBMB (International Union of Biochemistry and Molecular Biology).

Ø  In the IUB system, each enzyme has a name and a unique identification number.

Ø  The systematic name of each enzyme consists of TWO parts.

$.   Name of the substrate(s)

$.   Followed by a word ending in ‘-ase’ specifying the type of reaction

Ø  Example: Alcohol Dehydrogenase

Ø  The recommended name of the enzyme for everyday uses is often an enzyme’s previously used name (common name)

Ø  The unique identification number of the enzyme is called Enzyme Commission Number (E.C. Number)

IUB System of Enzyme Classification

Ø  All enzymes were categorized into SEVEN major Classes (*previously six) based on the type of reaction they catalyze.

Ø  These groups were subdivided and further subdivided so many categories.

Ø  Based on this classification, a ‘four-digit unique number’ (called EC number) is assigned to each enzyme as an identification code (The concept of EC Number is described below).

Six Classes of Enzymes (IUB System)

(1). Oxidoreductases

(2). Transferases

(3). Hydrolases

(4). Lyases

(5). Isomerases

(6). Ligases

(7). Translocases

(1). Oxidoreductases

Ø  Oxidoreductases catalyze oxidation and reduction reactions (redox reactions).

Ø  This reaction involves the transfer of protons or electrons between substrates.

Ø  Example: Alcohol Dehydrogenase, Odidase

(2). Transferases

Ø  Transferases catalyze the transfer of a functional group from one substance to another.

Ø  The groups usually transferred by these enzymes are methyl group, ethyl group, amino group, phosphate group etc.)         

Ø  Example: Transaminase, Nucleoside Monophosphate Kinase (NMP Kinase)

(3). Hydrolases

Ø  Hydrolases catalyze the hydrolysis (breakdown) reaction with water (transfer of functional groups to water)

Ø  Example: Lipase, Amylase, Peptidase

(4). Lyases

Ø  Lyases catalyze the addition of groups to double bonds and formation of double bonds by the removal of groups.

Ø  Example: Fumarase, Decarboxylase

(5). Isomerase:

Ø  Isomerases catalyze the transfer of groups within molecules to yield isomeric forms (isomeric reactions).

Ø  It catalyzes the intra-molecular (within the molecule) group transfer.

Ø  Example: Triose phosphate isomerase, Phosphoglucomutase

(6). Ligase

Ø  Ligases catalyze the condensation (joining) of two molecules with the expense of energy from ATP hydrolysis.

Ø  It catalyzes the formation of C – C, C – S, C – O and C – N bonds by the condensation reaction coupled with ATP cleavage.

Ø  Example: Aminoacyl-tRNA synthetase, DNA ligase

(7*). Translocases

Ø  *This class is a newly added major class of IUBMB enzyme classification.

Ø  Translocases catalyse the movement of ions or molecules across membranes or their separation within membranes.

Ø  Example: ATP synthase

ATP Synthase (Source: Wikipedia)

Features of IUB System of Classification of Enzymes

Ø  All enzymes have been classified into 7 major classes.

Ø  Each major class is divided into sub-classes.

Ø  Each sub-class is further divided into sub-sub-classes.

Ø  Each enzyme has been assigned with a specific code number.

Ø  This code number is called Enzyme Commission Number (EC number).

Ø  EC number consists of 4 digits, separated by periods.

Ø  Each digit in the EC number indicates a specific category in the classification.

$.   Example: Alcohol Dehydrogenase (EC No. 1.1.1.1)

$.   First digit indicate the major class

$.   Second digit indicates sub-class

$.   Third digit indicates the sub-sub-class

$.   Forth digit indicates the systematic specific name of the enzyme.

Ø  The systematic specific name of the enzyme consists of TWO parts.

$.   The first part indicates the name of the substrate.

$.   The second part indicates the nature of the reaction.

$.   Example: Alcohol Dehydrogenases (ADH)

E.C. Number Example:

Ø  Consider the following reaction in Glycolysis.

ATP + D-glucose    →   ADP + D-glucose 6-phosphate

Ø  Enzyme responsible for this reaction is Hexokinase.

Ø  New name of hexokinase according to IUMB is ATP-Glucose phospho-transferase.

Ø  The name indicates the transfer of phosphoryl group from ATP to glucose.

Ø  E.C. Number of Hexokinase  is 2.7.1.1

$.   First number (2) indicates the class name (Transferases).

$.   Second number (7): sub-class (Phosphotransferases).

$.   Third number (1) a phosphotransferase with a hydroxyl group as acceptor.

$.   Fourth number (1) D glucose as the phosphoryl group acceptor.

Ø  For any enzyme, a trivial name is more commonly used.

Ø  Here the name is Hexokinase.

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References

Lehninger A.B., (2018), Textbook of Biochemistry, Ed. 5, Pearson International, New York

Berg, J.M., Tymoczko, J.L. and Stryer, L., 2012. Biochemistry/Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; with Gregory J. Gatto, Jr.

Voet, D., Voet, J.G. and Pratt, C.W., 2013. Fundamentals of biochemistry: life at the molecular level