ENZYME CLASSIFICATION AND SUBCLASSES

1.Oxidoreductases are involve in oxidation and reduction: A red + B ox → A ox + B red

a)oxidases: use oxygen as an electron acceptor but do not incorporate it into the substrate

b)dehydrogenases: use molecules other than oxygen(NAD+) as an electron acceptor.

c)Oxygenases: directly incorporate oxygen into substrate

d)peroxidases: use H2O2 as electron acceptor

2.Transferases-transfer functional groups( example: amino or phosphate groups)

A-B + C → A + B - C
a)methyltransferases: transfer one carbon units between substrates

b)aminotransferases: transfer NH2 from amino acids to keto acids

c)kinases: transfer PO3 from ATP to substrate

d)phophorylases: transfer PO3 from inorganic phosphate to a substrate

3. Hydrolases-transfer water, that is, they catalyze the hydrolysis of a substrate

A-B + H2O → A-H + B-OH

a)phosphatases: remove PO3 from a substrate

b)phoaphodiesterases: cleave phosphodiester bonds such as those in nucleic acids

c)proteases: cleave amide bonds such as those in proteins

4.Lyases- add or remove the elements of water, ammonia, CO2 to(or from) double bonds
A(XH)-B → A-X + B-H

a)Decarboxylases: produce CO2 via elimination reactions

b)aldolases: produce aldehydes via elimination reactions

c)Synthases: link two molecules without the involvement of ATP

5.Isomerases- catalyze rearrangement of atoms within a molecule

a)racemases: interconvert L and D stereoisomers

b)mutases: transfer groups between atoms within a molecule

6.LIGASES- JOIN TWO MOLECULES

A + B + ATP → A-B + ADP + Pi ATP supplies the energy needs of the reaction

a)carboxylases: use CO2 as a substrate

 b)synthetases-link two molecules via an ATP-dependent reaction

NOMENCLATURE OF ENZYME
A.Enzyme Commission Classification system for enzymes(class names, Enzyme commission types
numbers, and type of reactions catalyzed.)
1.Oxidoreductases(oxidation-reduction reactions)
1.1 acting on -CH-OH
1.2acting on -C=O
1.3 Acting on -CH=CH-
1.4 Acting on -CH-NH2
1.5 Acting on -CH-NH
1.6 Acting on NADH;NADPH
2.Transferases(transfer of functional groups)
2.1 One-carbon groups
2.2 Aldehyde or ketonic groups
2.3 Acyl groups
2.4 glycosyl groups
----------------------
2.7 phosphate groups
2.8 S-containing groups
3.Hydrolases(hydrolysis reactions)
3.1 Esters
3.2 Glycosidic bonds
------------------
3.4peptide bonds
3.5 other C-N bonds
3.6 acid anhydrides
-----------------------
4.Lyases(addition to double bonds)
4.1 -C=C-
4.2 -C=O
4.3 C=N-
5. Isomerases(isomerization reactions)
5.1 racemases
------------------
6. Ligases(formation of bonds with ATP cleavage)
6.1C-O
6.2 C-S
6.3 C-N
6.4 C-C
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2. Recommended name: the most commonly used name for the enzyme.

3.Systematic name
The six major classes and subclasses developed by IUBMB (International Union of Biochemistry and
Molecular Biology) use a suffix -ase to completely describe the chemical reaction catalyzed. The IUBMB
outline governing nomenclature of enzymes is outlined:
a. Reactions and the enzymes that catalyzed them form six classes, each having subclasses.
b. The enzyme name has two parts: the first names the substrate or substrates and the second
with suffix -ase indicate the type of reaction catalyzed
c. Additional information to clarify the reaction follow in parenthesis.
d. Each enzyme has four digit code: class(first digit), subclass(second digit), subsubclass(third digit)
and the fourth digit for the specific enzyme.

To avoid possible confusions, cause by these numerous system on enzyme identification, let us not
forget what catalyst is.
1.Catalyst is a substance which increases the rate of chemical reaction without undergoing a permanent
chemical change.
2.Catalyst does NOT affect reaction equilibrium.
Note: equilibrium concentration can be calculated ONLY using the thermodynamic properties of the
substrates and products.

ENZYME STRUCTURE
1.Active sites. This contain amino acid side chains that create three dimensional surface complementary
to the substrate. Active site binds the substrate forming enzyme-substrate complex and converted to
enzyme product, which subsequently dissociates to enzyme and product.

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2.Cofactors. Some enzymes require a nonprotein cofactor for enzymatic activity. Common cofactors
include metal ions and organic molecules called coenzymes which are usually derivatives of vitamins
Ca2+ a-amylase(swine pancreas)

Collagenase
Lipase
Micrococcal nuclease
Co2+ Glucose isomerase(Bacillus coagulans)(also
requires Mg2+)
Cu2+( Cu+) Galactose oxidase
Tyrosinase
Fe2+ or Fe 3+ Catalase
Cytochromes
Peroxidase
Mg2+ Deoxiribonuclease(bovine pancreas)
Mn2+ Arginase
Na+ Plasma membrane ATPase(also require K+
and Mg 2+)
Zn2+ Alcohol dehydrogenase
Alkaline phosphatase
carboxypeptidase

3.Holoenzyme refer to enzyme and its cofactor.

4.Apoenzyme refer to the protein portion of the holoenzyme. In the absence of the appropriate
cofactor, apoenzyme does not show activity

5.Prosthetic group. A tightly bond coenzyme that does not dissociate from the enzyme

6. Allosteric site. Additional or other active site for interaction with regulated molecule.

Allas: other name

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SPECIFICITY of enzyme is determined by the functional groups of the substrate, functional groups of the
enzyme and the physical proximity of these functional groups.

Lock and Key theory (Emil Fischer 1899)

The enzyme AS is complementary in conformation to the substrate, the enzyme and substrate recognize
one another.
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Induced-fit theory (Daniel Koshland, 1958)

The enzyme changes shape on binding substrate so that the E-S conformation is only complementary
AFTER binding.

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TRIVIA
a) Biological catalysis was first recognized in the late 1700s.
b) 1800, examination of the conversion of starch to sugar by saliva and various plant extract.
c) In 1850, Louis Pasteur: fermentation of sugar into alcohol by yeast is catalyzed by “ferments’. He
postulated that ferments were inseparable from the structure of living yeast cells. (Vitalism/Vitalistic
theory still prevailed)
d) In 1897, Eduard Buchner discovered that yeast extract could ferment sugar to alcohol, proves that
fermentation continued to function when molecules are removed from cells.
e) Frederick W. Kuhne called these molecules molecules.

Enzymes are protein catalyst endowed with enormous catalytic power. Enzymes increase the rate of
chemical reaction and are not consumed during the reaction they catalyze.

Bisubstrate Reaction
Bi-bi ordered mechanism
Ping pong mechanism

Ternary Reaction Mechanism(3 substrates)

Ter-ter mechanism
Uni-uni-bi-bi
Bi-bi-uni-uni
Bi-uni-uni-bi
Hexa uni pingpong

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