Lec 1 Enzyme and Its Classification

ENZYME AND ITS
CLASSIFICATION
Enzymology
Sadia Din
What are Enzymes?
■ Biological catalysts
■ Highly specialized proteins or RNA
■ Extraordinary catalytic power
■ High degree of specificity
■ Accelerate chemical reactions tremendously
■ Function in aqueous solutions under very mild conditions of temperature and pH
■ Very few non-biological molecules have all these properties
What are Enzymes?
■ Enzymes are catalysts
■ Increase reaction rates without being used up
■ Most enzymes are globular proteins
■ However, some RNA (ribozymes and ribosomal RNA)
also catalyze reactions
■ Study of enzymatic processes is the oldest field of
biochemistry, dating back to late 1700s.
What are Enzymes?
■ Some enzymes need other chemical groups
■ Cofactors – either one or more inorganic ions
■ Coenzymes – complex organic or metalloorganic molecules
■ Some enzymes require both
■ Prosthetic group – a coenzyme or cofactor that is very tightly (or covalently) bound to an
enzyme
■ Holoenzyme – a complete active enzyme with its bound cofactor or coenzyme
■ Apoprotein – the protein part of a holoenzyme
What are Enzymes?
■ Enzyme classification
■ Common names (DNA polymerase, urease;
pepsin; lysozyme, etc.)
■ 6 classes each with subclasses
Enzyme Classification
and Nomenclature
■ Enzyme nomenclature, Malcolm Dixon and Edwin Webb, in 1958, took a step that was
radically different from that used in other branches of nomenclature by classifying
enzymes in terms of the reactions they catalysed, rather than by their structures.
■ This system has been adopted and developed by the International Union of
Biochemistry and Molecular Biology (IUBMB), through its Joint Nomenclature
Committee with the International Union of Pure and Applied Chemistry (IUPAC) into
the Enzyme Nomenclature list of enzymes.
■ This material is also made available in a modified form through the SWISSPROT
ENZYME on-line database.
■ https://enzyme.expasy.org/
General Classification Structure
■ EC number: The classification number, which is made up of

four digits, identifies the enzyme by the reaction catalysed.
■ This is also valuable for relating the information to other
databases.
■ The EC code is represented with 4 digits, for instance a’b’c’d.

Where ‘a’ is represented ‘class’ and rest of the four digits as
subclasses.
EC number
■ The tripeptide aminopeptidases have the code "EC 3.4.11.4", whose

components indicate the following groups of enzymes:
■ EC 3 enzymes are hydrolases (enzymes that use water to break up some other
molecule)
■ EC 3.4 are hydrolases that act on peptide bonds
■ EC 3.4.11 are those hydrolases that cleave off the amino-terminal amino acid
from a polypeptide
■ EC 3.4.11.4 are those that cleave off the amino-terminal end from a tripeptide
Recommended name
■ The most commonly used name for the enzyme is usually

used, provided that it is unambiguous.
■ 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.
Systematic name
■ This attempts to describe in unambiguous terms what the enzyme

actually catalyses.
■ 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, ligase.
Examples
■ ATP + D-glucose ADP + D-glucose 6-phosphate
■ Formal name: ATP:glucose phosphotransferase
■ Common name: hexokinase
■ E.C. number (enzyme commission): 2.7.1.1
■ 2 class name (transferases)
■ 7 subclass (phosphotransferases)
■ 1 phosphotransferase with –OH as acceptor
■ 1 D-glucose is the phosphoryl group acceptor
Enzyme Classes and Definitions
Class 1. –.–.– Oxidoreductases
■ This class contains the enzymes catalysing oxidation reactions.
■ 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 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.
■ For subclasses 1.13 and 1.14, a different classification scheme is used since these enzymes
catalyse the incorporation of oxygen into the substrate. The recommended names are
generally monooxygenase or dioxygenase, depending on whether one or two atoms of
oxygen are incorporated into the substance oxidized
Example
■ EC 1.1.1.14
■ Recommended name: l-iditol 2-dehydrogenase
■ Reaction: l-iditol 1 NAD 5 l-sorbose 1 NADH2
■ Other name(s): polyol dehydrogenase; sorbitol
dehydrogenase
■ Systematic name: l-iditol:NAD 2-oxidoreductase
1. 1.–.– Acting on the CH–OH group of donors
1. 1. 1.– With NAD or NADP as acceptor
1. 1. 2.– With a cytochrome as acceptor
1. 1. 3.– With oxygen as acceptor
1. 1. 4.– With a disulfide as acceptor
1. 1. 5.– With a quinone or similar compound as acceptor
1. 1.99. – With other acceptors
1. 2. –.– Acting on the aldehyde or oxo group of donors

1. 2. 1.– With NAD or NADP as acceptor
1. 2. 2.– With a cytochrome as acceptor
1. 2. 3.– With oxygen as acceptor
1. 2. 4.– With a disulfide as acceptor
1. 2. 7.– With an iron–sulfur protein as acceptor
1. 2.99.– With other acceptors
Class 2.–.–.– Transferases
■ These enzymes transfer a group from one substrate (the donor) to another (the acceptor) according to
the general reaction [II]:
■ X–YZ XY–Z [II]
■ Example EC 2.1.1.114
■ Recommended name: hexaprenyldihydroxybenzoate methyltransferase
■ Reaction: S-adenosyl-l-methionine 1 3-hexaprenyl- 4,5-dihydroxybenzoate 5 S-adenosyl-l-
homocysteine 1 3-hexaprenyl-4-hydroxy-5-methoxybenzoate
■ Other name(s): 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase;
dihydroxyhexaprenylbenzoate methyltransferase
■ Systematic name: S-adenosyl-l-methionine:3-hexaprenyl- 4,5-dihydroxylate O-methyltransferase
2. 1. –.– Transferring one-carbon groups
2. 1. 1. – Methyltransferases
2. 1. 2. – Hydroxymethyl-, formyl- and related transferases
2. 1. 3. – Carboxyl- and carbamoyltransferases
2. 1. 4. – Amidinotransferases
2. 2. –.– Transferring aldehyde or ketone residues

2. 2. 1. – a single subclass containing the transaldolases and transketolases
2. 3. –.– Acyltransferases
2. 3. 1. – Acyltransferases
2. 3. 2. – Aminoacyltransferases
Class 3. –. –. – Hydrolases
■ These enzymes catalyse 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 hydrolysed, 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),
Examples
■ EC 3.1.2.23
■ Recommended name: 4-hydroxybenzoyl-CoA thioesterase
■ Systematic name: 4-hydroxybenzoyl-CoA hydrolase
Acting on ester bonds
3.1. 1. – Carboxylic ester hydrolases
3.1. 2. – Thiolester hydrolases
3.1. 3. – Phosphoric monoester hydrolases
3.1. 4. – Phosphoric diester hydrolases
3.1. 5. – Triphosphoric monoester hydrolases
3.1. 6. – Sulfuric ester hydrolases
3.1. 7. – Diphosphoric monoester hydrolases
3.1. 8. – Phosphoric triester hydrolases
3.1.11. – Exodeoxyribonucleases producing 5′-phosphomonoesters
3.1.13. – Exoribonucleases producing 5′-phosphomonoesters
3.1.14. – Exoribonucleases producing other than 5′-phosphomonoesters
3.1.15. – Exonucleases active with either ribo- or deoxyribonucleic acids and producing 5′-phosphomonoesters
3.1.16. – Exonucleases active with either ribo- or deoxyribonucleic acids and producing other than 5′-phosphomonoesters
3.1.21. – Endodeoxyribonucleases producing 5′-phosphomonoesters
3.1.22. – Endodeoxyribonucleases producing other than 5′-phosphomonoesters
3.1.25. – Site-specific endodeoxyribonucleases specific for altered bases
3.1.26. – Endoribonucleases producing 5′-phosphomonoesters
3.1.27. – Endoribonucleases producing other than 5′-phosphomonoesters
3.1.30. – Endonucleases active with either ribo- or deoxyribonucleic acid and producing 5′-phosphomonoesters
3.1.31. – Endonucleases active with either ribo- or deoxyribonucleic acid and producing other than 5′-phosphomonoesters
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’.
Example
■ EC 4.1.2.39
■ Recommended name: hydroxynitrilase
■ Other name(s): hydroxynitrile lyase; oxynitrilase
■ Systematic name: 2-hydroxyisobutyronitrile
acetonelyase
4. 1. –.– Carbon–carbon lyases
4. 1. 1 – Carboxy-lyases
4. 1. 2 – Aldehyde-lyases
4. 1. 3 – Oxo-acid-lyases
4. 1.99 – Other carbon–carbon lyases
4. 2. –.– Carbon–oxygen lyases

4. 2. 1 – Hydro-lyases
4. 2. 2 – Acting on polysaccharides
4. 2.99 – Other carbon–oxygen lyases
Class 5. –. –.– Isomerases
■ These enzymes catalyse 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.
Example
■ EC 5.1.99.4
■ Recommended name: a-methylacyl-CoA
racemase
■ Systematic name: 2-methylacyl-CoA 2-
epimerase
5. 1. –.– Racemases and epimerases
5. 1. 1. – Acting on amino acids and
derivatives
5. 1. 2. – Acting on hydroxy acids and
derivatives
5. 1. 3. – Acting on carbohydrates and
derivatives
5. 1.99. – Acting on other compounds
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 (XDPor XMP-forming).
■ Example
■ EC 6.2.1.33
■ Recommended name: 4-chlorobenzoate-CoA ligase Reaction: 4-chlorobenzoate 1
CoA 1 ATP 5 4- chlorobenzoyl-CoA 1 AMP 1 diphosphate
■ Systematic name: 4-chlorobenzoate : CoA ligase
6. 1. –.– Forming carbon–oxygen bonds
6. 1. 1. – Ligases forming aminoacyl-tRNA and
related
compounds
6. 2. –.– Forming carbon–sulfur bonds

6. 2. 1. – Acid–thiol ligases
The End

Lec 1 Enzyme and Its Classification

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ENZYME AND ITS

■ EC number: The classification number, which is made up of

■ The EC code is represented with 4 digits, for instance a’b’c’d.

■ The tripeptide aminopeptidases have the code "EC 3.4.11.4", whose

■ The most commonly used name for the enzyme is usually

■ This attempts to describe in unambiguous terms what the enzyme

1. 2. –.– Acting on the aldehyde or oxo group of donors

2. 2. –.– Transferring aldehyde or ketone residues

4. 2. –.– Carbon–oxygen lyases

■ These enzymes catalyse geometric or structural

6. 2. –.– Forming carbon–sulfur bonds

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