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Lec 1 Enzyme and Its Classification
Lec 1 Enzyme and Its Classification
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 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
■ 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
■ 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