2. Historical aspects
Escherichia coli : 4288 proteins, 2656 (62%) proteins are characterized
1632 proteins; hypothetical, unclassified, unknown
Fisher proposed “lack and key” hypothesis (1894)
Koshland proposed “induced fit” theory (1958)
Urease; the first enzyme to be crystallized (1926 by Summer), two Ni2+/active site
(NH2)2CO + H2O → CO2 + 2NH3
3-D structure of lysozyme was deuced by X-ray crystallography (1965)
Chemical synthesis of ribonuclease (1969)
Recombinant DNA technology
RNA-catalyzed reaction (1986 by Coch); Ribozyme: self-splicing, tRNA process,
splicing of RNA viral genomes, transphosesterification, phosphate ester hydrolysis,
peptidyl transferase activity
9. 9
Enzymes have specific substrates, a property known as substrate
specificity. For example, the active site of hexokinase reacts with
D-glucose, but will not react with L-glucose
Enzymes are specific for one enantiomer of the substrate
Remarkable properties of enzymes as catalysts
Specificity
13. 13
Remarkable properties of enzymes as catalysts
beta-phenylanine binding site of beta-TABG within 4 Ao was
selected and high-lighted as stick representation. Active site amino
acid residues are highlighted in black; PLP and beta-phenylalanine
are represented in pink and green sticks respectively.
Stereoselectivity
15. Remarkable properties of enzymes as catalysts
Regulation
Catalytic activity is regulated by small ions or molecular, or by covalent
modification
ex) Regulation of Pyruvate Dehydrogenase
16. Cofactors
A cofactor is a non-protein chemical compound that is required for the
protein's biological activity
Tightly bound cofactors (which can not be removed by dialysis or which is
covalently bound) are often termed prosthetic groups.
Holoenzyme = apoenzyme + cofactor
Any small molecule or other species which can reversibly bind ; ligand
19. Name of Enzymes
End in –ase
Identifies a reacting substance
sucrase – reacts sucrose
lipase - reacts lipid
Describes function of enzyme
oxidase – catalyzes oxidation
hydrolase – catalyzes hydrolysis
Common names of digestion enzymes still use –in
pepsin, trypsin
20. Classification of Enzymes
Enzyme Reaction example
oxidoreductoases oxidation-reduction lactate dehydorgenase
transferases transfer group of atoms hexokinase
hydrolases hydrolysis adenosinetriphosphate
lyases add/remove atoms to/from
a double bond
fructose-bisphosphate aldolase
isomerases rearrange atoms triose phosphate isomerase
ligases combine molecules using
ATP
Isoleucine-tRNA ligase
21. • In the 1950’s the increasing amounts of known enzymes
were causing confusion. No official nomenclature system
for enzymes.
• The IUBMB created the International Commission on
Enzymes in 1956 to deal with enzyme nomenclature
• Later replaced with the Nomenclature Committee of the
International Union of Biochemistry and Molecular
Biology (NC-IUBMB)
NC-IUBMB
22. • NC-IUBMB developed the Enzyme Classification
number system (EC)
• Classification system is based on the reactions the
enzymes catalyzed
• Classification:
Classes
Subclasses
Sub-subclasses
EC numbers (Enzyme Commission)
• Example EC 1.1.1.1
EC Numbers
23. • EC 1 – Oxidoreductases; catalyze oxidation/reduction reactions.
• EC 2 – Transferases; transfer a functional group e.g. Methyl group.
• EC 3 – Hydrolases; catalyse the hydrolysis of various bonds.
• EC 4 – Lyases; cleave various bonds by means other than hydrolysis
and oxidation
• EC 5 – Isomerases; catalyse changes within one molecule.
• EC 6 – Ligases; joining of two molecules with concomitant hydrolysis
of the diphosphate bond in ATP or a similar triphosphate.
Classification - Classes
