Chymotrypsin: Difference between revisions

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The active site of an enzyme is the location where the substrate binds and where the chemical reaction occurs. Active site residues are those amino acid residues demonstrated to have importance for catalysis or substrate binding. Chymotrypsin contains three residues, Ser 195, His 57 and Asp 102, which are known as its <scene name='Chymotrypsin/Chymotrypsin_triad/2'>catalytic triad</scene>. Similar three-dimensional arrangements of a serine, a histidine and an aspartate are observed in many other proteases, and the role of these three residues in catalysis has been studied extensively. Serine acts as a nucleophile (contributing the electron pair for a new bond) attacking the carbonyl carbon of the peptide bond to be hydrolyzed. Histidine and aspartate turn serine into a better nucleophile by assisting in removing a hydrogen ion from serine.

==Substrate binding and catalysis==

Features of the substrate binding site can be seen in structure of bovine chymotrypsin bound to the inhibitor N-acetyl-L-leucyl-L-phenylalanyl trifuoromethyl kentone (Ac-Leu-Phe-CF<sub>3</sub>), which resembles a peptide substrate. This scene shows the three peptide chains of the enzyme in spacefill and colored tuquoise, beige, and violet, and the inhibitor shown in CPK ball & stick is sitting in the active site. In this <scene name='38/387136/Bovine_chymotrypsin_active_sit/1'>closeup of the active site</scene>, the residues of catalytic triad are shown in CPK ball & stick and labelled, and the inhibitor is in light gray ball & stick with its phenyl group in orchid. By moving the stucture back and forth with your mouse, it is easy to see that the phenyl group is located in the hydrophobic binding pocket of the enzyme. The binding pocket determines the preference for cleavage of peptides on the C-terminal side of aromatic residues.

This view shows the carbonyl group of the inhibitor<scene name='38/387136/Bovine_chymotrypsin_active_sit/3'>carbonyl group of the inhibitor</scene> in CPK colors. The triflouromethyl group is bound to the carbon via the yellow bond. In a peptide substrate, the triflouromethyl group would be replaced by the first amino acid residue of the rest of the peptide chain, and the yellow bond is the bond that would be cleaved. The carbonyl carbon is 1.95 Å away from the side chain oxygen of serine 195 and this indicates they are covalently bound. Thus this structure is similar to the tetrahedryl intermediate that is formed during the cleavage reaction. The negative charge that develops on the carbonyl oxygen of the substrate is stablized by hydrogen bonds to the backbone nitrogens of Ser 195 and Gly 193, shown in blue spacefill. The hydrogen atoms involved in these hydrogen bonds are not shown.

== 3D Structures of Chymotrypsin ==

Chymotrypsin: Difference between revisions

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 The active site of an enzyme is the location where the substrate binds and where the chemical reaction occurs. Active site residues are those amino acid residues demonstrated to have importance for catalysis or substrate binding. Chymotrypsin contains three residues, Ser 195, His 57 and Asp 102, which are known as its <scene name='Chymotrypsin/Chymotrypsin_triad/2'>catalytic triad</scene>. Similar three-dimensional arrangements of a serine, a histidine and an aspartate are observed in many other proteases, and the role of these three residues in catalysis has been studied extensively. Serine acts as a nucleophile (contributing the electron pair for a new bond) attacking the carbonyl carbon of the peptide bond to be hydrolyzed. Histidine and aspartate turn serine into a better nucleophile by assisting in removing a hydrogen ion from serine.
+==Substrate binding and catalysis==
+<Structure load='7gch' size='300' frame='true' align='right' caption='Bovine chymotrypsin with bound inhibitor' scene='38/387136/Bovine_chymotrypsin_overview/2' />
+Features of the substrate binding site can be seen in structure of bovine chymotrypsin bound to the inhibitor N-acetyl-L-leucyl-L-phenylalanyl trifuoromethyl kentone (Ac-Leu-Phe-CF<sub>3</sub>), which resembles a peptide substrate. This scene shows the three peptide chains of the enzyme in spacefill and colored tuquoise, beige, and violet, and the inhibitor shown in CPK ball & stick is sitting in the active site.  In this <scene name='38/387136/Bovine_chymotrypsin_active_sit/1'>closeup of the active site</scene>, the residues of catalytic triad are shown in CPK ball & stick and labelled, and the inhibitor is in light gray ball & stick with its phenyl group in orchid. By moving the stucture back and forth with your mouse, it is easy to see that the phenyl group is located in the hydrophobic binding pocket of the enzyme. The binding pocket determines the preference for cleavage of peptides on the C-terminal side of aromatic residues.
+This view shows the carbonyl group of the inhibitor<scene name='38/387136/Bovine_chymotrypsin_active_sit/3'>carbonyl group of the inhibitor</scene> in CPK colors. The triflouromethyl group is bound to the carbon via the yellow bond. In a peptide substrate, the triflouromethyl group would be replaced by the first amino acid residue of the rest of the peptide chain, and the yellow bond is the bond that would be cleaved. The carbonyl carbon is 1.95 Å away from the side chain oxygen of serine 195 and this indicates they are covalently bound. Thus this structure is similar to the tetrahedryl intermediate that  is formed during the cleavage reaction. The negative charge that develops on the carbonyl oxygen of the substrate is stablized by hydrogen bonds to the backbone nitrogens of Ser 195 and Gly 193, shown in blue spacefill. The hydrogen atoms involved in these hydrogen bonds are not shown.
 == 3D Structures of Chymotrypsin ==