Chymotrypsin: Difference between revisions

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==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.

[[Image:LPFstructure.jpg|left]]

Features of the substrate binding site can be seen in the structure of bovine chymotrypsin bound to the inhibitor N-acetyl-L-leucyl-L-phenylalanyl trifuoromethyl ketone (Ac-Leu-Phe-CF<sub>3</sub>), which resembles a peptide substrate (see structure in left figure). The colored backgrounds in the figure indicate the four components of structure and shows the bond (yellow on black background) that is position to be cleaved. The default scene shows the three peptide chains of chymotrypsin in spacefill and colored tuquoise, beige, and violet. The inhibitor, which is 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 structure 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 enzyme's 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.

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 carbonyl 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 would be the bond that is cleaved. The carbonyl carbon of the inhibitor is 1.95 Å away from the side chain oxygen of serine 195, and this indicates they are covalently bound (bond indicated by dotted line). Thus, this structure is similar to the tetrahedral intermediate that is formed during the cleavage reaction. The negative charge that develops on the carbonyl oxygen of the substrate is stabilized 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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@@ Line 40: / Line 40: @@
 ==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' />
+<Structure load='7gch' size='300' frame='true' align='right' caption='[[7gch]] 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.
+[[Image:LPFstructure.jpg|left]]
+Features of the substrate binding site can be seen in the structure of bovine chymotrypsin bound to the inhibitor N-acetyl-L-leucyl-L-phenylalanyl trifuoromethyl ketone (Ac-Leu-Phe-CF<sub>3</sub>), which resembles a peptide substrate (see structure in left figure). The colored backgrounds in the figure indicate the four components of structure and shows the bond (yellow on black background) that is position to be cleaved. The default scene shows the three peptide chains of chymotrypsin in spacefill and colored tuquoise, beige, and violet. The inhibitor, which is 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 structure 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 enzyme's 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.
+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 carbonyl 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 would be the bond that is cleaved. The carbonyl carbon of the inhibitor is 1.95 Å away from the side chain oxygen of serine 195, and this indicates they are covalently bound (bond indicated by dotted line). Thus, this structure is similar to the tetrahedral intermediate that is formed during the cleavage reaction. The negative charge that develops on the carbonyl oxygen of the substrate is stabilized 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 ==