(Modeling proteins) (Chymotrypsin Mechanism: Step 1, Step 2, Step 3, Step 4, Step 5, Step 6)
This structure can be summarized as follows: Ser195 has reacted with the substrate, forming a covalent bond with the carbonyl carbon of Trp252, and the hydroxyl hydrogen atom that had been on Ser195 has now migrated to the nitrogen atom of the CH3-NH- group at the Trp252 end of the substrate. (PDB file) (ARC file)
(A) Most important, the carbonyl carbon of Trp252 now has a tetrahedral coordination. Because of this, the carbonyl oxygen has a formal charge of -1, although the partial charge is, of course, much smaller.
(B) Both hydrogen bonds from Gly193 and Ser195 of the oxyanion hole to the anionic carbonyl oxygen of Trp252 are now stronger, the Gly193 bond shortening from 1.81Å to 1.77Å, and the Ser195 bond shortening from 2.02Å to 1.88Å.
(C) A quite long, 2.32Å, hydrogen bond now exists between the Zwitterionic nitrogen atom and His57.
(D) The C-N bond between the tetrahedral carbon and the Zwitterionic nitrogen has increased in length from the normal 1.36Å in the starting model to 1.64Å, reflecting the weakening of the peptide bond.
|
Toggle display all Toggle center picture Fit to screen Interesting parts:
Catalytic triad:
Substrate:
Oxyanion hole plus substrate:
Tetrahedral intermediate:
Ser195 forms two bonds with Trp252, first, the ester bond between the hydroxyl oxygen and the carbonyl carbon of Trp252, forming the tetrahedral intermediate, carbon atom 3485, and second, the hydrogen bond between Ser195 peptide hydrogen and Trp252's carbonyl oxygen. Gly193 forms a similar hydrogen bond. Between Gly 193 and Ser195 is the ionized Asp194, which forms a salt bridge with Ile16. The peptide bond between Trp252 and Thr253 is unusually long, 1.71Å, indicative of the weakening of the C-N interaction. Substrate in Hydrophobic pocket:
Toggle spin Toggle stereo |