(Modeling proteins) (Chymotrypsin Mechanism: Step 1, Step 2, Step 3, Step 4, Step 5, Step 6)

Step 3: Chymotrypsin Mechanism - the Tetrahedral Intermediate

 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)

Interesting features of the Tetrahedral Intermediate

(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:
His57 Asp102 Ser189 Gly193 Asp194
Ser195 Ser214 Ser214 Gly216 Ser217
Gly226 Gly250 Ala251 Trp252 Thr253
H2O

Catalytic triad:
His57 Asp102 Ser195

Substrate:
Gly250 Ala251 Trp252 Thr253


Oxyanion hole plus substrate:
Gly193 Asp194 Ser195 Gly250 Ala251
Trp252 Thr253

Tetrahedral intermediate:
Gly193 Asp194 Ser195 Trp252 Thr253

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:
Ser189 Gly216 Ser217 Gly226 Gly250
Ala251 Trp252

Toggle spin Toggle stereo