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

Step 2: Chymotrypsin Mechanism - Tetrahedral Intermediate with His57 ionized

A postulated stationary point in the reaction of Ser195 with the peptide bond to form the Zwitterionic tetrahedral intermediate involves the migration of the hydroxyl proton to His57 to form a histidinium or imidazolium cation.  This is predicted to be a stationary point, and examination of the predicted structure does in fact show the expected features: Asp102 is anionic, His57 is cationic, and Trp252 is anionic. (PDB file) (ARC file)

Interesting features of the Tetrahedral Intermediate

(A) Most important, the carbonyl carbon of Trp252 now has a tetrahedral coordination. The carbonyl oxygen now has a formal negative charge.

(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 hydrogen bond now exists between Ser195 and His57, although it is quite long, at 2.31Å.

(D) The C-N bond involving the tetrahedral carbon has increased in length only slightly from the normal 1.36Å in the starting model to 1.47Å, suggesting a slight weakening of the peptide bond.

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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.

Substrate in Hydrophobic pocket:
Ser189 Gly216 Ser217 Gly226 Gly250
Ala251 Trp252

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