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

Step 5: Chymotrypsin Mechanism - Chymotrypsin pre-acid plus histidinium 57

 After the peptide bund is broken, the amine fragment, here CH3-NH2, migrates out of the active site.  This leaves behind an ester composed of Ser195 reacting with Trp252.   A water molecule now reacts with this ester, adding a hydroxyl group to the carboxylic carbon, forming a tetrahedral carbon again.  At the same time, the proton adds to His57 to form histidinium again.  (PDB file) (ARC file)

Interesting features of the new tetrahedral intermediate

(A) This is a predicted intermediate.  There is no mention of it in the literature, so it should be regarded as a new idea, and therefore viewed with some skepticism.

(B) The carbonyl carbon of Trp252 now has a tetrahedral coordination once more.  In place of the weakened peptide bond, there is now the hydroxyl group from the water that will be used in the hydrolysis.  As with the earlier tetrahedral intermediate, the carbonyl oxygen has a formal charge of -1.

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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


Active site plus substrate:
Gly193 Asp194 Ser195 Gly250 Ala251
Trp252 Thr253 H2O


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.

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