Question

Serine proteases......
A) use an Asp, Lys, Ser catalytic triad
B) use a Shiff base-enzyme intermediate
C) cleave the Cα-carbonyl C bond

D) all of the above
E) B and C

F) none of the above

Answer 1

At least four distinct protein folds as illustrated by trypsin, subtilisin, prolyl oligopeptidase, and ClpP peptidase utilize the Asp-His Ser catalytic triad in identical configuration to catalyze hydrolysis of peptide bonds. Many serine proteases employ a simpler dyad mechanism where Lys or His is paired with the catalytic Ser. Other serine proteases mediate catalysis via novel triads of residues, such as a pair of His residues combined with the nucleophilic Ser.

The polypeptide substrate binds to the surface of the serine protease so that the scissile bond is inserted into the active site with the carbonyl carbon of this bond positioned near the nucleophilic serine. The serine -OH attacks the carbonyl carbon, and the nitrogen of the histidine accepts the hydrogen from the -OH of the serine and a pair of electrons from the double bond of the carbonyl oxygen moves to the oxygen and a tetrahedral intermediate is generated. The bond joining the nitrogen and the carbon in the peptide bond is broken. The covalent electrons creating this bond move to attack the hydrogen of the histidine, breaking the connection.

The electrons that previously moved from the carbonyl oxygen double bond move back from the negative oxygen to recreate the bond, generating an acyl-enzyme intermediate. Now, water replaces the N-terminus of the cleaved peptide, and attacks the carbonyl carbon. Again, the electrons from the double bond move to the oxygen making it negative, as the bond between the oxygen of the water and the carbon is formed. This is coordinated by the nitrogen of the histidine, which accepts a proton from the water. Overall, this generates another tetrahedral intermediate.

Finally the bond formed in the first step between the serine and the carbonyl carbon moves to attack the hydrogen that the histidine just acquired. The now electron-deficient carbonyl carbon re-forms the double bond with the oxygen. As a result, the C-terminus of the peptide is now ejected.