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A protease is an enzyme that cleaves peptide bonds. A Serine protease is an enzyme that uses an active site serine, in catalysis. They cleave on the C-terminals of specific residues. Trypsin cleaves on the C-terminal of the positively charged amino acids Lysine and Arginine. Chymotrypsin cleaves on the C-terminals of the large aromatic amino acids Phenylalanine, Tyrosine, and Tryptophan. Other Serine proteases include; elastase, thrombin, plasmin and kallikrien.

Key Components of the Enzyme Are:

Catalytic Triad
The active site consists of three invariant amino acids, known as the catalytic triad. These three amino acids are Serine 195, Histidine 57 and Aspartic Acid 102. The residues Ser195 and His57 are essential for function, this means that the enzyme's function will be destroyed if there is a point mutation, which changes one of these residues, or if a compound that reacts with one is added. A point mutation in Asp102 decreases the efficiency of the enzyme. In the enzyme this residue is unprotonated, and it serves to properly orient His57 by hydrogen bonding with it.

Oxyanion Hole
This is a region of the active site formed by the amide hydrogens of the residues Serine 195 and Glycine 193. They serve to stabilize the negative charge that forms on the carbonyl oxygen.11:42 PM 10/26/2001

Specificity Pocket
This is a pocket that gives each enzyme it's ability to cut at the C-terminal of only specific amino acids. In trypsin the amino acid Aspartic Acid 189 is located in the specificity pocket, it stabilizes the positive charges of the residues lysine and arginine. Chymotrypsin's specificity pocket is large and nonpolar, this stabilizes the large hydrophobic aromatic residues that chymotrypsin cleaves after.

A Sketch of the Active Site:

The sketch is a little off scale but should give a fairly good idea of what the arrangement of the active site is.

... = Hydrogen bond

               |     |-----|
               N     |     | 
 oxyanion      |     |     | specificty pocket 
   hole        H ____|     |_____
  Ser195 N-H        

His57 ||   \\
  \   ||    /
         - O

The Mechanism of the Enzyme:

1) In the first step His57 acts as a general base partially abstracting the hydroxyl proton of Ser195. This causes the hydroxyl group on Ser195 to nucleophilically attack the Carbonyl carbon of the scissile bond forming the tetrahedral intermediate. In this intermediate the negative charge on the carbonyl oxygen is stabilized by the oxyanion hole, and His57 is protonated.

2) In the second step the amino end of the scissile bond acts as a leaving group, this is the actual cleavage of the peptide bond. His57 acts as a general acid by protonating this leaving group. At the end of this step His57 is unprotonated, a free peptide fragment has been released, and the hydroxy O of Ser195 is covalently bound to the Carbonyl carbon of the scissile bond.

3) In the third step His57 once again acts as a general base by abstracting a proton from a water molecule, this causes the oxygen of the water molecule to nucleophilically attack the carbonyl carbon. The negative charge on the carbonyl oxygen is once again stabilized by the oxyanion hole. At the end of this step His57 is once again protonated, and another tetrahedral intermediate is formed.

4) In the fourth and final step the hydroxyl oxygen of Ser195 acts as a leaving group, and is protonated by His57 acting as a general acid. This releases a second peptide fragment and regenerates the active site as seen in the diagram.

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