Serine protease

From Academic Kids

In biochemistry, a serine proteases or serine endopeptidases (newer name) are a class of peptidases which are characterised by the presence of a serine residue in the active center of the enzyme. Serine proteases participate in a wide range of functions in the body, including blood clotting, inflammation as well as digestive enzymes in both prokaryotes and eukaryotes.


Digestive serine proteases


There are three serine proteases that are well understood, namely chymotrypsin, trypsin, and elastase. All three enzymes are synthesized by the pancreatic acinar cells, secreted in the small intestine and are responsible for catalyzing the hydrolysis of peptide bonds. All three of these enzymes are similar in structure, as shown through their X-ray structures. The differing aspect lies in the scisile site. The different enzymes, like most enzymes, are highly specific in the reactions they catalyze. Each of these digestive serine proteases targets different regions of the polypeptide chain, based upon the amino acid residues and side chains surrounding the site of cleavage:

  • Trypsin is responsible for cleaving peptide bonds flanked with positively charged amino acid residues. Instead of having the hydrophobic pocket of the "chymotrypsin", there exists an aspartic acid residue at the back of the pocket. This can then interact with positively charged residues such as arginine and lysine.
  • Elastase is responsible for cleaving peptide bonds flanked with small neutral amino acid resideues. Alanine, glycine and valine are all major amino acid residues that are nearly otherwise indigestible, forming much of the connective tissues in meat. The pocket that is in "trypsin" and "chymotrypsin" is now lined with valine and threonine, rendering it a mere depression, which can accommodate these smaller amino acid residues.

A combination of these three make an incredibly effective digestive team, and are primarily responsible for the digestion of proteins.

Catalytic mechanism

The main player in the catalytic mechanism in the three digestive serine proteases mentioned above is the catalytic triad. This particular structure, preserved in all three of the enzymes, is a coordinated structure consisting of three essential amino acids: histidine (His 57), serine (Ser 195) (hence the name "serine protease") and aspartic acid (Asp 102). Located near the heart of the enzyme, these three key amino acids each play an essential role in the cleaving ability of the proteases.

In the event of catalysis, an ordered mechanism occurs in which several intermediates are generated. The catalysis of the peptide cleavage can be seen as a ping-pong catalysis, in which a substrate binds (in this case, the polypeptide being cleaved), a product is released (the N-terminus "half" of the peptide), another substrate binds (in this case, water), and another product is released (the C-terminus "half" of the peptide).

Each amino acid in the triad performs a specific task in this process:

The whole reaction can be summarized as follows:

  • As the polypeptide enters, the above described process occurs: the serine -OH attacks the carbonyl carbon, 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. As a result, a tetrahedral intermediate is generated.
  • The bond joining the nitrogen and the carbon in the peptide bond is now 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 comes in to the reaction. Water replaces the N-terminus of the cleaved peptide, and attacks the carbonyl carbon. Once 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.
  • In a final reaction, 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.

Additional stabilizing effects

It was discovered that additional amino acids of the protease, Gly 193 and Ser 195, are involved in creating what is called an oxyanion hole. Both Gly 193 and Ser 195 have nitrogen-hydrogen bonds. When the tetrahedral intermediate of step 1 and step 3 are generated, the negative oxygen ion, having accepted the electrons from the carbonyl double bond fits perfectly into the oxyanion hole. In effect, serine proteases preferentially bind the transition state and the overall structure is favored, driving the reaction forward to completion. It should be noted that this "preferential binding" is responsible for much of the catalytic efficiency of the enzyme.


There are certain inhibitors which resemble the tetrahedral intermediate, and thus fill up the specificity pocket, preventing the enzyme from working properly. Trypsin is generated in the pancrease. As stated above, these are powerful digestive enzymes. In order to prevent them from digesting the pancreas itself, inhibitors often come into play to prevent the organism from self-digestion.

Zymogens is a term referring to the precursors of an enzyme, usually inactive. So far, we have been discussing digestive enzymes. The reason behind a zymogen should be evident - if the digestive enzymes were active when synthesized, they would immediately start chewing up the organs and tissue that synthesized them. Acute pancreatitis is such a condition, in which there is premature activation of the digestive enzymes in the pancreas, resulting in self-digestion (autolysis). It also complicates postmortem investigations, as the pancreas often digests itself before it can be assessed visually.

Zymogens are large, inactive structures, which have the ability to break apart or change into the smaller activated enzymes. The difference between zymogens and the activated enzymes lies in the fact that the active site for catalysis of the zymogens is distorted. As a result, the substrate polypeptide cannot bind effectively, and proteolysis does not occur. Only after activation, during which the conformation and structure of the zymogen change and the active site is opened up, can proteolysis occur.

The zymogen for trypsin is trypsinogen. When trypsinogen enters the small intestine from the pancrease, secretions from the duodenal mucosa cleaves the lysine 15 - isoleucine 16 peptide bond of the zymogen. As a result, the zymogen trypsinogen breaks down into trypsin. Recall that trypsin is also responsible for cleaving lysine peptide bonds, and thus, once a small amount of trypsin is generated, it participates in cleavage of its own zymogen, generating even more trypsin. The process of trypsin activation can thus be called autocatalytic.

Chymotrypsinogen is the zymogen of chymotrypsin. After the Arg 15 - Ile 16 bond in the chymotrypsinogen zymogen is cleaved by trypsin, the newly generated structure called a pi-chymotrypsin undergoes autolysis (self digestion), yielding active chymotrypsin.

Proelastase is the zymogen of elastase, and it is activated by cleavage through trypsin.

As can be seen, trypsinogen activation to trypsin is essential, because it activates its own reaction, as well as the reaction of both chymotrypsin and elastase. It is therefore essential that this activation doesn't occur prematurely. There are several protective measures taken by the organism to prevent self-digestion:

  • The activation of trypsinogen by trypsin is relatively slow
  • The zymogens are stored in zymogen granules, capsules that have walls that are thought to be resistant to proteolysis.


Serine proteases are inhibited by serine protease inhibitors ("serpins"), a diverse group of enzymes that form a covalent bond with the serine protease, inhibiting its function. The best-studied serpins are antithrombin and alpha 1-antitrypsin, studied for their role in coagulation/thrombosis and emphysema/A1AT respectively.

Role in disease

Mutations may lead to decreased or increased activity of enzymes. This may have different consequences, depending on the normal function of the serine protease. Mutations in protein C, when leading to insufficient protein levels or activity, predispose to thrombosis.

Diagnostic use

Determination of serine protease levels may be useful in the context of particular diseases. Coagulation factor levels may be required in the diagnosis of hemorrhagic or thrombotic conditions.

Fecal elastase is employed to determine the exocrine activity of the pancreas, e.g. in cystic fibrosis or chronic pancreatitis.

Full list

Numbering follows the EC numbers in the Expasy enzyme list, category 3.4.21 ( (missing numbers were transferred or deleted):

External link


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