In biochemistry, serine proteases or serine endopeptidases (newer name) are a class of peptidases (enzymes that cleave peptide bonds in proteins) that are characterised by the presence of a serine residue in the active center of the enzyme. Serine proteases are grouped into clans that share structural homology and then further subgrouped into families that share close sequence homology. The major clans found in humans include the chymotrypsin-like, the subtilisin-like, the alpha/beta hydrolase, and signal peptidase clans. Serine proteases participate in a wide range of functions in the body, including blood clotting, immunity, and inflammation, as well as contributing to digestive enzymes in both prokaryotes and eukaryotes.
Digestive serine proteases
The three serine proteases of the chymotrypsin-like clan that have been studied in greatest detail are 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 scissile 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:
- Chymotrypsin is responsible for cleaving peptide bonds flanked with bulky hydrophobic amino acid residues. Preferred residues include phenylalanine, tryptophan and tyrosine, which fit into a snug hydrophobic pocket.
- 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 residues. 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.
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 serine has an -OH group that is able to act as a nucleophile, attacking the carbonyl carbon in the potential peptide bond.
- The pair of electrons on the nitrogen histidine has the ability to accept the hydrogen from the serine -OH group, thus coordinating the attack of the peptide bond
- The carboxylic group on the aspartic acid in turn hydrogen bonds with the histidine, making the pair of electrons mentioned above much more electronegative.
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, lowering the activation energy of the reaction. 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.
Zymongens 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.
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. For example, mutations in protein C, when leading to insufficient protein levels or activity, predispose to thrombosis.
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.
- Prostate specific antigen is used to determine prostate cancer risk
Numbering follows the EC numbers in the ExPasy enzyme list, category 3.4.21 (missing numbers were transferred or deleted):
- 1 - Chymotrypsin
- 2 - Chymotrypsin C.
- 3 - Metridin
- 4 - Trypsin
- 5 - Thrombin
- 6 - Coagulation factor Xa
- 7 - Plasmin
- 9 - Enteropeptidase
- 10 - Acrosin
- 12 - Alpha-lytic endopeptidase
- 19 - Glutamyl endopeptidase
- 20 - Cathepsin G
- 21 - Coagulation factor VIIa
- 22 - Coagulation factor IXa
- 25 - Cucumisin
- 26 - Prolyl oligopeptidase
- 27 - Coagulation factor XIa
- 32 - Brachyurin
- 34 - Plasma kallikrein
- 35 - Tissue kallikrein.
- 36 - Pancreatic elastase
- 37 - Leukocyte elastase
- 38 - Coagulation factor XIIa
- 39 - Chymase
- 41 - Complement subcomponent C1r.
- 42 - Complement subcomponent C1s.
- 43 - Classical complement pathway C3/C5 convertase.
- 45 - Complement factor I.
- 46 - Complement factor D.
- 47 - Alternate complement pathway C3/C5 convertase.
- 48 - Cerevisin
- 49 - Hypodermin C
- 50 - Lysyl endopeptidase
- 53 - Endopeptidase La
- 54 - Gamma-renin
- 55 - Venombin AB
- 57 - Leucyl endopeptidase
- 59 - Tryptase
- 60 - Scutelarin
- 61 - Kexin
- 62 - Subtilisin
- 63 - Oryzin
- 64 - Endopeptidase K
- 65 - Thermomycolin
- 66 - Thermitase
- 67 - Endopeptidase So
- 68 - T-plasminogen activator
- 69 - Protein C (activated).
- 70 - Pancreatic endopeptidase E
- 71 - Pancreatic elastase II
- 72 - IgA-specific serine endopeptidase.
- 73 - U-plasminogen activator
- 74 - Venombin A
- 75 - Furin
- 76 - Myeloblastin
- 77 - Semenogelase
- 78 - Granzyme A
- 79 - Granzyme B
- 80 - Streptogrisin A
- 81 - Streptogrisin B
- 82 - Glutamyl endopeptidase II
- 83 - Oligopeptidase B
- 84 - Limulus clotting factor C
- 85 - Limulus clotting factor B
- 86 - Limulus clotting enzyme
- 87 - Omptin
- 88 - Repressor lexA.
- 89 - Signal peptidase I.
- 90 - Togavirin.
- 91 - Flavivirin.
- 92 - Endopeptidase Clp.
- 93 - Proprotein convertase 1
- 94 - Proprotein convertase 2
- 95 - Snake venom factor V activator.
- 96 - Lactocepin.
- 97 - Assemblin.
- 98 - Hepacivirin.
- 99 - Spermosin.
- 100 - Pseudomonalisin.
- 101 - Xanthomonalisin.
- 102 - C-terminal processing peptidase.
- 103 - Physarolisin.