Crystal structure of Trypsin, a typical serine protease.

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 site 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. Image File history File links 1UTN.png‎ Summary X-ray crystallographic structure of Trypsin. ... Image File history File links 1UTN.png‎ Summary X-ray crystallographic structure of Trypsin. ... X-ray crystallography or single-crystal X-ray diffraction is an analytical technique which uses the diffraction pattern produced by bombarding a single crystal with X-rays to solve the crystal structure. ... Trypsin (EC 3. ... Biochemistry is the study of the chemical processes and transformations in living organisms. ... Peptidases (proteases [pronounced pro-tea-aces] and proteolytic enzymes are also commonly used) are enzymes which break peptide bonds of proteins. ... Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Serine is one of the 20 natural amino acids. ... Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... Chymotrypsin (bovine γ chymotrypsin: PDB 1AB9, EC 3. ... Subtilisin is a proteolytic enzyme obtained from . ... The coagulation of blood is a complex process during which blood forms solid clots. ... Immunity is medical term that describes a state of having sufficient biological defenses to avoid infection, disease, or other unwanted biological invasion. ... Inflammation is the first response of the immune system to infection or irritation and may be referred to as the Innate immune system and as healthy nor unhealthy on its own: Inflammation helps fight disease, but it comes at the cost of suspending the bodys normal immune and catabolic... This article or section does not adequately cite its references or sources. ... Prokaryotes are unicellular (in rare cases, multicellular) organisms without a nucleus. ... Kingdoms Eukaryotes are organisms with complex cells, in which the genetic material is organized into membrane-bound nuclei. ...

Digestive serine proteases

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Chymotrypsin-clan

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 peptide bond which is being cleaved, which is called the scissile bond. The different enzymes, like most enzymes, are highly specific in the reactions they catalyze. Each of these digestive serine proteases targets different regions of a polypeptide chain, based upon the side chains of the amino acid residues surrounding the site of cleavage: Chymotrypsin (bovine γ chymotrypsin: PDB 1AB9, EC 3. ... Trypsin (EC 3. ... Protein Crystal Growth Porcine Elastase In molecular biology, elastase is an enzyme from the class of proteases (or better peptidases) that break down proteins. ... Neuraminidase ribbon diagram An enzyme (in Greek en = in and zyme = blend) is a protein, or protein complex, that catalyzes a chemical reaction and also controls the 3D orientation of the catalyzed substrates. ... The pancreas is an organ in the digestive and endocrine system that serves two major functions: exocrine (producing pancreatic juice containing digestive enzymes) and endocrine (producing several important hormones, including insulin). ... In biology the small intestine is the part of the gastrointestinal tract (gut) between the stomach and the large intestine. ... Hydrolysis is a chemical reaction or process in which a molecule is split into two parts by reacting with a molecule of water, which has the chemical formula H2O. One of the parts gets an OH- from the water molecule and the other part gets an H+ from the water. ... A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ... X-ray crystallography is a technique in crystallography in which the pattern produced by the diffraction of x-rays through the closely spaced lattice of atoms in a crystal is recorded and then analyzed to reveal the nature of that lattice. ... Neuraminidase ribbon diagram An enzyme (in Greek en = in and zyme = blend) is a protein, or protein complex, that catalyzes a chemical reaction and also controls the 3D orientation of the catalyzed substrates. ... Peptides are the family of molecules formed from the linking, in a defined order, of various amino acids. ...

• Chymotrypsin is responsible for cleaving peptide bonds following a bulky hydrophobic amino acid residue. Preferred residues include phenylalanine, tryptophan and tyrosine, which fit into a snug hydrophobic pocket.

• Trypsin is responsible for cleaving peptide bonds following a positively-charged amino acid residue. Instead of having the hydrophobic pocket of the chymotrypsin, there exists an aspartic acid residue at the base of the pocket. This can then interact with positively-charged residues such as arginine and lysine on the substrate peptide to be cleaved.

• Elastase is responsible for cleaving peptide bonds following a small neutral amino acid residue, such as Alanine, glycine and valine. (These amino acid residues form much of the connective tissues in meat). The pocket that is in "trypsin" and "chymotrypsin" is now partially filled with valine and threonine, rendering it a mere depression, which can accommodate these smaller amino acid residues.

The combination of these three enzymes make an incredibly effective digestive team, and are primarily responsible for the digestion of proteins. Chymotrypsin (bovine γ chymotrypsin: PDB 1AB9, EC 3. ... Phe redirects here. ... Tryptophan is an amino acid and essential in human nutrition. ... Tyrosine (from the Greek tyros, meaning cheese, as it was first discovered in 1846 by German chemist Justus von Liebig in cheese[1][2]), 4-hydroxyphenylalanine, or 2-amino-3(4-hydroxyphenyl)-propanoic acid, is one of the 20 amino acids that are used by cells to synthesize proteins. ... In chemistry, hydrophobic or lipophilic species, or hydrophobes, tend to be electrically neutral and nonpolar, and thus prefer other neutral and nonpolar solvents or molecular environments. ... Trypsin (EC 3. ... In chemistry, hydrophobic or lipophilic species, or hydrophobes, tend to be electrically neutral and nonpolar, and thus prefer other neutral and nonpolar solvents or molecular environments. ... Aspartic acid (Asp), also known as aspartate, the name of its anion, is one of the 20 natural proteinogenic amino acids which are the building blocks of proteins. ... Arginine (symbol Arg or R) is an α-amino acid. ... Lysine is one of the 20 amino acids normally found in proteins. ... Protein Crystal Growth Porcine Elastase In molecular biology, elastase is an enzyme from the class of proteases (or better peptidases) that break down proteins. ... Alanine (Ala, A) also 2-aminopropanoic acid is a non-essential α-amino acid. ... For the plant, see Glycine (plant). ... Valine is one of the 20 natural amino acids, and is coded for in DNA. Nutritionally, valine is also an essential amino acid. ... Valine is one of the 20 natural amino acids, and is coded for in DNA. Nutritionally, valine is also an essential amino acid. ... Threonine is one of the 20 natural amino acids. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ...

Subtilisin

Subtilisin is a serine protease in prokaryotes. Subtilisin is evolutionary unrelated to the chymotrypsin-clan, but shares the same catalytic mechanism utilising a catalytic triad, to create a nucleophilic serine. This is the classic example used to illustrate convergent evolution, since the same mechanism evolved twice independently during evolution. Prokaryotes are unicellular (in rare cases, multicellular) organisms without a nucleus. ... Three amino acid residues found inside the active site of certain proteases. ... Serine is one of the 20 natural amino acids. ... In evolutionary biology, convergent evolution is the process whereby organisms not closely related, independently evolve similar traits as a result of having to adapt to similar environments or ecological niches. ... This article is about evolution in biology. ...

Catalytic mechanism

The main player in the catalytic mechanism in the chymotrypsin and subtillisin clan enzymes mentioned above is the catalytic triad. The triad is located in the active site of the enzyme, where catalysis occurs, and is preserved in all serine protease enzymes. The triad 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 very near one another near the heart of the enzyme, these three key amino acids each play an essential role in the cleaving ability of the proteases. Three amino acid residues found inside the active site of certain proteases. ... In chemistry, an amino acid is any molecule that contains both amino and carboxylic acid functional groups. ... Histidine is one of the 20 most common natural amino acids present in proteins. ... Serine is one of the 20 natural amino acids. ... Aspartic acid (Asp), also known as aspartate, the name of its anion, is one of the 20 natural proteinogenic amino acids which are the building blocks of proteins. ...

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). Regional competition level table tennis, showing table, net, and player getting ready to return the ball with a winning backhand topspin stroke. ... In biochemistry, a substrate is a molecule upon which an enzyme acts. ...

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 of the scissile peptide bond of the substrate. Image File history File links Size of this preview: 676 × 600 pixel Image in higher resolution (1002 × 889 pixel, file size: 18 KB, MIME type: image/png) the serine protease reaction mechanism. ... Serine is one of the 20 natural amino acids. ... In chemistry, a nucleophile (literally nucleus lover) is a reagent which is attracted to centres of positive charge. ... Carbonyl group In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom. ... A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ...

• A pair of electrons on the histidine nitrogen has the ability to accept the hydrogen from the serine -OH group, thus coordinating the attack of the peptide bond.
• The carboxyl 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: Histidine is one of the 20 most common natural amino acids present in proteins. ... This article is about the chemistry of hydrogen. ... Serine is one of the 20 natural amino acids. ... A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ... A carboxyl or carboxylic group is a functional group consisting of a carbon atom and an oxygen atom doubly bonded to each other. ... Aspartic acid (Asp), also known as aspartate, the name of its anion, is one of the 20 natural proteinogenic amino acids which are the building blocks of proteins. ... In chemistry, a hydrogen bond is a type of attractive intermolecular force that exists between two partial electric charges of opposite polarity. ... Histidine is one of the 20 most common natural amino acids present in proteins. ... It has been suggested that this article or section be merged with electronegativity. ...

• The polypeptide substrate binds to the surface of the serine protease enzyme such that scissile bond is inserted into the active site of the enzyme, 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. 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.

Peptides are the family of molecules formed from the linking, in a defined order, of various amino acids. ... In chemistry, a nucleophile (literally nucleus lover) is a reagent which is attracted to centres of positive charge. ... Serine is one of the 20 natural amino acids. ... Serine is one of the 20 natural amino acids. ... Carbonyl group In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom. ... Histidine is one of the 20 most common natural amino acids present in proteins. ... Carbonyl group In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom. ... Histidine is one of the 20 most common natural amino acids present in proteins. ... Carbonyl group In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom. ... The N-terminal end refers to the extremity of a protein or polypeptide terminated by an amino acid with a free amine group (NH2). ... Carbonyl group In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom. ... Histidine is one of the 20 most common natural amino acids present in proteins. ... Serine is one of the 20 natural amino acids. ... Carbonyl group In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom. ... Histidine is one of the 20 most common natural amino acids present in proteins. ... Carbonyl group In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom. ... The C-terminal end refers to the extremity of a protein or polypeptide terminated by an amino acid with a free carboxyl group (COOH). ...

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. Definition An oxyanion is a polyatomic ion with a negative charge that contains oxygen. ... The general structure of a tetrahedral molecule, with the central atom labelled pink. ... Carbonyl group In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom. ... The transition state of a chemical reaction is a particular configuration along the reaction coordinate. ...

Zymogens

There are certain inhibitors that resemble the tetrahedral intermediate, and thus fill up the specificity pocket,^[clarify] preventing the enzyme from working properly. Trypsin, a powerful digestive enzyme, is generated in the pancreas. Inhibitors prevent self-digestion of the pancreas itself. HIV protease in a complex with the protease inhibitor ritonavir. ...

Zymogens are the usually inactive precursors of an enzyme. 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. A zymogen or a proenzyme, is an inactive enzyme precursor. ... An autopsy, also known as a post-mortem examination or an obduction, is a medical procedure that consists of a thorough examination of a corpse to determine the cause and manner of a persons death and to evaluate any disease or injury that may be present. ...

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, can proteolysis occur. Proteolysis is the directed degradation (digestion) of proteins by cellular enzymes called proteases or by intramolecular digestion. ... Proteolysis is the directed degradation (digestion) of proteins by cellular enzymes called proteases or by intramolecular digestion. ...

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: Trypsin (EC 3. ... In biology the small intestine is the part of the gastrointestinal tract (gut) between the stomach and the large intestine. ... Lysine is one of the 20 amino acids normally found in proteins. ... A single chemical reaction is said to have undergone autocatalysis, or be autocatalytic, if the reaction product is itself the catalyst for that reaction. ... Chymotrypsin (bovine γ chymotrypsin: PDB 1AB9, EC 3. ... In chemistry, autolysis is the production of a substance which catalyses the reaction it was made in, or catalyzes its own transformation into another compound. ... Protein Crystal Growth Porcine Elastase In molecular biology, elastase is an enzyme from the class of proteases (or better peptidases) that break down proteins. ...

• 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.

Inhibition

Serine proteases are inhibited by a diverse group of inhibitors, including synthetic chemical inhibitors for research or therapeutic purposes, and also natural proteinaceous inhibitors. One family of natural inhibitors called "serpins" (abbreviated from serine protease inhibitors) can 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. Artificial irreversible small molecule inhibitors include AEBSF and PMSF. Look up inhibition, inhibitor in Wiktionary, the free dictionary. ... Serine protease inhibitors or serpins (short for serine protease inhibitor) are a group of proteins that inhibit peptidases (old name: proteases). ... Covalent bonding is a form of chemical bonding characterized by the sharing of one or more pairs of electrons between atoms, in order to produce a mutual attraction, which holds the resultant molecule together. ... Image:Antithrombin. ... Alpha 1-antitrypsin or α1-antitrypsin (A1AT) is a serine protease inhibitor (serpin). ... The coagulation of blood is a complex process during which blood forms solid clots. ... Thrombosis is the formation of a clot or thrombus inside a blood vessel, obstructing the flow of blood through the circulatory system. ... Alpha 1-antitrypsin or α1-antitrypsin (A1AT) is a serine protease inhibitor (serpin). ... This article or section does not cite its references or sources. ... PMSF (phenylmethylsulphonylfluoride) is a serine protease inhibitor. ...

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. Protein C is a major physiological anticoagulant. ... Thrombosis is the formation of a clot or thrombus inside a blood vessel, obstructing the flow of blood through the circulatory system. ...

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.
• Prostate specific antigen is used to determine prostate cancer risk

Coagulation is the thickening or congealing of any liquid into solid clots. ... Fecal elastase refers to the testing of the concentration of the pancreatic elastase-1 enzyme found in fecal matter with an enzyme-linked immunosorbent assay (ELISA). ... Chronic pancreatitis can present as episodes of acute inflammation in a previously injured pancreas, or as chronic damage with persistent pain or malabsorption. ... Prostate specific antigen (PSA, also known as kallikrein III, seminin, semenogelase, γ-seminoprotein and P-30 antigen) is a protein manufactured almost exclusively by the prostate gland; PSA is produced for the ejaculate where it liquifies the semen and allows sperm to swim freely. ... Prostate cancer is a disease in which cancer develops in the prostate, a gland in the male reproductive system. ...

External link

• Serine protease site of the Washington University in St. Louis (WUSTL)
• MeSH Serine+proteases