Structural Biochemistry/Enzyme/Serine Proteases
Serine proteases are proteases that have serine, an amino acid, bonded at the active site. Their main function in humans is digestion, however they also function in processes such as inflammation, blood clotting, and the immune system in both prokaryotes and eukaryotes. Serine proteases are grouped depending on their structure. Major groups of serine proteases include alpha hydrolase, beta hydrolase, and signal peptidase. The serine proteases is the enzyme that catalyze the hydrolysis of ester or amide. This reaction involves the reaction of acylation of the hydroxyl group of Ser-195. The substrate forms a tetrahedral intermediate by attacking of Ser-195 on the carboxyl group of the substrate since the active site of the enzyme is complementary to the transition state of the reaction.
Proteases, proteinases, peptidases describe the same group of enzymes that catalyze the hydrolysis of covalent peptide bonds. Serine proteases are grouped into clans that share structural homology and then further subgrouped into families that share close sequence homology. In the case of serine protease, the mechanism of the protease is based on the nucleophilic attack of the targeted peptidic bond by a serine.
Cysteine, threonine or water molecules associated with aspartate or metals may also play this role. In many cases the nucleophilic property of the group is improved by the presence of a histidine, held in a "proton acceptor state" by an aspartate. Aligned side chains of serine, histidine and aspartate build the catalytic triad common to most serine proteases.
The active site of serine proteases is shaped as a cleft where the polypeptide substrate binds. Schechter and Berger  labeled amino acid residues from N to C term of the polypeptide substrate (Pi, ..., P3, P2, P1, P1', P2', P3', ..., Pj) and their respective binding sub-sites Si,..., S3, S2, S1, S1', S2', S3',..., Sj) . The cleavage is catalyzed between P1 and P1'.
Many proteases are synthesized and secreted as inactive forms called zymogens and subsequently activated by proteolysis. This changes the architecture of the active site of the enzyme.
Few examples are: Chymotrypsin, trypsin, and elastase.
Synthesized as inactive proenzymes (chymotrypsinogen)
Formation of key acyl-enzyme intermediate
Catalytic residues are Ser195 and His57
~240-residue monomeric proteins, 4 disulfide bridges
Two folded domains with antiparallel b-sheets (barrel-like) and little helix
Catalytic triad - His57 and Ser195 located at substrate binding site along with Asp102, which is buried in solventinaccessible pocket.
Chymotrypsin - prefers bulky Phe, Trp, or Tyr in hydrophobic pocket.
Trypsin - prefers Arg and Lys in binding pocket (Ser189 replaced by Asp).
Elastase - prefers Ala, Gly, Val in its depression site
Bound substrate is attacked by nucleophilic Ser195 forming transition state complex (tetrahedral intermediate), His57 takes up H+, which is facilitated by Asp102.
Tetrahedral intermediate decomposes to acyl-enzyme intermediate by His57 (general acid).
Acyl-enzyme intermediate is deacylated by reverse of above steps, release of carboxylate product, H2O is nucleophile and Ser195 is leaving group.
Enzyme prefers binding transition state to either Michaelis complex or acyl-enzyme intermediate forms.
Catalytic triad serves to form low-barrier hydrogen bonds in the transition state (assisted by hydrophobic environment).
Inactive (proenzyme) forms
Enzyme inhibitors (pancreatic trypsin inhibitor) or zymogen granules prevent activation
Active sites are distorted
Serine proteases are sequence specific. While cascades of protease activations control blood clotting and complement, other proteasesare involved in signalling pathways, enzyme activation and degradative functions in different cellular or extracellular compartments.