Human beta tryptase is a mast-cell specific serine protease. A mast cell or mastocyte, is a resident cell of connective tissue that contains many granules rich in histamine and heparin. These cells play a role in allergy and anaphylaxis, wound healing and pathogenic defense mechanisms. Human beta tryptase is released from the cell after cellular activation. It is thought that this protein may be involved in causing asthma and other allergic and inflammatory disorders.

Human beta tryptase is an unique enzyme for two reasons. First it can only be active as a heparin-stabilized tetramer. And second it is resistant to all known endogenous proteinase inhibitors.

The tetramer has four chains, each with two domains. There are hydrophobic and polar interactions that contribute to the intermolecular contacts between the monomers. There is symmetry in the flat, square protein; chain A (red) equals chain C(green) and chain B(orange) equals chain D (blue). The active centers are arranged to face toward the central pore. This structure is complexed with a synthetic inhibitor: 4-aminophenyl pyruvic acid (APPA). This is inhibitor is located at the active sites. Its purpose is to prevent catalysis in order to obtain the crystal structure.

Human beta tryptase hydrolyzes a number of peptide substrates using a typical serine protease mechanism. It cleaves the peptide bonds following Arg and Lys. The catalytic residues are Ser195, His57 and Asp102. These are found at the junction between two beta barrels that are perpendicular to each other. The His and Asp are on the loop of one barrel and the Ser is on a loop of the other barrel. These three amino acids make up the catalytic triad.

The reaction mechanism has four main steps. (1)The reaction starts when the peptide substrate binds and the hydroxyl group on the Ser195 nucleophilically attacks the peptide's carbonyl. The neighboring histidine extracts the hydroxyl hydrogen, making the hydroxyl group more nucleophilic, with the assistance from Asp102. A covalent bond forms between Ser195 and the substrate to form a tetrahedral intermediate which is stabilized by to amide hydrogens. (2) The tetrahedral intermediate quickly decomposes back to a planar carbonyl group when the bond to serine dissolves or the nitrogen bonds break from the C-terminus and form an ester linkage to the N-terminus of the substrate. This is called an acyl-enzyme intermediate. (3) The ester bond is broke by water nucleophilically attacking the carbonyl. The water transfers one hydrogen to the histidine while forming a covalent bond to the carbonyl carbon. The result is another tetrahedral intermediate stabilized by amide groups. (4) In the final step, the bond from the serine hydroxyl group is broken, decomposing the tetrahedral intermediate. The hydrogen held by the histidine is transferred to the serine and the substrate is released with a carboxylic acid terminus. The enzyme is returned to its original state ready to bind the next protein.

The CATH classification of human beta tryptase is Class: mainly beta, Architecture: barrel, Topology: thrombine, subunit H, Homology: trypsine-like serine protease

The motif is: 2 sheets, 7 beta hairpins, 14 strands, 6 beta bulges, 5 helices, 35 beta turns, 1 gamma turn and 4 disulfides.