Trypsin active site region

Figure 5. Stereoview of the active site region of trypsin bound to the trypsin inhibitor complex. The lys 16 sidechain extends back into the receptor cavity (cf. Figure 7 for a better view). The proton relay chain, asp 102-his 57-ser 195 arches from right to center with ser 195 appearing in the center. The partially tetrahedral geometry of the carbonyl carbon atom of lys 16 may be seen with some difficulty. The hexapeptide from the trypsin inhibitor protein (Figure 8) is drawn intensely for emphasis central H bridges are drawn as dashed vectors.

Fig. 4 AutoSolve solution for a fragment hit against trypsin. The initial mF0 — DFC difference Fourier contoured at 3a is shown for the active site region. Despite the pseudosymmetric shape of the electron density, AutoSolve correctly orientates the ligand to satisfy the most likely hydrogen bonding pattern with the protein (denoted by dashed lines). Figure adapted from Mooij et al. [45]...

Comparison (or alignment) of amino acid sequences, also called homology search, often provides first-hand information on such conserved structural features and enables one to classify enzymes into families and predict the possible function of a new enzyme (86). A family of enzymes usually folds into similar 3-D structures, at least at the active site region. A typical example is the serine protease family whose members—trypsin, chymotrypsin, elastase, and subtilisin—commonly contain three active-site residues, Asp/His/Ser, which are known as the catalytic triad or charge relay system. Another example is the conserved features of catalytic domains of the highly diverse protein kinase family. In this kinase family, the ATP-binding (or phosphate-anchoring) sites present a consensus sequence motif of Gly-X-Gly-X-X-Gly (67,87). 

The proteases are secreted as inactive zymogens the active site of the enzyme is masked by a small region of its peptide chain, which is removed by hydrolysis of a specific peptide bond. Pepsinogen is activated to pepsin by gastric acid and by activated pepsin (autocatalysis). In the small intestine, trypsinogen, the precursor of trypsin, is activated by enteropeptidase, which is secreted by the duodenal epithelial cells trypsin can then activate chymotrypsinogen to chymotrypsin, proelas-tase to elastase, procarboxypeptidase to carboxypepti-dase, and proaminopeptidase to aminopeptidase. 

Ecotin (eco) is a potent inhibitor of serine proteases that is derived from Escherichia coli. It was originally named for its ability to inhibit trypsin (E. coli trypsin inhibitor), but it is known to interact with and inhibit virtually all characterized tryp-sin-fold serine proteases. It is insensitive to the active site PI preference of the protease (the amino acid N-terminal to the cleaved or scissile bond ) and inhibits proteases with specificity towards basic, large hydrophobic, small aliphatic and acidic amino acids [2]. This remarkable breadth of inhibition classifies eco as a fold-specific inhibitor. It forms a unique tetrameric complex consisting of two protease molecules and two inhibitor molecules (the E2P2 complex), binding in a bi-dentate manner with two surface loop regions known as the primary and secondary sites (3) (Fig. 7.1). Eco itself is a 142 amino acid protein that forms a stable... 

Trypsin and factor Xa (fXa) are two members of the chymotrypsin family that have 38% sequence identity on the amino acid level and have distinguishable substrate specificities. Recently, the N-terminal 13-barrel of fXa and the C-terminal /3-barrel of trypsin were fused at a rationally designed site in the linker region between the two domains in order to create a hybrid fXa-trypsin protease (Hopfner et al., 1998). The fXa-trypsin hybrid was highly active and more active than either parent on three of the ten substrates assayed, as determined by k /Km. For most substrates, the activity of fXa-trypsin was an admixture of the two parents, probably because trypsin had higher activity than fXa for all the substrates tested. 

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