Three-dimensional structures chymotrypsin

Serine proteinases such as chymotrypsin and subtilisin catalyze the cleavage of peptide bonds. Four features essential for catalysis are present in the three-dimensional structures of all serine proteinases a catalytic triad, an oxyanion binding site, a substrate specificity pocket, and a nonspecific binding site for polypeptide substrates. These four features, in a very similar arrangement, are present in both chymotrypsin and subtilisin even though they are achieved in the two enzymes in completely different ways by quite different three-dimensional structures. Chymotrypsin is built up from two p-barrel domains, whereas the subtilisin structure is of the a/p type. These two enzymes provide an example of convergent evolution where completely different loop regions, attached to different framework structures, form similar active sites. 

This is nicely illustrated by members of the chymotrypsin superfamily the enzymes chymotrypsin, trypsin, and elastase have very similar three-dimensional structures but different specificity. They preferentially cleave adjacent to bulky aromatic side chains, positively charged side chains, and small uncharged side chains, respectively. Three residues, numbers 189, 216, and 226, are responsible for these preferences (Figure 11.11). Residues 216... 

Matthews, B.W., Sigler, P.B., Henderson, R., Blow, D.M. Three-dimensional structure of tosyl-a-chymotrypsin. Nature 214 652-656, 1967. 

Bovine pancreatic chymotrypsin (Mr 25,191) is a protease, an enzyme that catalyzes the hydrolytic cleavage of peptide bonds. This protease is specific for peptide bonds adjacent to aromatic amino acid residues (Trp, Phe, Tyr). The three-dimensional structure of chymotrypsin is shown in Figure 6-18, with functional groups in the active site emphasized. The reaction catalyzed by this enzyme illustrates the principle of transition-state stabilization and also provides a classic example of general acid-base catalysis and covalent catalysis. 

Thiosulfate cyanide sulfurtransferase symmetry in 78 TTiiouridine 234 Three-dimensional structures of aconitase 689 adenylate kinase 655 aldehyde oxido-reductase 891 D-amino acid oxidase 791 a-amylase, pancreatic 607 aspartate aminotransferase 57,135 catalytic intermediates 752 aspartate carbamyltransferase 348 aspartate chemoreceptor 562 bacteriophage P22 66 cadherin 408 calmodulin 317 carbonic acid anhydrase I 679 carboxypeptidase A 64 catalase 853 cholera toxin 333, 546 chymotrypsin 611 citrate synthase 702, 703 cutinase 134 cyclosporin 488 cytochrome c 847 cytochrome c peroxidase 849 dihydrofolate reductase 807 DNA 214, 223,228,229, 241 DNA complex... 

Fig. 2. Mapping of conserved features onto three-dimensional structure. The sequence differences between chymotrypsin and its closest homologs are mapped onto a surface representation of the structure of chymotrypsin (PDB lab9). Apeptide ligand (TPGVY) is show in stick format.

Thrombin is a proteolytic enzyme and has a remarkable similarity in its overall three-dimensional structure to the digestive serine proteases, trypsin, and chymotrypsin [11-13]. Trypsin and thrombin share a common primary specificity for proteolysis next to arginine or lysine residues. Structural data of thrombin and trypsin have demonstrated strong resemblance in their substrate sites, and many small organic inhibitors are comparably active against both the enzymes [14,15]. For this reason, no or low inhibition of trypsin is viewed as a required condition for a compoimd to be a successful orally bioavailable thrombin inhibitor [16]. 

Trypsin was named more than 100 years ago. It and chymotrypsin were among the first enzymes to be crystallized, have their amino acid sequences determined, and have their three-dimensional structure outlined by x-ray diffraction. Furthermore, both enzymes hydrolyze not only proteins and peptides but a variety of synthetic esters, amides, and anhydrides whose hydrolysis rates can be measured conveniently, precisely and, in some instances, extremely rapidly. As a result, few enzymes have received more attention from those concerned with enzyme kinetics and reaction mechanisms. The techniques developed by the pioneers in these various fields have enabled other serine proteases to be characterized rapidly, and the literature on this group of enzymes has become immense. It might be concluded that knowledge of serine proteases is approaching completeness and that little remains but to fill in minor details. 

The amino acid sequence of the enzyme is homologous with those of the pancreatic enzymes and has been shown by model building to be compatible with a chymotrypsin-like three-dimensional structure and catalytic site (36). The homology in sequence is particularly well marked around His-57. The enzyme s catalytic properties are virtually indistinguishable from those of pancreatic elastase. 

This discussion of the metalloexopeptidases has focused on the general role of these enzymes in the conversion of dietary proteins into amino acids. In particular, the apparent synergistic relationship which the pancreatic carboxypeptidases have with the major endopeptidases, trypsin, chymotrypsin, and pepsin, in order to facilitate formation of essential amino acids has been stressed. The chemical characteristics, metalloenzyme nature, and mechanistic details of a representative of each class of exopeptidase have been presented. Leucine aminopeptidase from bovine lens was shown to be subject to an unusual type of metal ion activation which may be representative of a more general situation. Carboxypeptidase A of bovine pancreas was discussed in terms of its three-dimensional structure, the implications of x-ray crystallography to mecha ... 

Kolodziej SJ, et al. The three-dimensional structure of die human alpha 2-macroglobulin dimer reveals its structural organization in the tetrameric native and chymotrypsin alpha 2-macroglobulin complexes. J. Biol. Chem. 2002 277 28031-28037. 

Figure 9.6. Three-Dimensional Structure of Chymotrypsin. The three chains are shown in ribbon form in orange, blue, and green. The side chains of the catalytic triad residues, including serine 195, are shown as ball-and-stick representations, as are two intrastrand and interstrand disulfide bonds.

Figure 37.1. Three-dimensional structure of a-chymotrypsin. Histidine-57, serine-195, and isoleucine-16 are shaded. The hydrophobic pocket lies to the right of histidine-57 and erine-196, where M is marked it is bounded by residues 1S4-191 and 214-227.

Chymotrypsin and subtilisin also differ in their amino acid sequences, number of disulfide bridges (chymotrypsin has five, whereas subtilisin has none), and overall three-dimensional structures. The striking difference in structure and common catalytic mechanism are taken as evidence of an independent but convergent evolutionary process. 

The three-dimensional structure of chymotrypsin was solved by David Blow in 1967. Overall, chymotrypsin is roughly spherical and comprises three polypeptide chains, Jinked by disulfide bonds. It is synthesized as a single polypeptide, termed chymotrypainogm, which is activated by the... 

Much but not all of this work has dealt with proteins the three-dimensional structures of which have been determined by x ray lysozyme, ribonuclease, myoglobin, hemoglobin, cytochrome C, carboxy-peptidase, chymotrypsin, concanavalin, trypsin, elastase, and sub-tilisin. The principal nucleus has been the proton, but more recently 13 C has been studied by several groups. Other nuclei, such as 19 F, 31P, and 35Cl, have found limited application in special studies. 

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