Three-dimensional structure chymosin

It is clear that a great deal of work is still required in the field of acid proteases before we reach the level of understanding attained for other groups of proteolytic enzymes. Fortunately the amino acid sequence work on at least three enzymes—pepsin, chymosin, and penicillopepsin— is well advanced, and complete three-dimensional structures should become available in the near future. A tentative structure for rhizopus-pepsin has been obtained, but in the absence of sufficient sequence information interpretation of the electron density maps is difficult. We can... 

Fig. 16.2. A section of the alignment of sequences of aspartic proteinases achieved by comparing the three-dimensional structures using COMPARER [14]. HIV human immunodeficiency virus RSV Rous sarcoma virus APE endothiapepsin APP penicillopepsin APR rhizopuspepsin PEP hexagonal porcine pepsin CHY calf chymosin. The last letter refers to the amino (N) or car-boxy (C) terminal domains of the pepsins. The coordinates of the three-dimensional structures were obtained from the PDB databank [24]. The amino acid code is the standard one-letter code (see Appendix C) formatted using the following conventions [7] ...

Central to the study of mechanism and specificity of the acid proteinases is a knowledge of the three-dimensional structures of enzymes with different physiological roles. The availability of acid proteinases with either extracellular or intracellular roles in vertebrates as well as similar enzymes from plants, protozoa, and fungi allows a wide range of comparative studies. In our laboratory we have undertaken the x-ray analysis of fungal enzymes, those from Endothia parasitica and Mucor pusillus, and some vertebrate enzymes including chymosin and chicken pepsin, and are beginning work with cathepsin D. 

The evidence from the rotation function that the enzyme from Endothia parasitica is homologous with chymosin and therefore with pepsin is supported by two further arguments. First, a comparison of the three-dimensional structure with that of the enzyme from Rhizopus chinensis shows a striking similarity (see Ref.20 and Chapter 3 in this book) as the first 40 residues of the Rhizopus enzyme are clearly homologous with pepsin, a similar homology for the enzyme from Endothia parasitica is implied. Secondly, the polypeptide chain is of similar length to that of pepsin and visits the centre of the cleft in a way which brings two residues equivalent to Asp-32 and Asp-215 into correlations between the structure of the Endothia parasitica enzyme and pepsin. 

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