Proteinase structure

One common Ca -binding site is found in all of the subtilisin-like serine proteinase structures, except proteinase K (2PRK). Four of the... 

Beppu, T., Park, Y.-N., Aikawa, J., Nishiyama, M., and Horinouchi, S. (1995). Tyrosine 75 on the flap contributes to enhance catalytic efficiency of a fungal aspartic proteinase, Mucor pusillus pepsin. In Aspartic Proteinase Structure, Function, Biology, and Biomedical Implications. Takahashi, T. (Ed.), (pp. 559-563). New York Plenum Press. 

Tong, L., Wengler, G., and Rossmann, M. G. (1993). Refined structure of Sindbis virus core protein and comparison with other chymotrypsin-like serine proteinase structures. J. Mol Biol 230, 228-247. 

Proteinases Structure, Function, Biology, and Biomedical Implications, Ed. by K. Takahashi,Plenum Press, New York, 1995, pp. 549-554. 

McPhalen, C. A., James, M. N. G. Structural comparison of two serine proteinase-protein inhibitor complexes Eglin-C-Subtilisin Carlsberg and CI-2-subtilisin novo. Biochemistry 27 (1988) 6582-6598... 

In the first edition of this book this chapter was entitled "Antiparallel Beta Structures" but we have had to change this because an entirely unexpected structure, the p helix, was discovered in 1993. The p helix, which is not related to the numerous antiparallel p structures discussed so far, was first seen in the bacterial enzyme pectate lyase, the stmcture of which was determined by the group of Frances Jurnak at the University of California, Riverside. Subsequently several other protein structures have been found to contain p helices, including extracellular bacterial proteinases and the bacteriophage P22 tailspike protein. 

In these p-helix structures the polypeptide chain is coiled into a wide helix, formed by p strands separated by loop regions. In the simplest form, the two-sheet p helix, each turn of the helix comprises two p strands and two loop regions (Figure 5.28). This structural unit is repeated three times in extracellular bacterial proteinases to form a right-handed coiled structure which comprises two adjacent three-stranded parallel p sheets with a hydrophobic core in between. 

Figure 6.23 Schematic diagram illustrating the active site loop regions (red) in three forms of the serpins. (a) In the active form the loop protrudes from the main part of the molecuie poised to interact with the active site of a serine proteinase. The first few residues of the ioop form a short p strand inserted between ps and pis of sheet A. (h) As a result of inhibiting proteases, the serpin molecules are cleaved at the tip of the active site ioop region, in the cleaved form the N-terminal part of the loop inserts itself between p strands 5 and 15 and forms a long p strand (red) in the middie of the p sheet, (c) In the most stable form, the latent form, which is inactive, the N-terminai part of the ioop forms an inserted p strand as in the cleaved form and the remaining residues form a ioop at the other end of the p sheet. (Adapted from R.W. Carreii et ai., Structure 2 257-270, 1994.)...

The serine proteinases have been very extensively studied, both by kinetic methods in solution and by x-ray structural studies to high resolution. From all these studies the following reaction mechanism has emerged. 

Four important structural features are required for the catalytic action of serine proteinases... 

The serine proteinases have four important structural features that facilitate this mechanism of catalysis (Figure 11.6). 

The serine proteinases all have the same substrate, namely, polypeptide chains of proteins. However, different members of the family preferentially cleave polypeptide chains at sites adjacent to different amino acid residues. The structural basis for this preference lies in the side chains that line the substrate specificity pocket in the different enzymes. 

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. 

Choi, H.-K., et al. Structure of Sindbis virus core protein reveals a chymotrypsin-like serine proteinase and the organization of the virion. Nature 354 37-43, 1991. 

How do the mutations identified by phage display improve binding specificity There is as yet no direct stmctural information on the phage-selected inhibitors however they can be modeled using data from the crystal structures of other Kunitz domains bound to serine proteinases. These studies lead to the conclusion that the mutations identified by phage display improve binding specificity by maximizing complementarity between the... 

Lesk, A. M., and Fordham, W. D., 1996. Conservation and variability in the structures of serine proteinases of die chymotrypsin family. Journal of Molecular Biology 258 501—537. 

Anand K, Ziebuhr J, Wadhwani P, Masters JR, Hilgenfeld R (2003). Coronavirus main proteinase (3CLpro) structure basis for design of anti-SARS drugs. Science (New York, N.Y 300 1763-1767... 

Anand K, Palm GJ, Mesters JR, SiddeU SG, Ziebuhr J, HUgenfeld R (2002) Structure of coron-avirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-heUcal domain. EMBO J 21 3213-3224... 

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