Proteinase domain structures

Although the many components of the hemostatic system inevitably create a high level of complexity, the functional and structural similarities between and among the different molecules permit the simplification described above. Simplification can be obtained by representing many of the molecules as ellipses, the two-dimensional representations of the generally ellipsoid shapes of the molecules in solution (see Figure 36-9 below). However, the common motifs and similar proteinase domain structures can be presented even more simply in the form of bar diagrams, which are usually used in the descriptions of reactions that follow. 

Cicero DO, Barbato G, Koch U, Ingallinella P, Bianchi E, Nandi MC, Steinkuhler C, Cortese R, Matassa V, De Francesco R, Pessi A, Bazzo R, Structural characterization of the interactions of optimized product inhibitors with the N-terminal proteinase domain of the Hepatitis C Virus (HCV) NS3 protein by NMR and modelling studies, J. Mol. Biol., 289 385-396, 1999. 

In our low-resolution picture, the proteinase domains differ most obviously from the pancreatic proteinases in that they contain inserted sequences. These insertions are found primarily on the surfaces of the proteinase domains and are responsible for the high specificity that the coagulation proteinases have for their protein substrates, all of which are cleaved at Arg (or Lys) residues. Conventional secondary structure cartoons that illustrate the differences between trypsin and thrombin are shown in Figure 36-4. 

Also see color figure.) Tissue factor-factor Vila complex. The three-dimensional structure of the complex of factor Vila and tissue factor (minus the transmembrane polypeptide domain of the tissue factor) in the absence of membrane surface. It is approximately 115 A in length and has a diameter of 40-50 A. Factor Vila shows its four distinct domains the Gla domain, two EGF-like domains, and the proteinase domain. Tissue factor contacts factor VHa via the interface between the two fibronectin type Ill-like domains. All four domains of factor Vila appear to be involved in the interaction between tissue factor and factor Vila. The Gla domain of factor Vila is folded very similarly to the Gla domain of prothrombin (Gla domain of prothrombin fragment 1). Activation of factor VII can be catalyzed by thrombin, factor Xa, factor Vila, and factor Xlla—all by cleavage at Arg -Ile . Secondary structures are shown in the center diagram two views of the close interactions between TF and factor Vila are shown in the two diagrams at each side. 

Friedrich R, Fuentes-Prior P, Ong E, Coombs G, Hunter M, Oehler R, Pierson D, Gonzales R, Huber R, Bode W, Madison EL. Catalytic domain structures of MT-SP1/ matriptase, a matrix-degrading transmembrane serine proteinase. J Biol Chem 2002 277 2160-2168. 

Although the sequence similarity between the HIV protease and each of the two symmetrical domains of several cellular aspartic proteinases was low, several residues, in addition to the catalytic triad of Asp-Thr/Ser-Gly, critical to the structure and conserved in aspartic proteinase domains and retroviral proteinases, were identified. " There were many uncertainties in the alignment arising fi-om the fact that HTV proteinase had a sequence of only 99 amino acid residues compared to about 160 for a lobe of the pepsin-like aspartic proteinases, but the majority of the deletions could be acconunodated in surface regions. 

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. 

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... 

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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