Domain flexibility in aspartic proteinases

Abstract

Comparison of the three-dimensional structures of native endothiapepsin (EC 3.4.23.6) and 15 endothiapepsin oligopeptide inhibitor complexes defined at high resolution by X-ray crystallography shows that endothiapepsin exists in two forms differing in the relative orientation of a domain comprising residues 190-302. There are relatively few interactions between the two parts of the enzyme; consequently, they can move as separate rigid bodies. A translational, librational, and screw analysis of the thermal parameters of endothiapepsin also supports a model in which the two parts can move relative to each other. In the comparison of different aspartic proteinases, the rms values are reduced by up to 47% when the two parts of the structure are superposed independently. This justifies description of the differences, including those between pepsinogen and pepsin (EC 3.4.34.1), as a rigid movement of one part relative to another although considerable distortions within the domains also occur. The consequence of the rigid body movement is a change in the shape of the active site cleft that is largest around the S3 pocket. This is associated with a different position and conformation of the inhibitors that are bound to the two endothiapepsin forms. The relevance of these observations to a model of the hydrolysis by aspartic proteinases is briefly discussed.

Active‐site mobility in human immunodeficiency virus, type 1, protease as demonstrated by crystal structure of A28S mutant

“…A potential dichotomy from this line of argument is the fact that pepsin-like enzymes also have diverse substrate sequences, yet no active-site mobility has been observed. However, endothiapepsin and pepsin exhibit rigid body movements of their two domains relative to each other upon the binding of transition-state analogue inhibitors (Sali et al, 1992;Fujinaga et al, 1995). The mode and amplitude of the movement, which are dependent upon the structure of the inhibitors, would result in different relative positions of the inhibitor or substrate to the catalytic apparatus (Sali et al, 1992).…”

“…However, endothiapepsin and pepsin exhibit rigid body movements of their two domains relative to each other upon the binding of transition-state analogue inhibitors (Sali et al, 1992;Fujinaga et al, 1995). The mode and amplitude of the movement, which are dependent upon the structure of the inhibitors, would result in different relative positions of the inhibitor or substrate to the catalytic apparatus (Sali et al, 1992). The domain movement may provide adjustment of the substrate position relative to the nucleophilic water in pepsin-like proteases.…”

Structure of a secreted aspartic protease from C. albicans complexed with a potent inhibitor: Implications for the design of antifungal agents

“…The approximate relative orientation of the segment of residues between 190 and 301 (pepsin numbering) is an important element in the structural variability observed within the carboxy domain of the monomeric aspartic proteinases (Sali et al, 1989(Sali et al, , 1992Abad-Zapatero et al, 1990;Sielecki et al, 1990). After the rigid body domain 1 (RBI, 1-189 and 301-326) has been superimposed between a certain pair, the relative orientation of rigid body domain 2 can range widely among the different enzymes.…”

An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins

“…The structure (PDB code, 4APE) consists of five antiparallel @sheets; there are two @sheets in each of the N-and C-terminal domains and a further sheet (the central motif) at their interface (Eilundell et al, 1990). From a subjective analysis of the interresidue contact matrices, Sali et al (1992) conclude that the central motif should be considered separately. Figure 4 shows the C" trace of the endothiapepsin structure and the dendrogram of the secondary structures.…”

“…The relative disposition of domains in a protein may be important for the function and/or ligand binding (Lesk & Chothia, 1988; for a recent paper see Gerstein et al, 1994); for example, domain movements important to function have been described in aspartic proteinases (Sali et al, 1992) and in T4-lysozyme (Dixon et al, 1992). Domains of recently evolved proteins are frequently encoded by exons, reflecting gene fusion of simpler modules.…”