Section 23.4.4.1.1. Serine proteases of the trypsin family

The serine proteases have an especially large number of buried water molecules. Using a probe sphere of radius 1.4 Å, an iterative procedure was used to delete all accessible surface waters for each structure of chymotrypsin, chymotrypsinogen, trypsin, trypsinogen, elastase, kallikrein, rat tonin and rat mast cell protease. A total of 58 non-equivalent sites containing buried water molecules were found in the 35 crystal structures included in the study. Of these, 16 sites were common to all of the structures, with five additional sites common to proteins sharing the primary specificity of trypsin. A protein environment was defined for each of these 21 water sites to consist of the set of non-hydrogen protein atoms within 5 Å of the water oxygen atom. There is an average of 29 protein atoms per buried water molecule. Of these, 87% consist of main-chain atoms or conserved amino-acid side-chain atoms. The highly conserved nature of the amino-acid residues lining these water-binding sites suggests that the corresponding water molecules are important components of the protein tertiary structure and are likely to be present in all of the members of the trypsin family of serine proteases (Sreenivasan & Axelsen, 1992). Proteins in this family have two β-sheet domains, with the active site in the cleft between these domains. A large portion of the conserved buried water molecules occur in this cleft, mediating the interaction between the domains (Fig. 23.4.4.1). Conserved buried water molecules in other areas are found to bridge secondary-structure elements. These water molecules have been analysed extensively for elastase and are discussed in more detail below (Bellamacina et al., 1999).

Figure 23.4.4.1| top | pdf | Stereoview of the set of 21 highly conserved buried waters in eukaryotic serine proteases. The trypsin backbone is represented as a stick drawing, with the catalytic triad at the centre (filled circles). Water molecules are represented as open circles. Reprinted with permission from Sreenivasan & Axelsen (1992). Copyright (1992) American Chemical Society.