Section 23.4.4.2.4. Ribonuclease A

Ribonuclease A is not homologous to ribonuclease T1 in either sequence or structure, but both have evolved to catalyse the same reaction with specificity for different substrates (compare Figs. 23.4.4.10 and 23.4.4.11). Ribonuclease A cleaves RNA after pyrimidines, while ribonuclease T1 cleaves specifically after guanine. Therefore, the information obtained from a study of the solvent structure in ribonuclease A is completely independent from that described above for ribonuclease T1. A collection of ten crystal structures of ribonuclease A, derived from five different crystal forms, were compared pairwise after least-squares superposition (Zegers et al., 1994). 17 conserved water molecules were found to be within a sphere of 0.5 Å of each other in all of the ten structures and are shown in Fig. 23.4.4.11. These water molecules were found in small clusters of two or three or as part of a larger solvent network. Not surprisingly, they form multiple hydrogen bonds with the protein and generally have low temperature factors. Of the 17 structurally conserved sites, 13 are associated with one of the three α-helices. Most of these link the helices to one of the β-strands. Three water molecules are involved in hydrogen bonding with unpaired amido and carbonyl groups on the protein, and one is found on top of the β-pleated sheet. These interactions result in bringing together elements of secondary structure and in stabilizing distortions within these elements. Conserved water molecules are also responsible for bridging the N-terminal helix to the C-terminal β-strand, which form the two halves of the active site.

Figure 23.4.4.10| top | pdf | Three-dimensional structure of RNase T1. Secondary structure is denoted as follows: α1, α-helix; βn, strands of β-sheet structure; Ln, loops. Drawn using MOLSCRIPT (Kraulis, 1991). Residue numbers indicate the beginning and end of secondary-structure elements. Reprinted with permission from Pletinckx et al. (1994). Copyright (1994) American Chemical Society.

Figure 23.4.4.11| top | pdf | Overall structure of RNase A. The overall structure of the d(CpA) complex of RNase A is shown as a ribbon drawing using MOLSCRIPT (Kraulis, 1991). The conserved water molecules are shown as white spheres and the d(CpA) inhibitor in black. The three helices are labelled H1, H2 and H3. Reprinted with the permission of Cambridge University Press from Zegers et al. (1994). Copyright (1994) The Protein Society.