The structure of the RNA binding site of ribosomal proteins S8 and S15

Proteins S8 and S15 from the 30 S ribosomal subunit of Escherichia coli were bound to 16 S RNA and digested with ribonuclease A. A ribonucleoprotein complex was isolated which contained the two proteins and three noncontiguous RNA subfragments totaling 93 nucleotides, that could be unambiguously located in the 16 S RNA sequence. We present a secondary structural model for the RNA moiety of the binding site complex, in which the two smaller fragments are extensively base-paired, respectively, to the two halves of the large fragment, to form two disconnected duplexes. Each of the two duplexes is interrupted by a small internal loop. This model is supported by (i) minimum energy considerations, (ii) sites of cleavage by ribonuclease A, and (iii) modification by the single strand-specific reagent kethoxal. The effect of protein binding on the topography of the complex is reflected in the kethoxal reactivity of the RNA moiety. In the absence of the proteins, 5 guanines are modified; 4 of these, at positions 663, 732, 733, and 741, are strongly protected from kethoxal when protein S15 is bound.