Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA.
Transfer RNA protects a characteristic set of bases in 16 S rRNA from chemical probes when it binds to ribosomes. We used several criteria, based on construction of well-characterized in vitro ribosome-tRNA complexes, to assign these proteins to A or P-site binding. All of these approaches lead to similar conclusions. In the A site, tRNA caused protection of G529, G530, A1492 and A1493 (strongly), and A1408 and G1494 (weakly). In the P site, the protected bases are G693, A794, C795, G926 and G1401 (strong), and A532, G966, G1338 and G1339 (weak). In contrast to what is observed for 23 S rRNA, blocking the release of EF-Tu.GDP from the ribosome by kirromycin has no detectable effect on the protection of bases in 16 S rRNA.
Thimann Laboratories, University of California Santa Cruz 95064.
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D001345:Autoradiography; D001665:Binding Sites; D002250:Carbon Radioisotopes; D004926:Escherichia coli / Q000378:metabolism*; D007700:Kinetics; D009690:Nucleic Acid Conformation; D012335:RNA, Ribosomal / Q000378:metabolism*; D012336:RNA, Ribosomal, 16S / Q000378:metabolism*; D012343:RNA, Transfer / Q000378:metabolism*; D012360:RNA, Transfer, Phe / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism*
D002250:Carbon Radioisotopes; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012360:RNA, Transfer, Phe; D012343:RNA, Transfer