Major groove binding of the tRNA/mRNA complex to the 16 S ribosomal RNA decoding site

We propose a detailed three-dimensional model, with atomic detail, for the structure of the Escherichia coli 16 S rRNA decoding site in a complex with mRNA and the A and P-site tRNAs. Model building began with four primary as sumptions: (1) A and P-site tRNA conformations are identical with those see n in the tRNA crystal structure; (2) A and P-site tRNAs adopt an S-type ori entation upon binding mRNA in the ribosome; (3) A1492 and A1493 bind non-sp ecifically to the mRNA through a series of hydrogen bonds; and (4) C1400 li es in close proximity to the P-site tRNA wobble base in order to satisfy a UV-induced photocrosslink formed between the two residues. We have models w ith both major groove and minor groove binding of the tRNA/mRNA complex to the decoding site RNA, and conclude that major groove binding is more likel y. Both classes of models maintain structural features reported in the NMR structure of the A-site region of the decoding site RNA with bound paromomy cin. We also present models for the tRNA/mRNA complex bound to the decoding site RNA in the presence of the aminoglycoside paromomycin. We discuss pos sible mechanisms for ribosomal proofreading and antibiotic disruption of th is proofreading. (C) 1999 Academic Press.