title: Purine bases at position 37 of tRNA stabilize codon-anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions.
abstract: The anticodon loop of tRNA contains a number of conserved or semiconserved nucleotides. In most tRNAs, a highly modified purine is found at position 37 immediately 3' to the anticodon. Here, we examined the role of the base at position 37 for tRNA(Phe) binding to the A site of Escherichia coli ribosomes. Affinities and rate constants of A-site binding of native yeast peptidyl-tRNA(Phe) with hypermodified G (wybutine), or of unmodified peptidyl-tRNA(Phe) transcripts with G, A, C, or U, at position 37 were measured. The data indicate that purines stabilize binding due to stronger stacking and additional interactions with the ribosome mediated by Mg(2+) ions. Paromomycin, an antibiotic that binds to 16S rRNA in the decoding center, greatly stabilized tRNAs in the A site and abolished the Mg(2+)-dependence of binding. Comparison of binding enthalpies and entropies suggests that hypermodification of the base at position 37 does not affect stacking in the codon-anticodon complex, but rather decreases the entropic penalty for A-site binding. Substitution of purines with pyrimidines at position 37 increases the rates of tRNA binding to and dissociation from the A site. The data suggest that initial binding of tRNA to the A site is followed by a rate-limiting rearrangement of the anticodon loop or the ribosome decoding center that is favored by purines at position 37 and involves stronger stacking, additional Mg(2+) binding, and interactions with 16S rRNA.
authors.affiliation: Petersburg Nuclear Physics Institute, Russian Academy of Sciences, 188300 Gatchina, Russia.
authors.forename: Andrey L
authors.initials: AL
authors.lastname: Konevega
authors.forename: Natalia G
authors.initials: NG
authors.lastname: Soboleva
authors.forename: Valentin I
authors.initials: VI
authors.lastname: Makhno
authors.forename: Yuri P
authors.initials: YP
authors.lastname: Semenkov
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Wintermeyer
authors.forename: Marina V
authors.initials: MV
authors.lastname: Rodnina
authors.forename: Vladimir I
authors.initials: VI
authors.lastname: Katunin
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D000926:Anticodon; D001665:Binding Sites; D003062:Codon; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D008274:Magnesium / Q000378:metabolism*; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D009690:Nucleic Acid Conformation; D010303:Paromomycin / Q000494:pharmacology; D014176:Protein Biosynthesis; D011687:Purines / Q000737:chemistry / Q000378:metabolism*; D011743:Pyrimidines / Q000737:chemistry / Q000378:metabolism; D012331:RNA, Fungal; D012360:RNA, Transfer, Phe / Q000235:genetics / Q000378:metabolism*; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D013816:Thermodynamics
chemical_list: D000900:Anti-Bacterial Agents; D000926:Anticodon; D003062:Codon; D011687:Purines; D011743:Pyrimidines; D012331:RNA, Fungal; D012360:RNA, Transfer, Phe; D010303:Paromomycin; D008274:Magnesium