title: Codon reading by tRNAAla with modified uridine in the wobble position.
abstract: tRNAs reading four-codon families often have a modified uridine, cmo(5)U(34), at the wobble position of the anticodon. Here, we examine the effects on the decoding mechanism of a cmo(5)U modification in tRNA(1B)(Ala), anticodon C(36)G(35)cmo(5)U(34). tRNA(1B)(Ala) reads its cognate codons in a manner that is very similar to that of tRNA(Phe). As Ala codons are GC rich and Phe codons AU rich, this similarity suggests a uniform decoding mechanism that is independent of the GC content of the codon-anticodon duplex or the identity of the tRNA. The presence of cmo(5)U at the wobble position of tRNA(1B)(Ala) permits fairly efficient reading of non-Watson-Crick and nonwobble bases in the third codon position, e.g., the GCC codon. The ribosome accepts the C-cmo(5)U pair as an almost-correct base pair, unlike third-position mismatches, which lead to the incorporation of incorrect amino acids and are efficiently rejected.
authors.affiliation: Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany.
authors.forename: Ute
authors.initials: U
authors.lastname: Kothe
authors.forename: Marina V
authors.initials: MV
authors.lastname: Rodnina
mesh_terms: D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D006160:Guanosine Triphosphate / Q000378:metabolism; D006868:Hydrolysis; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010455:Peptides / Q000378:metabolism; D012344:RNA, Transfer, Ala / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016364:Reading Frames / Q000235:genetics*; D014529:Uridine / Q000737:chemistry / Q000378:metabolism*
chemical_list: D003062:Codon; D010455:Peptides; D012344:RNA, Transfer, Ala; D006160:Guanosine Triphosphate; D014529:Uridine