A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs.
Phylogenetic and chemical probing data indicate that a modular RNA motif, common to loop E of eucaryotic 5 S ribosomal RNA (rRNA) and the alpha-sarcin/ricin loop of 23 S rRNA, organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs. The motif occurs in the 3' domain of 16 S rRNA at positions 1345-1350/1372-1376 (Escherichia coli numbering), within the three-way junction loop, which binds ribosomal protein S7, and which contains nucleotides that help to form the binding site for P-site tRNA in the ribosome. The motif also helps to structure a three-way junction within domain I of 23 S, which contains many universally conserved bases and which lies close in the primary and secondary structure to the binding site of r-protein L24. Several other highly conserved hairpin, internal, and multi-helix loops in 16 S and 23 S rRNA contain the motif, including the core junction loop of 23 S and helix 27 in the core of 16 S rRNA. Sequence conservation and range of variation in bacteria, archaea, and eucaryotes as well as chemical probing and cross-linking data, provide support for the recurrent and autonomous existence of the motif in ribosomal RNAs. Besides its presence in the hairpin ribozyme, the loop E motif is also apparent in helix P10 of bacterial RNase P, in domain P7 of one sub-group of group I introns, and in domain 3 of one subgroup of group II introns.
Chemistry Department, Bowling Green State University, Bowling Green, OH, 43403, USA. neocles@rosalind.bgsu.edu
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Leontis
E
E
Westhof
D002384:Catalysis; D020134:Catalytic Domain; D004926:Escherichia coli / Q000737:chemistry* / Q000378:metabolism; D020459:Genes, rRNA / Q000502:physiology; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012329:RNA, Bacterial / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D012338:RNA, Ribosomal, 23S / Q000737:chemistry* / Q000145:classification / Q000378:metabolism
D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S