The structure of helix III in Xenopus oocyte 5 S rRNA: An RNA stem containing a two-nucleotide bulge

The solution structure of an oligonucleotide containing the helix Ill seque nce from Xenopus oocyte 5 S rRNA has been determined by NMR spectroscopy. H elix III includes two unpaired adenosine residues, flanked on either side b y G:C base-pairs, that are required for binding of ribosomal protein L5. Th e consensus conformation of helix Ill in the context provided by this oligo nucleotide has the two adenosine residues located in the miner groove and s tacked upon the 3' flanking guanosine residue, consistent with biochemical studies of free 5 S rRNA in solution. A distinct break in stacking that occ urs between the first adenosine residue of the bulge and the flanking 5' gu anosine residue exposes the base of the adenosine residue in the minor groo ve and the base of the guanosine residue in the major groove. The major gro ove of the helix is widened at the site of the unpaired nucleotides and the helix is substantially bent; nonetheless, the G:C base-pairs flanking the bulge are intact. The data indicate that there may be conformational hetero geneity centered in the bulge region. The corresponding adenosine residues in the Haloarcula marismortui 50 S ribosomal subunit form a dinucleotide pl atform, which is quite different from the motif seen in solution. Thus, the conformation of helix Ill probably changes when 5 S rRNA is incorporated i nto the ribosome. (C) 2001 Academic Press.