Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs

Abstract

Analysis of atomic resolution structures of the rRNAs within the context of the 50S and the 30S ribosomal subunits have revealed the presence of nine examples of a recurrent structural motif, first observed in the TΨC loop of tRNAs. The key component of this T-loop motif is a UA trans Watson–Crick/Hoogsteen base pair stacked on a Watson–Crick pair on one side. This motif is stabilized by several noncanonical hydrogen bonds, facilitating RNA–RNA as well as RNA–protein interactions. In particular, the sugar edge of the purine on the 3′ side of the pivotal uridine in the UA pair frequently forms a noncanonical base pair with a distant residue. The bulged-out bases, usually seen as part of the motif, also use their Watson–Crick edges to interact with nearby residues via base-specific hydrogen bonds. In certain occurrences, a backbone reversal is stabilized by specific hydrogen bonds as is observed in the U-turn motifs and the adenosine residue of the key UA pair interacts with a third base via its Watson–Crick edge, essentially generating a base triple.