A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex

The yeast Saccharomyces cerevisiae ribosomal protein L30 negatively autoreg ulates its production by binding to a helix-loop-helix structure formed in its pre-mRNA and its mRNA. A three-dimensional solution structure of the L3 0 protein in complex with its regulatory RNA has been solved using NMR spec troscopy. In the complex, the helix-loop-helix RNA adopts a sharply bent co nformation at the internal loop region. Unusual RNA features include a puri ne stack, a reverse Hoogsteen base pair (C11(anti)-G56(syn)) and highly dis torted backbones. The L30 protein is folded in a three-layer alpha/beta/alp ha sandwich topology, and three loops at one end of the sandwich make base- specific contacts with the RNA internal loop. The protein-RNA binding inter face is divided into two clusters, including hydrophobic and aromatic stack ing interactions centering around G56, and base-specific hydrogen-bonding c ontacts to A57, G58 and C10-U60 wobble base pair. Both the protein and the RNA exhibit a partially induced fit for binding, where loops in the protein and the internal loop in the RNA become more ordered upon complex formatio n. The specific interactions formed between loops on L30 and the internal l oop on the mRNA constitute a novel loop-loop recognition motif where an int imate! RNA-protein interface is formed between regions on both molecules th at lack regular secondary structure.