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

Abstract

The yeast Saccharomyces cerevisiae ribosomal protein L30 negatively autoregulates 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 L30 protein in complex with its regulatory RNA has been solved using NMR spectroscopy. In the complex, the helix-loop-helix RNA adopts a sharply bent conformation at the internal loop region. Unusual RNA features include a purine stack, a reverse Hoogsteen base pair (G11anti -G56syn) and highly distorted backbones. The L30 protein is folded in a three-layer α/β/α sandwich topology, and three loops at one end of the sandwich make base-specific contacts with the RNA internal loop. The protein–RNA binding interface is divided into two clusters, including hydrophobic and aromatic stacking interactions centering around G56, and base-specific hydrogen-bonding contacts to A57, G58 and G10–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 formation. The specific interactions formed between loops on L30 and the internal loop on the mRNA constitute a novel loop-loop recognition motif where an intimate RNA–protein interface is formed between regions on both molecules that lack regular secondary structure.

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Figure 1: Sequences of the S. cerevisiae L30 protein and the regulatory pre-mRNA site.
Figure 2: Schematic representation of the complex structure.
Figure 3: The overall structural views of the L30 protein and the RNA internal loop conformation.
Figure 4: Close-up view of the purine base stack.
Figure 5: Two specific contacts between the RNA and the protein.
Figure 6: Recognition differences between L30 and U1A complexes.

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Acknowledgements

We would like to thank K. Dayie, C. Turner and J. Chung for assistance with NMR experiments, and R. Plachikkat and J. Schnell for valuable discussions in structural calculations. This work was supported by grants from the National Science Foundation to S.A.W. and the National Institutes of Health to J.R.W.

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Correspondence to James R. Williamson.

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Mao, H., White, S. & Williamson, J. A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex. Nat Struct Mol Biol 6, 1139–1147 (1999). https://doi.org/10.1038/70081

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