Local folding coupled to RNA binding in the yeast ribosomal protein L30

The ribosomal protein L30 from yeast Saccharomyces cerevisiae auto-regulates its own synthesis by binding to a structural element in both its premRNA and its mRNA. The three-dimensional structures of L30 in the free (fL30) and the pre-mRNA bound (bL30) forms have been solved by nuclear magnetic resonance spectroscopy. Both protein structures contain four alternating alpha-helices and four beta-strands segments and adopt an overall topology that is an alpha beta alpha three-layer sandwich, representing a unique fold. Three loops on one end of the alpha beta alpha sandwich have been mapped as the RNA binding site on the basis of structural comparison, chemical shift perturbation and the inter-molecular nuclear Overhauser effects to the RNA. The structural and dynamic comparison of fL30 and bL30 reveals that local dynamics may play an important role in the RNA binding. The fourth helix in bL30 is longer than in fL30, and is stabilized by RNA binding. The exposed hydrophobic surface that is buried upon RNA binding may provide the energy necessary to drive secondary structure formation, and may account for the increased stability of bL30. (C) 1999 Academic Press.