THE RNA-BINDING DOMAIN OF RIBOSOMAL-PROTEIN L11 - 3-DIMENSIONAL STRUCTURE OF THE RNA-BOUND FORM OF THE PROTEIN AND ITS INTERACTION WITH 23-S-RIBOSOMAL-RNA

The three-dimensional solution structure has been determined by NMR sp ectroscopy of the 75 residue C-terminal domain of ribosomal protein L1 1 (L11-C76) in its RNA-bound state. L11-C76 recognizes and binds tight ly to a highly conserved 58 nucleotide domain of 23 S ribosomal RNA, w hose secondary structure consists of three helical stems and a central junction loop. The NMR data reveal that the conserved structural core of the protein, which consists of a bundle of three alpha-helices and a two-stranded parallel beta-sheet four residues in length, is nearly the same as the solution structure determined for the non-liganded fo rm of the protein. There are however, substantial chemical shift pertu rbations which accompany RNA binding, the largest of which map onto an extended loop which bridges the C-terminal end of alpha-helix 1 and t he first strand of parallel beta-sheet. Substantial shift perturbation s are also observed in the N-terminal end of alpha-helix 1, the interv ening loop that bridges helices 2 and 3, and alpha-helix 3. The four c ontact regions identified by the shift perturbation data also displaye d protein-RNA NOEs, as identified by isotope-filtered three-dimensiona l NOE spectroscopy. The shift perturbation and NOE data not only impli cate helix 3 as playing an important role in RNA binding, but also ind icate that regions flanking helix 3 are involved as well. Loop 1 is of particular interest as it was found to be flexible and disordered for L11-C76 free in solution, but not in the RNA-bound form of the protei n, where it appears rigid and adopts a specific conformation as a resu lt of its direct contact to RNA. (C) 1997 Academic Press Limited.