The RNA binding domain of ribosomal protein L11: three-dimensional structure of the RNA-bound form of the protein and its interaction with 23 S rRNA

J Mol Biol. 1997 Nov 21;274(1):101-13. doi: 10.1006/jmbi.1997.1379.

Abstract

The three-dimensional solution structure has been determined by NMR spectroscopy of the 75 residue C-terminal domain of ribosomal protein L11 (L11-C76) in its RNA-bound state. L11-C76 recognizes and binds tightly to a highly conserved 58 nucleotide domain of 23 S ribosomal RNA, whose 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 form of the protein. There are however, substantial chemical shift perturbations which accompany RNA binding, the largest of which map onto an extended loop which bridges the C-terminal end of alpha-helix 1 and the first strand of parallel beta-sheet. Substantial shift perturbations are also observed in the N-terminal end of alpha-helix 1, the intervening loop that bridges helices 2 and 3, and alpha-helix 3. The four contact regions identified by the shift perturbation data also displayed protein-RNA NOEs, as identified by isotope-filtered three-dimensional NOE spectroscopy. The shift perturbation and NOE data not only implicate helix 3 as playing an important role in RNA binding, but also indicate 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 protein, where it appears rigid and adopts a specific conformation as a result of its direct contact to RNA.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Magnetic Resonance Spectroscopy
  • Molecular Sequence Data
  • Protein Conformation*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA / metabolism*
  • RNA, Ribosomal, 23S / metabolism*
  • RNA-Binding Proteins / chemistry*
  • Ribosomal Proteins / chemistry*
  • Ribosomal Proteins / metabolism*
  • Solutions

Substances

  • RNA, Ribosomal, 23S
  • RNA-Binding Proteins
  • Ribosomal Proteins
  • Solutions
  • ribosomal protein L11
  • RNA