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

Andrew P. Hinck, Michelle A. Markus, Shengrong Huang, Stephan Grzesiek, Irina Kustonovich, David E. Draper, Dennis A. Torchia

Research output: Contribution to journalArticlepeer-review

45 Scopus citations

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 α-helices and a two-stranded parallel β-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 α-helix 1 and the first strand of parallel β-sheet. Substantial shift perturbations are also observed in the N-terminal end of α-helix 1, the intervening loop that bridges helices 2 and 3, and α-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.

Original languageEnglish (US)
Pages (from-to)101-113
Number of pages13
JournalJournal of Molecular Biology
Volume274
Issue number1
DOIs
StatePublished - Nov 21 1997

Keywords

  • 23 S ribosomal RNA
  • Heteronuclear NMR
  • L11
  • Protein-RNA
  • Ribosome

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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