title: NMR characterisation of a highly conserved secondary structural RNA motif of Halobacterium halobium 23S rRNA.
abstract: The highly conserved 29-mer RNA motif corresponding to the peptidyl transferase central circle region of the domain V of Halobacterium halobium 23S rRNA has been characterised by multidimensional NMR spectroscopy. The NMR structure has a good all atom average RMSD of 1.28 Å and a stable A-form helical conformation. The NMR structure differs from the X-ray crystal structure of an analogous motif, contained within the Escherichia coli ribosome, as none of the bases are flipped out and a number of non-canonical base pairs are formed in the solution structure. Thus in the observed NMR structure, the predicted A7 to U30 base pair is not seen and a non-canonical U6 to U30 base pair was formed in its place. Similarly the predicted A9 to U26 base pair was also not observed and another non-canonical A9 to A27 base pair was formed. It was also seen from the conformational analysis that the steps near the bulges had the greatest deviation from the canonical Watson-Crick base pair step parameters. Despite these differences, the 29-mer structure provides a working model of the RNA within the ribosome in a more natural solution state than that observed in the intact ribosome crystal structures, particularly around the A27 residue. The NMR structure determination of the 29-mer RNA motif provides a solid foundation for determining the NMR structure of the RNA-amicetin complex in the next step. To extend the above study, a fully (13)C and (15)N isotopically labelled 37-mer RNA version of the Halobacterium halobium RNA sample has been characterised using ultra high field 1 GHz spectroscopy. The results have been used to demonstrate the advantages conferred by the use of a 1 GHz spectrometer frequency over 800 MHz in terms of superior sensitivity and greater spectral dispersion achieved in the spectrum of the RNA.
authors.affiliation: School of Chemistry, University of Manchester, Manchester, UK.
authors.forename: John
authors.initials: J
authors.lastname: King
authors.forename: Christos
authors.initials: C
authors.lastname: Shammas
authors.forename: Misbah
authors.initials: M
authors.lastname: Nareen
authors.forename: Moreno
authors.initials: M
authors.lastname: Lelli
authors.forename: Vasudevan
authors.initials: V
authors.lastname: Ramesh
mesh_terms: D018360:Crystallography, X-Ray; D006217:Halobacterium / Q000737:chemistry*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012338:RNA, Ribosomal, 23S / Q000737:chemistry*
chemical_list: D012338:RNA, Ribosomal, 23S