Issue 20, 2013

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 13C and 15N 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.

Graphical abstract: NMR characterisation of a highly conserved secondary structural RNA motif of Halobacterium halobium 23S rRNA

Supplementary files

Article information

Article type
Paper
Submitted
08 Feb 2013
Accepted
20 Mar 2013
First published
20 Mar 2013

Org. Biomol. Chem., 2013,11, 3382-3392

NMR characterisation of a highly conserved secondary structural RNA motif of Halobacterium halobium 23S rRNA

J. King, C. Shammas, M. Nareen, M. Lelli and V. Ramesh, Org. Biomol. Chem., 2013, 11, 3382 DOI: 10.1039/C3OB40295A

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