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Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action

Nature Structural Biology volume 9, pages 397–403 (2002)Cite this article

Abstract

Long-range interactions involving the P5.1 hairpin of Bacillus RNase P RNA are thought to form a structural truss to support RNA folding and activity. We determined the structure of this element by NMR and refined the structure using residual dipolar couplings from a sample weakly oriented in a dilute liquid crystalline mixture of polyethylene glycol and hexanol. Dipolar coupling refinement improved the global precision of the structure from 1.5 to 1.2 Å (to the mean), revised the bend angle between segments of the P5.1 stem and corroborated the structure of the loop region. The UGAGAU hexaloop of P5.1 contains two stacks of bases on opposite sides of the loop, distinguishing it from GNRA tetraloops. The unusual conformation of the juxtaposed uracil residues within the hexaloop may explain their requirement in transactivation assays.

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Figure 1: P5.1 hairpin excised from RNase P for tranactivation and NMR studies, along with conservation of loops of P5.1 and its P15.1 contact partner.
Figure 2: Transactivation of Δ5.1 RNase P by P5.1 elements shows a tolerance for stem alterations but not for loop alterations.
Figure 3: T1ρ relaxation times of aromatic 13C6/8 peaks suggest relative mobility of bases.
Figure 4: Stero view of ensembles of P5.1 structures calculated with and without dipolar couplings.
Figure 5: Stereo view comparison of the P5.1 hexaloop structure with other loops.

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Acknowledgements

This work was supported by the Univ. of Missouri Research Board (S.R.V.), NASA (F.J.S.), University of Missouri Molecular Biology Program pre-doctoral fellowship (T.C.L.) and the Missouri Agricultural Experiment Station. The 500 and 600 MHz spectrometers were purchased in part with grants from the National Science Foundation and Univeristy of Missouri Research Board.

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  1. Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, 65211, Missouri, USA

    Thomas C. Leeper, Matthew B. Martin, Hadong Kim, Shawn Cox, Valentyna Semenchenko, Francis J. Schmidt & Steven R. Van Doren

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Correspondence to Steven R. Van Doren.

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Leeper, T., Martin, M., Kim, H. et al. Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action. Nat Struct Mol Biol 9, 397–403 (2002). https://doi.org/10.1038/nsb775

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