Solution structure of RNase P RNA
- Alexei V. Kazantsev1,
- Robert P. Rambo2,
- Sina Karimpour1,
- John SantaLucia Jr.3,
- John A. Tainer4 and
- Norman R. Pace1
- 1Department of MCD Biology, University of Colorado, Boulder, Colorado 80309, USA
- 2Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- 3Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
- 4Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
Abstract
The ribonucleoprotein enzyme ribonuclease P (RNase P) processes tRNAs by cleavage of precursor-tRNAs. RNase P is a ribozyme: The RNA component catalyzes tRNA maturation in vitro without proteins. Remarkable features of RNase P include multiple turnovers in vivo and ability to process diverse substrates. Structures of the bacterial RNase P, including full-length RNAs and a ternary complex with substrate, have been determined by X-ray crystallography. However, crystal structures of free RNA are significantly different from the ternary complex, and the solution structure of the RNA is unknown. Here, we report solution structures of three phylogenetically distinct bacterial RNase P RNAs from Escherichia coli, Agrobacterium tumefaciens, and Bacillus stearothermophilus, determined using small angle X-ray scattering (SAXS) and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) analysis. A combination of homology modeling, normal mode analysis, and molecular dynamics was used to refine the structural models against the empirical data of these RNAs in solution under the high ionic strength required for catalytic activity.
Keywords
Footnotes
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Reprint requests to: Norman R. Pace, Department of MCD Biology, Campus box 347, University of Colorado, Boulder, CO 80309, USA; e-mail: nrpace{at}colorado.edu; fax: (303) 492-7744.
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.2563511.
- Received November 23, 2010.
- Accepted March 30, 2011.
- Copyright © 2011 RNA Society
