This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. All bacterial RNase P RNAs are composed of two independently folding domains. These domains pack against each other in the crystal structure of the Bacillus stearothermophilus RNase P RNA. This side-by-side packing is widely assumed to be the only native structure bacterial P RNAs can adapt. Here we show using small-angle X-ray scattering, in-line probing and molecular modeling that the P RNA from Bacillus subtilis, a close homolog of B. stearothermophilus, adopts two globally distinct native structures depending on the presence of monovalent cations. The structure under high ionic conditions (e100 mM) is 20% more compact as a result of a change in the relative orientation of the catalytic and specificity domains. This structure is well represented by the crystal structure. We also generate a molecular model for the structure under low ionic conditions structures that matches the molecular envelop obtained from the SAXS measurements. The agreement between the crystal structure and the models with the data is quantified using a cross-correlation function. Our results indicate that multi-domain RNAs can have more than one stable native structure. In the case of P RNA, these structures may be important in the assembly of the RNase P holoenzyme, a ribonucleoprotein particle.
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