Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage

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Abstract

Bacterial ribonuclease P (RNase P) is a ribonucleoprotein complex composed of one catalytic RNA (PRNA) and one protein subunit (P protein) that together catalyze the 5′ maturation of precursor tRNA. High-resolution X-ray crystal structures of the individual P protein and PRNA components from several species have been determined, and structural models of the RNase P holoenzyme have been proposed. However, holoenzyme models have been limited by a lack of distance constraints between P protein and PRNA in the holoenzyme-substrate complex. Here, we report the results of extensive cross-linking and affinity cleavage experiments using single-cysteine P protein variants derivatized with either azidophenacyl bromide or 5-iodoacetamido-1,10-o-phenanthroline to determine distance constraints and to model the Bacillus subtilis holoenzyme-substrate complex. These data indicate that the evolutionarily conserved RNR motif of P protein is located near (<15 Å) the pre-tRNA cleavage site, the base of the pre-tRNA acceptor stem and helix P4 of PRNA, the putative active site of the enzyme. In addition, the metal binding loop and N-terminal region of the P protein are proximal to the P3 stem-loop of PRNA. Studies using heterologous holoenzymes composed of covalently modified B. subtilis P protein and Escherichia coli M1 RNA indicate that P protein binds similarly to both RNAs. Together, these data indicate that P protein is positioned close to the RNase P active site and may play a role in organizing the RNase P active site. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 RNA Society.

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Niranjanakumari, S., Day-Storms, J. J., Ahmed, M., Hsieh, J., Zahler, N. H., Venters, R. A., & Fierke, C. A. (2007). Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage. RNA, 13(4), 521–535. https://doi.org/10.1261/rna.308707

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