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

Somashekarappa Niranjanakumari; Jeremy J. Day-Storms; Mahiuddin Ahmed; John Hsieh; Nathan H. Zahler; Ronald A. Venters; Carol A. Fierke

doi:10.1261/rna.308707

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

¹Chemistry Department, University of Michigan, Ann Arbor, Michigan 48109, USA
²NMR Center, Levine Science Research Center, Duke University Medical School, Durham, North Carolina, USA

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.

Keywords

Footnotes

↵3 Present address: Department of Natural Sciences and Mathematics, Southeastern University, 1000 Longfellow Boulevard, Lakeland, FL 33801, USA.
↵4 Department of Biochemistry and Cell Biology, Center for Structural Biology, State University of New York at Stony Brook, Stony Brook, NY 11794, USA.
Reprint requests to: Carol A. Fierke, Chemistry Department, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA; e-mail: fierke{at}umich.edu; fax: (734) 647-4865.
Abbreviations: RNP, ribonucleoprotein; pre-tRNA, precursor tRNA; PRNA, the RNA component of the B. subtilis RNase P holoenzyme; P protein, the protein component of the B. subtilis RNase P holoenzyme; RNase P, ribonuclease P; Cu-OP, copper 1,10-o-phenanthroline; AOP, acetamido-1,10-o-phenanthroline; M1 RNA, the RNA component of the E. coli RNase P holoenzyme; C5 protein, the protein component of the E. coli RNase P holoenzyme; AzP, azidophenacyl moiety; C-domain, the PRNA catalytic domain; S-domain, the PRNA specificity domain; DTT, dithiothreitol; RNR, highly conserved region of the P protein consisting of arg/asn/arg; MBL, metal binding loop in the P protein; CC, central cleft of the P protein.
Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.308707.
- Received September 21, 2006.
- Accepted December 21, 2006.