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Crystal structure of the specificity domain of ribonuclease P

Nature volume 421, pages 760–764 (2003)Cite this article

Abstract

RNase P is the only endonuclease responsible for processing the 5′ end of transfer RNA by cleaving a precursor and leading to tRNA maturation1,2. It contains an RNA component and a protein component and has been identified in all organisms. It was one of the first catalytic RNAs identified3 and the first that acts as a multiple-turnover enzyme in vivo. RNase P and the ribosome are so far the only two ribozymes known to be conserved in all kingdoms of life. The RNA component of bacterial RNase P can catalyse pre-tRNA cleavage in the absence of the RNase P protein in vitro and consists of two domains: a specificity domain and a catalytic domain4,5. Here we report a 3.15-Å resolution crystal structure of the 154-nucleotide specificity domain of Bacillus subtilis RNase P. The structure reveals the architecture of this domain, the interactions that maintain the overall fold of the molecule, a large non-helical but well-structured module that is conserved in all RNase P RNA, and the regions that are involved in interactions with the substrate.

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Figure 1: Structure of the S domain of B. subtilis RNase P RNA.
Figure 2: The central junction and the P10.1 helix.
Figure 3: The J11/12–J12/11 module.
Figure 4: Surface representation of the S-domain structure.

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Acknowledgements

We thank X. Liu and Y. Xiao for technical assistance, A. Changela, H. Feinberg, V. Grum and members of DND–CAT for help with data collection, and A. Changela, C. Correll, V. Grum, E. Sontheimer, B. Taneja and J. Wedekind for comments and suggestions. Research was supported by the NIH (to A.M.) and an NIH NRSA Fellowship to A.K. Support from the R.H. Lurie Cancer Center of Northwestern University to the Structural Biology Center is acknowledged. Portions of this work were performed at the DuPont–Northwestern–Dow Collaborative Access Team (DND–CAT) Synchrotron Research Center at the Advanced Photon Source (APS) and at the Stanford Synchrotron Radiation Laboratory (SSRL). DND–CAT is supported by DuPont, Dow and the NSF, and use of the APS is supported by the DOE. SSRL is operated by the DOE, Office of Basic Energy Sciences. The SSRL Biotechnology Program is supported by the NIH and the DOE.

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Authors and Affiliations

  1. Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois, 60208, USA

    Andrey S. Krasilnikov, Xiaojing Yang & Alfonso Mondragón

  2. Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, Illinois, 60637, USA

    Tao Pan

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Correspondence to Alfonso Mondragón.

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Krasilnikov, A., Yang, X., Pan, T. et al. Crystal structure of the specificity domain of ribonuclease P. Nature 421, 760–764 (2003). https://doi.org/10.1038/nature01386

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