Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Crystal structure of the specificity domain of ribonuclease P


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.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

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.


  1. Altman, S. & Kirsebom, L. A. in The RNA World (eds Gesteland, R. F., Cech, T. R. & Atkins, J. F.) 351–380 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1999)

    Google Scholar 

  2. Frank, D. N. & Pace, N. R. Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu. Rev. Biochem. 67, 153–180 (1998)

    CAS  Article  Google Scholar 

  3. Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. & Altman, S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849–857 (1983)

    CAS  Article  Google Scholar 

  4. Loria, A. & Pan, T. Domain structure of the ribozyme from eubacterial ribonuclease P. RNA 2, 551–563 (1996)

    CAS  PubMed Central  Google Scholar 

  5. Pan, T. Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry 34, 902–909 (1995)

    CAS  Article  Google Scholar 

  6. Qin, H., Sosnick, T. R. & Pan, T. Modular construction of a tertiary RNA structure: the specificity domain of the Bacillus subtilis RNase P RNA. Biochemistry 40, 11202–11210 (2001)

    CAS  Article  Google Scholar 

  7. Brown, J. W. et al. Comparative analysis of ribonuclease P RNA using gene sequences from natural microbial populations reveals tertiary structural elements. Proc. Natl Acad. Sci. USA 93, 3001–3006 (1996)

    ADS  CAS  Article  Google Scholar 

  8. Massire, C., Jaeger, L. & Westhof, E. Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J. Mol. Biol. 279, 773–793 (1998)

    CAS  Article  Google Scholar 

  9. Chen, J. L., Nolan, J. M., Harris, M. E. & Pace, N. R. Comparative photocross-linking analysis of the tertiary structures of Escherichia coli and Bacillus subtilis RNase P RNAs. EMBO J. 17, 1515–1525 (1998)

    CAS  Article  Google Scholar 

  10. Pan, T. Novel RNA substrates for the ribozyme from Bacillus subtilis ribonuclease P identified by in vitro selection. Biochemistry 34, 8458–8464 (1995)

    CAS  Article  Google Scholar 

  11. Barrera, A. et al. Dimeric and monomeric Bacillus subtilis RNase P holoenzyme in the absence and presence of pre-tRNA substrates. Biochemistry 41, 12986–12994 (2002)

    CAS  Article  Google Scholar 

  12. Nissen, P., Ippolito, J. A., Ban, N., Moore, P. B. & Steitz, T. A. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl Acad. Sci. USA 98, 4899–4903 (2001)

    ADS  CAS  Article  Google Scholar 

  13. Cate, J. H. et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273, 1678–1685 (1996)

    ADS  CAS  Article  Google Scholar 

  14. Odell, L., Huang, V., Jakacka, M. & Pan, T. Interaction of structural modules in substrate binding by the ribozyme from Bacillus subtilis RNase P. Nucleic Acids Res. 26, 3717–3723 (1998)

    CAS  Article  Google Scholar 

  15. LaGrandeur, T. E., Huttenhofer, A., Noller, H. F. & Pace, N. R. Phylogenetic comparative chemical footprint analysis of the interaction between ribonuclease P RNA and tRNA. EMBO J. 13, 3945–3952 (1994)

    CAS  Article  Google Scholar 

  16. Cate, J. H. et al. RNA tertiary structure mediation by adenosine platforms. Science 273, 1696–1699 (1996)

    ADS  CAS  Article  Google Scholar 

  17. Moore, P. B. Structural motifs in RNA. Annu. Rev. Biochem. 68, 287–300 (1999)

    CAS  Article  Google Scholar 

  18. Tanner, M. A. & Cech, T. R. An important RNA tertiary interaction of group I and group II introns is implicated in gram-positive RNase P RNAs. RNA 1, 349–350 (1995)

    CAS  PubMed Central  Google Scholar 

  19. Costa, M. & Michel, F. Frequent use of the same tertiary motif by self-folding RNAs. EMBO J. 14, 1276–1285 (1995)

    CAS  Article  Google Scholar 

  20. Costa, M. & Michel, F. Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: comparison with in vivo evolution. EMBO J. 16, 3289–3302 (1997)

    CAS  Article  Google Scholar 

  21. Chen, J.-L. & Pace, N. R. Identification of the universally conserved core of ribonuclease P RNA. RNA 3, 557–560 (1997)

    CAS  PubMed Central  Google Scholar 

  22. Brown, J. W. The Ribonuclease P Database. Nucleic Acids Res. 27, 314 (1999)

    CAS  Article  Google Scholar 

  23. Frank, D. N., Adamidi, C., Ehringer, M. A., Pitulle, C. & Pace, N. R. Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA. RNA 6, 1895–1904 (2000)

    CAS  Article  Google Scholar 

  24. Pan, T., Loria, A. & Zhong, K. Probing of tertiary interactions in RNA: 2′-hydroxyl-base contacts between the RNase P RNA and pre-tRNA. Proc. Natl Acad. Sci. USA 92, 12510–12514 (1995)

    ADS  CAS  Article  Google Scholar 

  25. Loria, A. & Pan, T. Recognition of the T stem-loop of a pre-tRNA substrate by the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry 36, 6317–6325 (1997)

    CAS  Article  Google Scholar 

  26. Nolan, J. M., Burke, D. H. & Pace, N. R. Circularly permuted tRNAs as specific photoaffinity probes of ribonuclease P RNA structure. Science 261, 762–765 (1993)

    ADS  CAS  Article  Google Scholar 

  27. Hendrickson, W. A. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 254, 51–58 (1991)

    ADS  CAS  Article  Google Scholar 

  28. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997)

    CAS  Article  Google Scholar 

  29. Brunger, A. T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    CAS  Article  Google Scholar 

  30. Haas, E. S., Banta, A. B., Harris, J. K., Pace, N. R. & Brown, J. W. Structure and evolution of ribonuclease P RNA in Gram-positive bacteria. Nucleic Acids Res. 24, 4775–4782 (1996)

    CAS  Article  Google Scholar 

Download references


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.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Alfonso Mondragón.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Krasilnikov, A., Yang, X., Pan, T. et al. Crystal structure of the specificity domain of ribonuclease P. Nature 421, 760–764 (2003).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing