Structure of the ubiquitous 3′ processing enzyme RNase Z bound to transfer RNA


The highly conserved ribonuclease RNase Z catalyzes the endonucleolytic removal of the 3′ extension of the majority of tRNA precursors. Here we present the structure of the complex between Bacillus subtilis RNase Z and tRNAThr, the first structure of a ribonucleolytic processing enzyme bound to tRNA. Binding of tRNA to RNase Z causes conformational changes in both partners to promote reorganization of the catalytic site and tRNA cleavage.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Crystal structure of RNase Z bound to tRNAThr.
Figure 2: Major conformational changes in complex compared to free RNase Z.

Accession codes

Primary accessions

Protein Data Bank

Referenced accessions

Protein Data Bank


  1. 1

    Condon, C. & Putzer, H. Nucleic Acids Res. 30, 5339–5346 (2002).

  2. 2

    Pellegrini, O., Nezzar, J., Marchfelder, A., Putzer, H. & Condon, C. EMBO J. 22, 4534–4543 (2003).

  3. 3

    Tavtigian, S.V. et al. Nat. Genet. 27, 172–180 (2001).

  4. 4

    Nashimoto, M. Nucleic Acids Res. 25, 1148–1154 (1997).

  5. 5

    Kunzmann, A., Brennicke, A. & Marchfelder, A. Proc. Natl. Acad. Sci. USA 95, 108–113 (1998).

  6. 6

    Schierling, K., Rosch, S., Rupprecht, R., Schiffer, S. & Marchfelder, A. J. Mol. Biol. 316, 895–902 (2002).

  7. 7

    Mohan, A., Whyte, S., Wang, X., Nashimoto, M. & Levinger, L. RNA 5, 245–256 (1999).

  8. 8

    Li de la Sierra-Gallay, I., Pellegrini, O. & Condon, C. Nature 433, 657–661 (2005).

  9. 9

    Ishii, R. et al. J. Biol. Chem. 280, 14138–14144 (2005).

  10. 10

    Schilling, O. et al. J. Biol. Chem. 280, 17857–17862 (2005).

  11. 11

    Minagawa, A., Takaku, H., Takagi, M. & Nashimoto, M. J. Biol. Chem. 279, 15688–15697 (2004).

  12. 12

    Nashimoto, M., Tamura, M. & Kaspar, R.L. Biochemistry 38, 12089–12096 (1999).

  13. 13

    Schiffer, S., Helm, M., Theobald-Dietrich, A., Giege, R. & Marchfelder, A. Biochemistry 40, 8264–8272 (2001).

  14. 14

    Westhof, E., Dumas, P. & Moras, D. Acta Crystallogr. A 44, 112–123 (1988).

  15. 15

    Shi, H. & Moore, P.B. RNA 6, 1091–1105 (2000).

Download references


We thank F.A. Wollman, D. Drapier, J.L. Popot, G. Hervé, D. Picot, T. Bizebard, F. Dardel, M. Springer, Y. Timsit, R. Giégé and V. Arluison for their contributions and L. Jacquamet at the European Synchrotron Radiation Facility. Funding was from the CNRS (UPR 9073), Université de Paris 7, the Association pour la Recherche sur le Cancer (grant 3506), ACI Jeunes Chercheurs and the Conseil Régionale de l'Ile de France.

Author information

Correspondence to Ciarán Condon.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Cleavage of tRNA reisolated from crystals (PDF 428 kb)

Supplementary Fig. 2

Crystal contacts between tRNA and RNase Z (PDF 68 kb)

Supplementary Fig. 3

Cleavage of tRNA precursor by RNase Z mutants (PDF 341 kb)

Supplementary Fig. 4

Conformational changes in RNase Z upon tRNA binding (PDF 300 kb)

Supplementary Table 1

Data collection and refinement statistics (PDF 61 kb)

Supplementary Discussion (PDF 60 kb)

Supplementary Methods (PDF 75 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Li de la Sierra-Gallay, I., Mathy, N., Pellegrini, O. et al. Structure of the ubiquitous 3′ processing enzyme RNase Z bound to transfer RNA. Nat Struct Mol Biol 13, 376–377 (2006).

Download citation

Further reading