Skip to main content

Thank you for visiting nature.com. 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.

  • Article
  • Published:

The structure of I-Crel, a Group I intron-encoded homing endonuclease

Abstract

The structure of I-Crel provides the first view of a protein encoded by a gene within an intron. This endonuclease recognizes a long DNA site 20 base pairs in length and facilitates the lateral transfer of that intron. The protein exhibits a DNA-binding surface consisting of four antiparallel β-strands that form a 20 Å wide groove which is over 70 Å long. The architecture of this fold is different from that of the TATA binding protein, TBP, which also contains an antiparallel β-saddle. The conserved LAGLIDADG motif, which is found in many mobile intron endonucleases, maturases and inteins, forms a novel helical interface and contributes essential residues to the active site.

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

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. Lambowitz, A.M. & Belfort, M. Introns as mobile genetic elements. Ann. Rev. Biochem. 62, 587–622 (1993).

    Article  CAS  Google Scholar 

  2. Mueller, J.E., Brysk, M., Loizos, N. & Belfort, M. Homing endonucleases. in Nucleases, 2nd Ed. (eds S.M. Linn, R.S. Lloyd & RJ. Roberts) 111–143 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY 1993).

    Google Scholar 

  3. Belfort, M., Reaban, M.E., Coetzee, T. & Dalgaard, J.Z. Mechanisms of intron mobility. J. Biol. Chem. 270, 30237–30240 (1995).

    Article  CAS  Google Scholar 

  4. Belfort, M. & Perlman, P.S. Prokaryotic introns and inteins: a panoply of form and function. J. Bacteriolgy 177, 3897–3903 (1995).

    Article  CAS  Google Scholar 

  5. Rochaix, J.D., Rahire, M. & Michel, F. The chloroplast ribosomal intron of Chlamydomonas reinhardtii codes for a polypeptide related to mitochondrial maturases. Nucleic Acids Res. 13, 975–984 (1985).

    Article  CAS  Google Scholar 

  6. Dürrenberger, F. & Rochaix, J.-D. Chloroplast ribosomal intron of Chlamydomonas reinhardtii: in vitro self-splicing, DNA endonuclease activity and in vivo mobility. EMBO J. 10, 3495–3501 (1991).

    Article  Google Scholar 

  7. Thompson, A.J. & Herrin, D.L. In vitro self-splicing reactions of the chloroplast group I intron Cr. LSU from Chlamydomonas reinhardtii and in vivo manipulation via gene replacement. Nucleic Acids Res. 19, 6611–6618 (1991).

    Article  CAS  Google Scholar 

  8. Michel, F. Jacquier, A. & Dujon, B. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie. 64, 867–881 (1982).

    Article  CAS  Google Scholar 

  9. Waring, R.B., Davies, R.W., Scazzocchio, C. & Brown, T.A. Internal structure of a mitochondrial intron of Aspergillus nidulans. Proc. Natl. Acad. Set. USA 79, 6332–6336 (1982).

    Article  CAS  Google Scholar 

  10. Hensgens, L.A.M., Bonen, L., de Haan, M., van der Horst, G. & Grivell, L. A. Two intron sequences in yeast mitochondrial COX1 gene: homology among URF-containing introns and strain-dependent variation in flanking exons. Cell 32, 379–389 (1983).

    Article  CAS  Google Scholar 

  11. Thompson, A.J., Yuan, X., Kudlicki, W. & Herrin, D.L. Cleavage and recognition pattern of a double-strand-specific endonuclease (I-CreI) encoded by the chloroplast 235 rRNA intron of Chlamydomonas reinhardtii . Gene 119, 247–251 (1992).

    Article  CAS  Google Scholar 

  12. Dürrenberger, F. & Rochaix, J.-D. Characterization of the cleavage site and the recognition sequence of the I-CreI DNA endonuclease encoded by the chloroplast ribosomal intron of Chlamydomonas reinhardtii . Mol. Gen. Genet. 236, 409–414 (1993).

    Article  Google Scholar 

  13. Lesk, A.M. Protein architecture: a practical approach. IRL Press: The practical approach series (eds D. Rickwood & B.D. Hames) 5–90 (Oxford, U.K.1991)

    Google Scholar 

  14. Phillips, S.E.V. The β-ribbon DNA recognition motif. Ann. Rev. Biophys. Biomol. Struct 23, 671–701 (1994).

    Article  CAS  Google Scholar 

  15. Nikolov, D.B. et al. Crystal structure of TFIID TATA-box binding protein. Nature 360, 40–46 (1992).

    Article  CAS  Google Scholar 

  16. Endrizzi, J.A. Cronk, J.D., Wang, W., Crabtree, G.R. & Alber, T. Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator. Science 268, 556–559 (1995).

    Article  CAS  Google Scholar 

  17. Hodges, R.A., Perler, F.B., Noren, C.J. & Jack, W.E. Protein splicing removes intervening sequences in an archaea DNA polymerase. Nucleic Acids Res. 20, 6153–6157 (1992).

    Article  CAS  Google Scholar 

  18. Gimble, F.S. & Stephens, B.W. Substitutions in conserved dodecapeptide motifs that uncouple the DNA binding and DNA cleavage activities of Pl-Scel endonuclease. J. Biol. Chem. 270, 5849–5856 (1995).

    Article  CAS  Google Scholar 

  19. Henke, R.M., Butow, R.A. & Perlman, P.S. Maturase and endonuclease functions depend on separate conserved domains of the bifunctional protein encoded by the group I intron al4a of yeast mitochondrial DNA. EMBO J. 14, 5094–5099 (1995).

    Article  CAS  Google Scholar 

  20. Gernert, K.M., Surles, M.C., Labean, T.H., Richardson, J. S. & Richardson, D.C. The Alacoil: A very tight, antiparallel coiled-coil of helices. Prat Sci. 4, 2252–2260 (1995).

    Article  CAS  Google Scholar 

  21. Gimble, F.S. & Thorner, J. Purification and characterization of VDE, a site-specific endonuclease from the yeast Saccharomyces cerevisiae . J. Biol. Chem. 268 (29), 21844–21853 (1993).

    CAS  PubMed  Google Scholar 

  22. Wende, W., Grindl, W., Christ, F., Pingoud, A. & Pingoud, V. Binding, bending and cleavage of DNA substrates by the homing endonuclease Pl-Scel. Nucleic Acids Res. 24, 4123–4132 (1996).

    Article  CAS  Google Scholar 

  23. Roberts, R.J. & Halford, S.E. Type II Restriction Endonucleases in Nucleases, 2nd ed. (S.M. Linn, R. S. Lloyd and R. J. Roberts, eds) 35–70 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1993)

    Google Scholar 

  24. Kim, Y.-C, Grable, J.C. Choi, P.J. Greene, P. & Rosenberg J.M. Refinement of EcoRI endonuclease crystal structure: a revised protein chain tracing. Science 249, 1307–1309 (1990).

    Article  CAS  Google Scholar 

  25. Newman, M., Strzelecka, T. Dorner, L.F., Schildkraut, I. & Aggarwal, A.K. Structure of SamHI endonuclease bound to DNA: partial folding and unfolding on DNA binding. Science 269, 656–663 (1995).

    Article  CAS  Google Scholar 

  26. Winkler, F. K. et al. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 122, 1781–1795 (1993).

    Article  Google Scholar 

  27. Cheng, X., Balendiran, K., Schildkraut, I. & Anderson, J.E. Structure of Pvull endonuclease with cognate DNA. EMBO J. 13, 3927–3935 (1995).

    Article  Google Scholar 

  28. Aggarwal, A.K. Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 5, 11–19 (1995).

    Article  CAS  Google Scholar 

  29. Anderson, J.E. Restriction endonucleases and modification methylases. Curr. Opin. Struct. Biol. 3, 24–30 (1993).

    Article  CAS  Google Scholar 

  30. Gerlt, J.A. Mechanistic principles of enzyme-catalyzed cleavage of phosphodiester bonds, in Nucleases. 2nd ed. (S.M. Linn, R. S. Lloyd and R. J. Roberts, ed) 1–34 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1993)

    Google Scholar 

  31. Studier, F.W., Rosenberg, A.H., Dunn, J.J. & Dubendorff, J.W. Use of T7 RNA Polymerase to Direct Expression of Cloned Genes. Methods in Enzymology 185, 60–89 (1990).

    Article  CAS  Google Scholar 

  32. Stephens, K.M., Monnat, R.J. Jr., Heath, P.J. & Stoddard, B.L. Crystallization and preliminary X-ray studies of I-Crel: a Group I intron-encoded endonuclease from C reinhardtii . Proteins in the press (1997).

    Google Scholar 

  33. Otwinowski, Z. DENZO. in Proceedings of the CCP4 Study Weekend: Data Collection and Processing, (eds L. Sawyer, N. Isaacs & S. Bailey) 56–62 (Warrington, UK: SERC Daresbury Laboratory, 1993).

  34. CCP4 The SERC (UK) Collaborative Computing Project No. 4, a suite of programs for protein crystallography. Daresbury Laboratory, Warrington WA4 4AD, UK (1979).

  35. QUANTA96 X-ray structure analysis user's reference. San Diego: Molecular Simulations (1996).

  36. Brünger, A. X-PLOR version 3.1: a system for X-ray crystallography and NMR. (New Haven, Connecticut, Yale University Press, 1992).

    Google Scholar 

  37. Brünger, A. Assessment of phase accuracy by cross validation: the free R value. Methods and applications. Acta Crystallogr. D49, 24–36 (1993).

    Google Scholar 

  38. Laskowski, R.J., Macarthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–290 (1993).

    Article  CAS  Google Scholar 

  39. Luthy, R., Bowie, J.U. & Eisenberg, D. Assessment of protein models with three-dimensional profiles. Nature 356, 83–85 (1992).

    Article  CAS  Google Scholar 

  40. Kleywegt, G.J. & Brünger, A.T. Checking your imagination: Applications of the free R value. Structure 4 (8), 897–904 (1996).

    Article  CAS  Google Scholar 

  41. Evans, S.V. SETOR: hardware-lighted three-dimensional solid model representations of macromolecules. J. Mol. Graphics 11, 134–138 (1993).

    Article  CAS  Google Scholar 

  42. Nicholls, A., Sharp, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281–296 (1991).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Heath, P., Stephens, K., Monnat, R. et al. The structure of I-Crel, a Group I intron-encoded homing endonuclease. Nat Struct Mol Biol 4, 468–476 (1997). https://doi.org/10.1038/nsb0697-468

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb0697-468

This article is cited by

Search

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