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:

Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA

Nature volume 401, pages 235–242 (1999)Cite this article

Abstract

The trp RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes of several bacilli by binding single-stranded RNA. The binding sequence is composed of eleven triplet repeats, predominantly GAG, separated by two or three non-conserved nucleotides. Here we present the crystal structure of a complex of TRAP and a 53-base single-stranded RNA containing eleven GAG triplets, revealing that each triplet is accommodated in a binding pocket formed by β-strands. In the complex, the RNA has an extended structure without any base-pairing and binds to the protein mostly by specific protein–base interactions. Eleven binding pockets on the circular TRAP 11-mer form a belt with a diameter of about 80 Å. This simple but elegant mechanism of arresting the RNA segment by encircling it around a protein disk is applicable to both transcription, when TRAP binds the nascent RNA, and to translation, when TRAP binds the same sequence within a non-coding leader region of the messenger RNA.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1: Transcription attenuation in bacilli2.
Figure 2: Overall structure of the TRAP–RNA complex.
Figure 3: RNA conformation.
Figure 4: Protein–RNA interactions.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

Data deposits

The structure factors and the refined coordinates of the TRAP–RNA complex have been deposited with the Protein Data Bank43; the accession codes are R1C9SSF and 1C9S, respectively.

References

  1. Yanofsky,C. Attenuation in the control of expression of bacterial operons. Nature 289, 751–758 (1981).

    Article  ADS  CAS  Google Scholar 

  2. Shimotsu,H., Kuroda,M. I., Yanofsky,C. & Henner,D. J. Novel form of transcription attenuation regulates expression of the Bacillus subtilis tryptophan operon. J. Bacteriol. 166, 461–471 (1986).

    Article  CAS  Google Scholar 

  3. Gollnick,P., Ishino,S., Kuroda,M. I., Henner,D. & Yanofsky,C. The mtr locus is a two gene operon required for transcription attenuation in the trp operon of Bacillus subtilis. Proc. Natl Acad. Sci. USA 87, 8726–8730 (1990).

    Article  ADS  CAS  Google Scholar 

  4. Otridge,J. & Gollnick,P. MtrB from Bacillus subtilis binds specifically to trp leader RNA in a tryptophan dependent manner. Proc. Natl Acad. Sci. USA 90, 128–132 (1993).

    Article  ADS  CAS  Google Scholar 

  5. Babitzke,P. & Yanofsky,C. Reconstitution of Bacillus subtilis trp attenuation in vitro with TRAP, the trp RNA-binding attenuation protein. Proc. Natl Acad. Sci. USA 90, 133–137 (1993).

    Article  ADS  CAS  Google Scholar 

  6. Babitzke,P., Stults,J. T., Shire,S. J. & Yanofsky,C. TRAP, the trp RNA-binding attenuation protein of Bacillus subtilis, is a multisubunit complex that appears to recognize G/UAG repeats in the trpEDCFBA and trpG transcripts. J. Biol. Chem. 269, 16597–16604 (1994).

    CAS  PubMed  Google Scholar 

  7. Babitzke,P., Yealy,J. & Campanelli D. Interaction of the trp RNA-binding attenuation protein (TRAP) of Bacillus subtilis with RNA: Effects of the number of GAG repeats, the nucleotides separating adjacent repeats and RNA structure. J. Bacteriol. 178, 5159–5163 (1996).

    Article  CAS  Google Scholar 

  8. Gollnick,P. Regulation of the Bacillus subtilis trp operon by an RNA-binding protein. Mol. Microbiol. 11, 991–997 (1994).

    Article  CAS  Google Scholar 

  9. Kuroda,M. I., Henner,D. & Yanofsky,C. cis-Acting sites in the transcript of the Bacillus subtilis trp operon regulate expression of the operon. J. Bacteriol. 170, 3080–3088 (1988).

    Article  CAS  Google Scholar 

  10. Merino,E., Babitzke,P. & Yanofsky,C. Trp RNA-binding attenuation protein (TRAP)-trp leader RNA interactions mediate translational as well as transcriptional regulation of the Bacillus subtilis trp operon. J. Bacteriol. 177, 6362–6370 (1995).

    Article  CAS  Google Scholar 

  11. Du,H. & Babitzke,P. Trp RNA-binding attenuation protein-mediated long distance RNA refolding regulates translation of trpE in Bacillus subtilis. J. Biol. Chem. 273, 20494–20503 (1998).

    Article  CAS  Google Scholar 

  12. Slock,J., Stahly,D. P., Han,C. Y., Six,E. W. & Crawford,I. P. An apparent Bacillus subtilis folic-acid biosynthetic operon containing pab, an amphibolic trpG gene, a third gene required for synthesis of para-aminobenzoic acid, and the dihydropteroate synthase gene. J. Bacteriol. 72, 7211–7226 (1990).

    Article  Google Scholar 

  13. Yang,M., de Saizieu,A., van Loon,A. P. G. M. & Gollnick,P. Translation of trpG in Bacillus subtilis is regulated by the trp RNA-binding attenuation protein (TRAP). J. Bacteriol. 177, 4272–4278 (1995).

    Article  CAS  Google Scholar 

  14. Antson,A. A. et al. Eleven-fold symmetry of the trp RNA-binding attenuation protein (TRAP) from Bacillus subtilis determined by X-ray analysis. J. Mol. Biol. 244, 1–5 (1994).

    Article  ADS  CAS  Google Scholar 

  15. Antson,A. A. et al. The three dimensional structure of trp RNA-binding attenuation protein. Nature 374, 693–700 (1995).

    Article  ADS  CAS  Google Scholar 

  16. Yang,M. et al. Alanine-scanning mutagenesis of Bacillus subtilis trp RNA-binding attenuation protein (TRAP) reveals residues involved in tryptophan binding and RNA binding. J. Mol. Biol. 270, 696–710 (1997).

    Article  CAS  Google Scholar 

  17. Chen,X.-P. et al. Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus. J. Mol. Biol. 289, 1003–1016 (1999).

    Article  ADS  CAS  Google Scholar 

  18. Dock-Bregeon,A. C. et al. High resolution structure of the RNA duplex [U(U - A)6A]2. Nature 335, 375–378 (1988).

    Article  ADS  CAS  Google Scholar 

  19. Oubridge,C., Ito,N., Evans,P. R., Teo,C.-H. & Nagai,K. Crystal-structure at 1.92 Angstrom resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature 372, 432–438 (1994).

    Article  ADS  CAS  Google Scholar 

  20. Valegard,K., Murray,J. B., Stockley,P. G., Stonehouse,N. J. & Liljas,L. Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature 371, 623–626 (1994).

    Article  ADS  CAS  Google Scholar 

  21. Rould,M. A., Perona,J. J. & Steitz,T. A. Structural basis of anticodon loop recognition by glutaminyl-transfer RNA-synthetase. Nature 352, 213–218 (1991).

    Article  ADS  CAS  Google Scholar 

  22. Pauling,L. & Corey,R. B. A proposed structure for the nucleic acids. Proc. Natl Acad. Sci. USA 39, 84–97 (1953).

    Article  ADS  CAS  Google Scholar 

  23. Allemand,J. F., Bensimon,D., Lavery,R. & Croquette,V. Stretched and overwound DNA forms a Pauling-like structure with exposed bases. Proc. Natl Acad. Sci. USA 95, 14152–14157 (1998).

    Article  ADS  CAS  Google Scholar 

  24. Baumann,C., Xirasagar,S. & Gollnick,P. The trp RNA-binding attenuation protein (TRAP) from B. subtilis binds to unstacked trp leader RNA. J. Biol. Chem. 272, 19863–19869 (1997).

    Article  CAS  Google Scholar 

  25. Baumann,C., Otridge,J. & Gollnick,P. Kinetic and thermodynamic analysis of the interaction between TRAP (t rp RNA-binding attenuation protein) and trp leader RNA from Bacillus subtilis. J. Biol. Chem. 271, 12269–12274 (1996).

    Article  CAS  Google Scholar 

  26. Babitzke,P., Bear,D. G. & Yanofsky,C. TRAP, the trp RNA-binding attenuation protein of Bacillus subtilis, is a toroid-shaped molecule that binds transcripts containing GAG or UAG repeats separated by 2 nucleotides. Proc. Natl Acad. Sci. USA 92, 7916–7920 (1995).

    Article  ADS  CAS  Google Scholar 

  27. Elliott,M. B., Gottlieb,P. A. & Gollnick,P. Probing the TRAP-RNA interaction with nucleoside analogues. RNA (in the press).

  28. Price,S. R., Evans,P. R. & Nagai,K. Crystal structure of the spliceosomal U2B″-U2A′ protein complex bound to a fragment of U2 small nuclear RNA. Nature 394, 645–650 (1998).

    Article  ADS  CAS  Google Scholar 

  29. Handa,N. et al. Structural basis for recognition of the tra mRNA precursor by the sex-lethal protein. Nature 398, 579–585 (1999).

    Article  ADS  CAS  Google Scholar 

  30. Bochkarev,A., Pfuetzner,R. A., Edwards,A. M. & Frappier,L. Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature 385, 176–181 (1997).

    Article  ADS  CAS  Google Scholar 

  31. Avis,J. M. et al. Solution structure of the N-terminal RNP domain of U1A protein: the role of C-terminal residues in structure stability and RNA binding. J. Mol. Biol. 257, 398–411 (1996).

    Article  CAS  Google Scholar 

  32. Puglisi,J. D., Chen,L., Blanchard,S. & Frankel,A. D. Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science 270, 1200–1203 (1995).

    Article  ADS  CAS  Google Scholar 

  33. Cavarelli,J., Rees,B., Ruff,M., Thierry,J.-C. & Moras,D. Yeast tRNAAsp recognition by its cognate class II aminoacyl-tRNA synthetase. Nature 362, 181–184 (1993).

    Article  ADS  CAS  Google Scholar 

  34. Biou,V., Yaremchuk,A., Tukalo,M. & Cusack,S. The 2.9 Å crystal structure of T. Termophilus seryl-tRNA synthetase complexed with tRNASer. Science 263, 1404–1410 (1994).

    Article  ADS  CAS  Google Scholar 

  35. Wimberly,B. T., Guymon,R., McCutcheon,J. P., White,S. W. & Ramakrishnan,V. A detailed view of a ribosomal active site: The structure of the L11-RNA complex. Cell 97, 491–502 (1999).

    Article  CAS  Google Scholar 

  36. Conn,G. L., Draper,D. E., Lattman,E. E. & Gittis,A. G. Crystal structure of a conserved ribosomal protein–RNA complex. Science 284, 1171–1174 (1999).

    Article  ADS  CAS  Google Scholar 

  37. Houman,F., Diaz-Torres,M. R. & Wright,A. Transcriptional antitermination in the bgl operon of E. coli is modulated by a specific RNA-binding protein. Cell 62, 1153–1163 (1990).

    Article  CAS  Google Scholar 

  38. Tomchick,D. R., Turner,R. J., Switzer,R. L. & Smith,J. L. Adaptation of an enzyme to regulatory function: structure of Bacillus subtilis PyrR, a pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase. Structure 6, 337–350 (1998).

    Article  CAS  Google Scholar 

  39. Ziehler,W. A. & Engelke,D. R. Synthesis of small RNA transcripts with discrete 5′ and 3′ ends. Biotechniques 20, 622–624 (1996).

    CAS  PubMed  Google Scholar 

  40. Brzozowski,A. M. Crystallization of a Humicola lanuginosa lipase-inhibitor with the use of poly(ethylene)glycol monomethyl ether. Acta Crystallogr. D 49, 352–354 (1993).

    Article  CAS  Google Scholar 

  41. Otwinowski,Z. & Minor,W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  42. CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994).

    Article  Google Scholar 

  43. Bernstein,F. C. et al. The protein data bank: a computer based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542 (1977).

    Article  CAS  Google Scholar 

  44. Oldfield,T. J. in Proceedings of the CCP4 Study Weekend (eds Bailey, S., Hubbard, R. & Waller, D.) (Daresbury Laboratory, Warrington, UK, 1994).

  45. Brunger,A. T. The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472–475 (1992).

    Article  ADS  CAS  Google Scholar 

  46. Brooks,B. R. et al. CHARMM—a program for macromolecular energy, minimization and dynamics calculation. J. Comp. Chem. 4, 187–217 (1983).

    Article  CAS  Google Scholar 

  47. Schneider,B., Neidle,S. & Berman,H. M. Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42, 113–124 (1997).

    Article  CAS  Google Scholar 

  48. Kraulis,P. J. MOLSCRIPT—a program to produce both detailed and schematic plots of proteins structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

  49. Esnouf,R. M. An extensively modified version of Molscript that includes greatly enhanced coloring capabilities. J. Mol. Graph. 15, 133–138 (1997).

    Google Scholar 

  50. Merritt,E. A. & Bacon,D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505–524 (1997).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by a Wellcome Trust career development fellowship to A.A.A., by an MRC grant to E.J.D. and by grants for the National Science Foundation and the Pew Charitable Trusts to P.G. We thank the BBSRC, UK for infrastructure support. We also thank the European Commission for support of the work at EMBL Hamburg through the HCMP Access to Large Installations Project. We thank A. J. Wilkinson, H. F. J. Savage and K. S. Wilson for critically reading the manuscript; C. S. Verma and L. S. D. Caves for discussions; S. J. P. Mumford for help with figure preparation; and N. Kouzmina for advice on artwork.

Author information

Author notes

  1. Xiao-ping Chen

    Present address: CuraGen Corp., 322 East Main Street, Branford, Connecticut, 06405, USA

Authors and Affiliations

  1. Department of Chemistry, York Structural Biology Laboratory, University of York, York, Y010 5DD, UK

    Alfred A. Antson, Eleanor J. Dodson, Guy Dodson & Richard B. Greaves

  2. Department of Biological Sciences, State University of New York, Buffalo, New York, 14260, USA

    Xiao-ping Chen & Paul Gollnick

Authors
  1. Alfred A. Antson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Eleanor J. Dodson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Guy Dodson
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Richard B. Greaves
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xiao-ping Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Paul Gollnick
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alfred A. Antson.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Antson, A., Dodson, E., Dodson, G. et al. Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA. Nature 401, 235–242 (1999). https://doi.org/10.1038/45730

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/45730

This article is cited by

Comments

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.

Search

Advanced 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