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:

1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAG

Abstract

The three-dimensional structure of a TATA box-binding protein (TBP) from Arabidopsis thaliana complexed with a fourteen base pair oligonucleotide bearing the Adenovirus major late promoter TATA element has been refined at 1.9 Å resolution, giving a final crystallographic R-factor of 19.4%. Binding of the monomeric, saddle-shaped α/β protein induces an unprecedented conformational change in the DNA. A detailed structural and functional analysis of this unusual protein-DNA complex is presented, with particular emphasis on the mechanisms of DNA deformation, TATA element recognition, and preinitiation complex assembly.

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. Sawadogo, M. & Sentenac, A. RNA polymerase B (II) and general transcription factors. Rev. Biochem. 59, 711–754 (1990).

    Article  CAS  Google Scholar 

  2. Zawel, L. & Reinberg, D. Advances in RNA polymerase II transcription. Curr. Opin. Cell Biol. 4, 488–495 (1992).

    Article  CAS  Google Scholar 

  3. Kaufmann, J. & Smale, S.T Direct recognition of initiator elements by a component of the transcription factor IID complex. Genes Dev. 8, 821–829 (1994).

    Article  CAS  Google Scholar 

  4. Purnell, B.A., Emanuel, P.A. & Gilmour, D.S. TFIID sequence recognition of the initiator and sequences farther downstream in Drosophila class II genes. Genes Dev. 8, 830–842 (1994).

    Article  CAS  Google Scholar 

  5. Verrijzer, C., Yokomori, K., Chen, J.-L. & Tjian, R. Drosophila TAFII150: Similarity to yeast gene TSM-1 and specific binding to core promoter DNA. Science 264, 933–941 (1994).

    Article  CAS  Google Scholar 

  6. Roeder, R.G. The complexities of eukaryotic transcription initiation: regulation of preinitiation complex assembly. Trends biochem. Sci. 16, 402–408 (1991).

    Article  CAS  Google Scholar 

  7. Nikolov, D.B. & Burley, S.K. 2.1 Å Resolution refined structure of a TATA box-binding protein. Nature struct. Biol. 1, 621–637 (1994).

    Article  CAS  Google Scholar 

  8. Buratowski, S. & Zhow, H. Transcription factor IID mutants defective for interaction with transcription factor IIA. Science 255, 1030–1032 (1992).

    Article  Google Scholar 

  9. Lee, D.K., DeJong, J., Hashimoto, S., Horikoshi, M. & Roeder, R.G. TFIIA induces conformational changes in TFIID via interactions with the basic repeat. Molec. Cell. Biol. 12, 5189–5196 (1992).

    Article  CAS  Google Scholar 

  10. Ha, I. et al. Multiple functional domains of human transcription factor IIB: distinct interactions with two general transcription factors and RNA polymerase II. Genes Dev. 7, 1021–1032 (1993).

    Article  CAS  Google Scholar 

  11. Usheva, A. et al. Specific interactions between the nonphosphorylated form of RNA polymerase II and the TATA-binding protein. Cell 69, 871–881 (1992).

    Article  CAS  Google Scholar 

  12. Koleske, A.J., Buratowski, S., Nonet, M. & Young, R.A. A Novel transcription factor reveals a functional link between the RNA polymerase II CTD and TFIID. Cell 69, 883–894 (1992).

    Article  CAS  Google Scholar 

  13. Hernandez, N. TBP, a universal transcription factor? Genes Dev. 7, 1291–1308 (1993).

    Article  CAS  Google Scholar 

  14. Hahn, S., Buratowski, S., Sharp, P.A. & Guarente, L. Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and nonconsensus DNA sequences. Proc. natn. Acad. Sci. U.S.A. 86, 5718–5722 (1989).

    Article  CAS  Google Scholar 

  15. Horikoshi, M. et al. Transcription factor TFIID induces DNA bending upon binding to the TATA element. Proc. natn. Acad. Sci. U.S.A. 89, 1060–1064 (1992).

    Article  CAS  Google Scholar 

  16. Starr, D.B. & Hawley, D.K. TFIID binds in the minor groove of the TATA box. Cell 67, 1231–1240 (1991).

    Article  CAS  Google Scholar 

  17. Lee, D.K., Horikoshi, M. & Roeder, R.G. Interaction of TFIID in the minor groove of the TATA element. Cell 67, 1241–1250 (1991).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  19. Chasman, D.I., Flaherty, K.M., Sharp, P.A. & Kornberg, R.D. Crystal structure of yeast TATA-binding protein and model for interaction with DNA. Proc. natn. Acad. Sci. U.S.A. 90, 8174–8178 (1993).

    CAS  Google Scholar 

  20. Geiger, J.H., Kim, Y., Hahn, S. & Sigler, P.B. Crystal structure of yeast TBP at 2.1 Å resolution. Biochemistry 33, in the press (1994).

  21. Kim, J.L., Nikolov, D.B. & Burley, S.K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365, 520–527 (1993).

    Article  CAS  Google Scholar 

  22. Kim, Y., Geiger, J.H., Hahn, S. & Sigler, P.B. Crystal structure of a yeast TBP/TATA-box complex. Nature 356, 512–520 (1993).

    Article  Google Scholar 

  23. Nagawa, F. & Fink, G.R. The relationship between the “TATA” sequence and transcription initiation sites at the HIS4 gene of Saccharomyces cerevisiae. Proc. natn. Acad. Sci. U.S.A. 82, 8557–8561 (1985).

    Article  CAS  Google Scholar 

  24. Luzzati, P.V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta. crystallogr. 5, 802–810 (1952).

    Article  Google Scholar 

  25. Lorch, Y. & Kornberg, R.D. Near-zero linking difference upon transcription factor IId binding to promoter DNA. Molec. Cell. Biol. 13, 1872–1875 (1993).

    Article  CAS  Google Scholar 

  26. Nelson, H.C.M., Finch, J.T., Luisi, B.F. & Klug, A. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature 330, 221–226 (1987).

    Article  CAS  Google Scholar 

  27. DiGabriele, A.D., Sanderson, M.R. & Steitz, T.A. Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. natn. Acad. Sci. U.S.A. 86, 1816–1820 (1989).

    Article  CAS  Google Scholar 

  28. DiGabriele, A.D. & Steitz, T.A. A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend. J. molec. Biol. 231, 1024–1039 (1993).

    Article  CAS  Google Scholar 

  29. Aggarwal, A.K., Rodgers, D.W., Drottar, M., Ptashne, M. & Harrison, S.C. Recognition of a DNA operator by the represser of Phage 434: A view at high resolution. Science 242, 899–907 (1988).

    Article  CAS  Google Scholar 

  30. Winkler, F.K. et al. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12, 1781–1795 (1993).

    Article  CAS  Google Scholar 

  31. Suck, D., Lahm, A. & Oefner, C. Structure refined to 2 Å of a nicked DNA octanucleotide complex with DNase I. Nature 332, 464–468 (1988).

    Article  CAS  Google Scholar 

  32. Hodel, A., Kim, S.-H. & Brunger, A.T. Model bias in macromolecular crystal structures. Acta crystallogr. A48, 851–858 (1992).

    Article  CAS  Google Scholar 

  33. Yamamoto, T. et al. A bipartite DNA binding domain composed of direct repeats in the TATA box binding factor TFIID. Proc. natn. Acad. Sci. U.S.A. 89, 2844–2848 (1992).

    Article  CAS  Google Scholar 

  34. Lilley, D.M.J. HMG has DNA wrapped up. Nature 357, 282–283 (1992).

    Article  CAS  Google Scholar 

  35. Crothers, D.M. Architectural elements in nucleoprotein complexes. Curr. Biol. 3, 675–676 (1993).

    Article  CAS  Google Scholar 

  36. Yang, C.-C. & Nash, H.A. The interaction of E. coli IHF protein with its specific binding sites. Cell 57, 869–880 (1989).

    Article  CAS  Google Scholar 

  37. Pil, P.M., Chow, C.S. & Lippard, S.J. High-mobility-group 1 protein mediates DNA bending as determined by ring closures. Proc. natn. Acad. Sci. U.S.A. 90, 9465–9469 (1993).

    Article  CAS  Google Scholar 

  38. Giese, K., Cox, J. & Grosschedl, R. The HMG domain of lympnoid enhancer factor 1 bends DNA and facilitates assembly of functional nucleoprotein structures. Cell 69, 185–195 (1992).

    Article  CAS  Google Scholar 

  39. Weir, H.M. et al. Structure of the HMG box motif in the B-domain of HMG-1. EMBO J. 12, 1311–1319 (1993).

    Article  CAS  Google Scholar 

  40. Read, C.M., Cary, P.D., Crane-Robinson, C., Driscoll, P.C. & Norman, D.G. Solution structure of a DNA-binding domain from HMG1. Nucleic Acids Res. 21, 3427–3436 (1993).

    Article  CAS  Google Scholar 

  41. King, C.-Y. & Weiss, M.A. The SRY high-mobility-group box recognizes DNA by partial intercalation in the minor groove: A topological mechanism of sequence specificity. Proc. natn. Acad. Sci. U.S.A. 90, 11990–11994 (1993).

    Article  CAS  Google Scholar 

  42. Tanaka, I., Appelt, K., Dijk, J., White, S.W. & Wilson, K.S. 3-Å resolution structure of a protein with histone-like properties in prokaryotes. Nature 310, 376–381 (1984).

    Article  CAS  Google Scholar 

  43. Steitz, T.A. Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q. Rev. Biophys. 23, 205–280 (1990).

    Article  CAS  Google Scholar 

  44. Harrison, S.C. A structural taxonomy of DNA-binding domains. Nature 353, 715–719 (1991).

    Article  CAS  Google Scholar 

  45. Wolberger, C. Transcription Factor Structure and DNA Binding. Curr. Opin. struct. Biol. 3, 3–10 (1993).

    Article  CAS  Google Scholar 

  46. Burley, S.K. DNA-binding motifs from eukaryotic transcription factors. Curr. Opin. struct. Biol. 4, 3–11 (1994).

    Article  CAS  Google Scholar 

  47. Spolar, R. & Record, M.T., Jr Science 263, 777–784 (1994).

    Article  CAS  Google Scholar 

  48. Ladbury, J., Wright, J., Sturtevant, J. & Sigler, P. A thermodynamic study of the trp repressor-operator interaction. J. molec. Biol. 238, 669–681 (1994).

    Article  CAS  Google Scholar 

  49. Livingston, J., Spolar, R. & Record, M.T., Jr. Biochemistry 30, 4237–4244 (1991).

    Article  Google Scholar 

  50. Hoopes, B.C., LeBlanc, J.F. & Hawley, D.K. Kinetic analysis of yeast TFIID-TATA box complex formation suggests a multi-step pathway. J. biol. Chem. 267, 11539–11546 (1992).

    CAS  Google Scholar 

  51. Shakked, Z. et al. Sequence-dependent conformation of an A-DNA double helix. J. molec. Biol. 166, 183–201 (1983).

    Article  CAS  Google Scholar 

  52. Ornstein, R.L., Rein, R., Breen, D.L. & MacElroy, R.D. An optimized potential function for the calculation of nucleic acid interaction energies. I. Base stacking. Biopolymers 17, 2341–2361 (1978).

    Article  CAS  Google Scholar 

  53. Yuan, H., Quintana, J. & Dickerson, R. Alternative structures for alternating poly(dA-DT) tracts: the structure of the B-DNA decamer C-G-A-T-A-T-A-T-C-G. Biotechemistry 31, 8009–8021 (1992).

    Article  CAS  Google Scholar 

  54. Wobbe, C.R. & Struhl, K. Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro. Molec. Cell. Biol. 10, 3859–3867 (1990).

    Article  CAS  Google Scholar 

  55. Poon, D. et al. Genetic and biochemical analyses of yeast TATA-binding protein mutants. J. biol. Chem. 268, 5005–5013 (1993).

    CAS  PubMed  Google Scholar 

  56. Strubin, M. & Struhl, K. Yeast and human TFIID with altered DNA-binding specificity for TATA elements. Cell 68, 721–730 (1992).

    Article  CAS  Google Scholar 

  57. Roy, A., Malik, S., Meisterernst, M. & Roeder, R. An alternative pathway for transcription initiation involving TFII-I. Nature 365, 355–359 (1993).

    Article  CAS  Google Scholar 

  58. Usheva, A. & Shenk, T. TATA-binding protein-independent initiation: YY1, TFIIB, and RNA polymerase II direct basal transcription on supercoiled template DNA. Cell 76, 1115–1121 (1994).

    Article  CAS  Google Scholar 

  59. Drew, H.R. & Travers, A.A. DNA bending and its relation to nucleosome positioning. J. molec. Biol. 186, 773–790 (1985).

    Article  CAS  Google Scholar 

  60. Satchwell, S.C., Drew, H.R. & Travers, A.A. Sequence periodicities in chicken nucleosome core DNA. J. molec. Biol. 191, 659–675 (1986).

    Article  CAS  Google Scholar 

  61. Workman, J.L. & Roeder, R.G. Binding of transcription factor TFIID to the major late promoter during In vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II. Cell 51, 613–622 (1987).

    Article  CAS  Google Scholar 

  62. Meisterernst, M., Horikoshi, M. & Roeder, R.G. Recombinant yeast TFIID, a general transcription factor, mediates activation by the gene-specific factor USF in a chromatin assembly assay. Proc. natn. Acad. Sci. U.S.A. 87, 9153–9157 (1990).

    Article  CAS  Google Scholar 

  63. Prioleau, M.-N., Huet, J., Sentenac, A. & Mechali, M. Competition between chromatin and transcription complex assembly regulates gene expression during early development. Cell 77, 439–449 (1994).

    Article  CAS  Google Scholar 

  64. Kopka, M., Yoon, C., Goodsell, D., Pjura, P. & Dickerson, R. The binding of an antitumor drug to DNA. Netropsin and CGCGAATTBrCGCG. J. molec. Biol. 183, 553–563 (1985).

    Article  CAS  Google Scholar 

  65. Coll, M., Aymami, J., Marel, G.v.d., Boom, J.v. & Wang, A.-J. Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment. Biochemistry 28, 310–320 (1989).

    Article  CAS  Google Scholar 

  66. Chen, X., Ramakrishnan, B., Sambhorao, T. & Sundaralingam, M. Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex. Nature struct. Biol. 1, 169–175 (1994).

    Article  CAS  Google Scholar 

  67. Chiang, S.-Y., Welch, J., Rauscher, F. & Beerman, T. Effects of minor groove binding drugs on the interaction of TATA box binding protein and TFIIA with DNA. Biochemistry 33, 7033–7040 (1994).

    Article  CAS  Google Scholar 

  68. Schultz, S.C., Shields, G.C. & Steitz, T.A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 °. Science 253, 1001–1007 (1991).

    Article  CAS  Google Scholar 

  69. Brunger, A.T. XPLOR Manual (Yale University, New Haven, 1992).

    Google Scholar 

  70. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta crystallogr. A47, 110–119 (1991).

    Article  CAS  Google Scholar 

  71. Brunger, A.T. The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472–474 (1992).

    Article  CAS  Google Scholar 

  72. Ramachandran, G.N. & Sasisekharan, V. Conformation of polypeptides and proteins. Advan. prot. Chem. 23, 283–437 (1968).

    Article  CAS  Google Scholar 

  73. Kraulis, P.J. Molscript: a program to produce both detailed and schematic plots of protein structures. J. appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  75. Gilson, M., Sharp, K. & Honig, B. Calculating the electrostatic potential of molecules in solution: method and error assessment. J. comput. Chem. 9, 327–335 (1988).

    Article  CAS  Google Scholar 

  76. Lavery, R. & Sklenar, H. Defining the structure of irregular nucleic acids: conventions and principles. J. biomolec. Struct. Dynamics 6, 655–667 (1989).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kim, J., Burley, S. 1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAG. Nat Struct Mol Biol 1, 638–653 (1994). https://doi.org/10.1038/nsb0994-638

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb0994-638

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