Co-crystal structure of TBP recognizing the minor groove of a TATA element

Abstract

The three-dimensional structure of a TATA-box binding polypeptide complexed with the TATA element of the adenovirus major late promoter has been determined by X-ray crystallography at 2.25 Å resolution. Binding of the saddle-shaped protein induces a conformational change in the DNA, inducing sharp kinks at either end of the sequence TATAAAAG. Between the kinks, the right-handed double helix is smoothly curved and partially unwound, presenting a widened minor groove to TBP's concave, antiparallel β-sheet. Side-chain/base interactions are restricted to the minor groove, and include hydrogen bonds, van der Waals contacts and phenylalanine–base stacking interactions.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1

    Sharp, P. A. Cell 68, 819–821 (1992).

    CAS  Article  Google Scholar 

  2. 2

    White, R. J. & Jackson, S. P. Trends Genet. 8, 284–288 (1992).

    CAS  Article  Google Scholar 

  3. 3

    Rigby, P. W. J. Cell 72, 7–10 (1993).

    CAS  Article  Google Scholar 

  4. 4

    Roeder, R. G. Trends biochem. Sci. 16, 402–408 (1991).

    CAS  Article  Google Scholar 

  5. 5

    Zawel, L. & Reinberg, D. Curr. Opin. Cell Biol. 4, 488–495 (1992).

    CAS  Article  Google Scholar 

  6. 6

    Hisatake, K. et al. Nature 362, 179–181 (1993).

    ADS  CAS  Article  Google Scholar 

  7. 7

    Ruppert, S., Wang, E. H. & Tjian, R. Nature 362, 175–179 (1993).

    ADS  CAS  Article  Google Scholar 

  8. 8

    Hoffmann, A. et al. Nature 346, 387–390 (1990).

    ADS  CAS  Article  Google Scholar 

  9. 9

    Peterson, M. G., Tanese, N., Pugh, B. F. & Tjian, R. Science 248, 1625–1630 (1990).

    ADS  CAS  Article  Google Scholar 

  10. 10

    Buratowski, S., Hahn, S., Guarente, L. & Sharp, P. A. Cell 56, 549–661 (1989).

    CAS  Article  Google Scholar 

  11. 11

    Nikolov, D. B. et al. Nature 360, 40–46 (1992).

    ADS  CAS  Article  Google Scholar 

  12. 12

    Yamamoto, T. et al. Proc. natn. Acad. Sci. U.S.A. 89, 2844–2848 (1992).

    ADS  CAS  Article  Google Scholar 

  13. 13

    Reddy, P. & Hahn, S. Cell 65, 349–357 (1991).

    CAS  Article  Google Scholar 

  14. 14

    Hahn, S., Buratowski, S., Sharp, P. A. & Guarente, L. Proc. natn. Acad. Sci. U.S.A. 86, 5718–5722 (1989).

    ADS  CAS  Article  Google Scholar 

  15. 15

    Lee, D. K., Horikoshi, M. & Roeder, R. G. Cell 67, 1241–1250 (1991).

    CAS  Article  Google Scholar 

  16. 16

    Starr, D. B. & Hawley, D. K. Cell 67, 1231–1240 (1991).

    CAS  Article  Google Scholar 

  17. 17

    Horikoshi, M. et al. Proc. natn. Acad. Sci. U.S.A. 89, 1060–1064 (1992).

    ADS  CAS  Article  Google Scholar 

  18. 18

    Cormack, B. P. & Struhl, K. Cell 69, 685–696 (1992).

    CAS  Article  Google Scholar 

  19. 19

    Schultz, M. C., Reeder, R. H. & Hahn, S. Cell 69, 697–702 (1992).

    CAS  Article  Google Scholar 

  20. 20

    Ziff, E. B. & Evans, R. M. Cell 15, 1463–1475 (1978).

    CAS  Article  Google Scholar 

  21. 21

    Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Acta. crystallogr. A47, 110–119 (1991).

    Article  Google Scholar 

  22. 22

    Brunger, A. T. XPLOR Manual (Yale Univ. Press, New Haven, 1992).

    Google Scholar 

  23. 23

    Ramachandran, G. N., Ramakrishnan, C. & Sasisekharan, V. J. molec. Biol. 7, 95–99 (1963).

    CAS  Article  Google Scholar 

  24. 24

    Travers, A. A. Curr. Opin. struct. Biol. 1, 114–122 (1991).

    CAS  Article  Google Scholar 

  25. 25

    Wu, H.-M. & Crothers, D. M. Nature 308, 509–513 (1984).

    ADS  CAS  Article  Google Scholar 

  26. 26

    Nelson, H. C. M., Finch, J. T., Luisi, B. F. & Klug, A. Nature 330, 221–226 (1987).

    ADS  CAS  Article  Google Scholar 

  27. 27

    DiGabriele, A. D. & Steitz, T. A. J. molec. Biol. 231, 1024–1039 (1993).

    CAS  Article  Google Scholar 

  28. 28

    Lavery, R. & Sklenar, H. J. biomolec. struct. Dyn. 7, 655–667 (1989).

    Article  Google Scholar 

  29. 29

    Lorch, Y. & Kornberg, R. D. Molec. cell. Biol. 13, 1872–1875 (1993).

    CAS  Article  Google Scholar 

  30. 30

    Ornstein, R. L., Rein, R., Breen, D. L. & MacElroy, R. D. Biopolymers 17, 2341–2360 (1978).

    CAS  Article  Google Scholar 

  31. 31

    Phillips, S. E. V. Curr. Opin. struct. Biol. 1, 89–98 (1991).

    CAS  Article  Google Scholar 

  32. 32

    Wolberger, C. Curr. Opin. struct. Biol. 3, 3–10 (1993).

    CAS  Article  Google Scholar 

  33. 33

    Wobbe, C. R. & Struhl, K. Molec. cell. Biol. 10, 3859–3867 (1990).

    CAS  Article  Google Scholar 

  34. 34

    Strubin, M. & Struhl, K. Cell 68, 721–730 (1992).

    CAS  Article  Google Scholar 

  35. 35

    Arndt, K. M., Ricupero, S. L., Eisenmann, D. M. & Winston, F. Molec. cell. Biol. 12, 2372–2382 (1992).

    CAS  Article  Google Scholar 

  36. 36

    Steitz, T. A. Q. Rev. Biophys. 23, 205–280 (1990).

    CAS  Article  Google Scholar 

  37. 37

    Schultz, S. C., Shields, G. C. & Steitz, T. A. Science 253, 1001–1007 (1991).

    ADS  CAS  Article  Google Scholar 

  38. 38

    Hegde, R. S., Grossman, S. R., Laimins, L. A. & Sigler, P. B. Nature 359, 505–512 (1992).

    ADS  CAS  Article  Google Scholar 

  39. 39

    Lieberman, P. M., Schmidt, M. C., Kao, C. C. & Berk, A. J. Molec. cell. Biol. 11, 63–74 (1991).

    CAS  Article  Google Scholar 

  40. 40

    Hooper, B. C., LeBlanc, J. F. & Hawley, D. K. J. biol. Chem. 267, 11539–11547 (1992).

    Google Scholar 

  41. 41

    Zenzie-Gregory, B., Khachi, A., Garraway, I. P. & Smale, S. T. Molec. cell. Biol. 13, 3841–3849 (1993).

    CAS  Article  Google Scholar 

  42. 42

    Lee, D. K., DeJong, J., Hashimoto, S., Horikoshi, M. & Roeder, R. G. Molec. cell. Biol. 12, 5189–5196 (1992).

    CAS  Article  Google Scholar 

  43. 43

    Buratowski, S. & Zhou, H. Science 255, 1030–1032 (1992).

    Article  Google Scholar 

  44. 44

    Flores, O., Maldonado, E., Burton, Z., Greenblatt, J. & Reinberg, D. J. biol. Chem. 264, 10812–10816 (1988).

    Google Scholar 

  45. 45

    Greenblatt, J. Cell 66, 1067–1070 (1991).

    CAS  Article  Google Scholar 

  46. 46

    Workman, J. L. & Roeder, R. G. Cell 51, 613–622 (1987).

    CAS  Article  Google Scholar 

  47. 47

    Meisterernst, M., Horikoshi, M. & Roeder, R. G. Proc. natn. Acad. Sci. U.S.A. 87, 9153–9157 (1990).

    ADS  CAS  Article  Google Scholar 

  48. 48

    Drew, H. R. & Travers, A. A. J. molec. Biol. 186, 773–790 (1985).

    CAS  Article  Google Scholar 

  49. 49

    Satchwell, S. C., Drew, H. R. & Travers, A. A. J. molec. Biol. 191, 659–675 (1986).

    CAS  Article  Google Scholar 

  50. 50

    Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P. & Dickerson, R. E. J. molec. Biol. 183, 553–563 (1985).

    CAS  Article  Google Scholar 

  51. 51

    Coll, M. et al. Biochemistry 28, 310–320 (1989).

    CAS  Article  Google Scholar 

  52. 52

    Kabsch, W. & Sander, C. Biopolymers 22, 2577–2637 (1983).

    CAS  Article  Google Scholar 

  53. 53

    Puglisi, J. D. & Tinoco, I. J. Meth. Enzym. 180A, 304–325 (1989).

    CAS  Article  Google Scholar 

  54. 54

    Terwilliger, T. & Eisenberg, D. Acta crystallogr. A39, 813–817 (1983).

    Article  Google Scholar 

  55. 55

    Kabsch, W., Mannherz, H. G., Suck, D., Pai, E. F. & Holmes, K. C. Nature 347, 37–44 (1990).

    ADS  CAS  Article  Google Scholar 

  56. 56

    Bernstein, F. C. et al. J. molec. Biol. 112, 535–542 (1977).

    CAS  Article  Google Scholar 

Download references

Author information

Affiliations

Authors

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kim, J., Nikolov, D. & Burley, S. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365, 520–527 (1993). https://doi.org/10.1038/365520a0

Download citation

Further reading

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.