2.1 Å resolution refined structure of a TATA box-binding protein (TBP) (original) (raw)

References

  1. Sentenac, A. Eukaryotic RNA polymerases. CRC Crit. Rev. Biochem. 18, 31–90 (1985).
    CAS PubMed Google Scholar
  2. Reeder, R.H. Regulation of transcription by RNA polymerase I. in Transcriptional regulation (eds McKnight, S. & Yamamoto, K.R.) 315–348 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1992).
    Google Scholar
  3. Roeder, R.G. The complexities of eukaryotic transcription initiation: regulation of preinitiation complex assembly. Trends biochem. Sci. 16, 402–408 (1991).
    Article CAS PubMed Google Scholar
  4. Zawel, Z. & Reinberg, D. Initiation of transcription by RNA polymerase II: a multi-step process. Prog. nucl. Acids Res. molec. Biol. 44, 67–108 (1993).
    CAS Google Scholar
  5. Gabrielsen, O.S. & Sentenac, A. RNA polymerase III (C) and its transcription factors. Trends biochem. Sci. 16, 412–416 (1991).
    CAS PubMed Google Scholar
  6. Hernandez, N. TBP, a universal transcription factor? Genes Dev. 7, 1291–1308 (1993).
    CAS PubMed Google Scholar
  7. Gill, G. & Tjian, R. Eukaryotic coactivators associated with the TATA box binding protein. Curr. Opin. Genetics Dev. 2, 236–242 (1992).
    CAS Google Scholar
  8. Matsui, T., Segall, J., Weil, P.A. & Roeder, R.G. Multiple factors required for accurate initiation of transcription by purified RNA polymerase II. J. biol. Chem 255, 11992–11996 (1980).
    CAS PubMed Google Scholar
  9. Buratowski, S. & Sharp, P.A. Initiation of transcription by RNA polymerase II. in Transcriptional Regulation (eds McKnight, S. & Yamamoto, K.R.) 227–246 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1992).
    Google Scholar
  10. Buratowski, S., Hahn, S., Guarente, L. & Sharp, P.A. Five intermediate complexes in transcription initiation by RNA polymerase II. Cell 56, 549–561 (1989).
    Article CAS PubMed Google Scholar
  11. Wang, W., Carey, M. & Gralla, J. Polymerase II promoter activation: closed complex formation and ATP-driven start site opening. Science 255, 450–453 (1992).
    CAS PubMed Google Scholar
  12. Dyke, M.W.V., Roeder, R.G. & Sawadogo, M. Physical analysis of transcription preinitiation complex assembly on a class II gene promoter. Science 241, 1335–1338 (1988).
    PubMed Google Scholar
  13. Ptashne, M. & Gann, A.A.F. Activators and targets. Nature 346, 329–331 (1990).
    CAS PubMed Google Scholar
  14. Wang, W., Gralla, J. & Carey, M. The acidic activator GAL4-AH can stimulate polymerase II transcription by promoting assembly of a closed complex requiring TFIID and TFIIA. Genes Dev. 6, 1716–1727 (1992).
    CAS PubMed Google Scholar
  15. Comai, L., Tanese, N. & Tjian, R. The TATA-binding protein and associated factors are integral components of the RNA polymerase I transcription factor, SL1. Cell 68, 965–976 (1992).
    CAS PubMed Google Scholar
  16. Nikolov, D.B. et al. Crystal structure of TFIID TATA box-binding protein. Nature 360, 40–46 (1992).
    Article CAS PubMed Google Scholar
  17. Hahn, S., Buratowski, S., Sharp, P.A. & Guarente, L. The 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).
    CAS Google Scholar
  18. Hooper, 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).
    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. Kim, Y., Geiger, J.H., Hahn, S. & Sigler, P.B. Crystal structure of a yeast TBP/TATA-box complex. Nature 356, 512–520 (1993).
    Google Scholar
  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 PubMed Google Scholar
  22. Klug, A. Opening the gateway. Nature 365, 486–487 (1993).
    CAS PubMed Google Scholar
  23. Kim, J.L. & Burley, S.K. 1.9 Å Refined structure of TBP recognizing the minor groove of TATAAAAG. Nature struct. Biol. 1, 638–653 (1994).
    CAS PubMed Google Scholar
  24. Sibanda, B.L., Blundell, T.L. & Thornton, J.M. Conformation of β-hairpins in protein structures: A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J. molec. Biol. 206, 759–777 (1989).
    Article CAS PubMed Google Scholar
  25. Janin, J. & Chothia, C. The structure of protein-protein recognition sites. J. biol. Chem. 265, 16027–16030 (1990).
    CAS PubMed Google Scholar
  26. Hoffmann, A. et al. Highly conserved core domain and unique N terminus with presumptive regulatory motifs in a human TATA factor (TFIID). Nature 346, 387–390 (1990).
    CAS Google Scholar
  27. Crowley, T.E. et al. A new factor related to TATA-binding protein has highly restricted expression patterns in Drosophila. Nature 361, 557–561 (1993).
    CAS PubMed Google Scholar
  28. McAndrew, M.B., Read, M., Sims, P.F.G. & Hyde, J.E. Characterization of the gene encoding an unusually divergent TATA-binding protein (TBP) from the extremely A+T rich human malaria parasite Plasmodium falciparum. Gene 124, 165–171 (1993).
    CAS PubMed Google Scholar
  29. Bowie, J.U., Luthy, R. & Eisenberg, D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253, 164–170 (1991).
    CAS PubMed Google Scholar
  30. Cormack, B.P. & Struhl, K. The TATA-binding protein is required for transcription by all three nuclear RNA polymerases in yeast cells. Cell 69, 685–696 (1992).
    CAS PubMed Google Scholar
  31. Schultz, M.C., Reeder, R.H. & Hahn, S. Variants of the TATA-binding protein can distinguish subsets of RNA polymerase I, II, and III promoters. Cell 69, 697–702 (1992).
    CAS PubMed Google Scholar
  32. Cormack, B.P. & Struhl, K. Regional codon randomization: defining a TATA-binding protein surface required for RNA polymerase III transcription. Science 262, 244–248 (1993).
    CAS PubMed Google Scholar
  33. Kim, T.K. & Roeder, R.G. Involvement of the basic repeat domain of TATA-binding protein (TBP) in transcription by RNA polymerase I, II, and III. J. biol. Chem. 269, 4891–4894 (1994).
    CAS PubMed Google Scholar
  34. Reddy, P. & Hahn, S. Dominant negative mutation in yeast TFIID define a bipartite DNA-binding region. Cell 65, 349–357 (1991).
    CAS PubMed Google Scholar
  35. 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
  36. Buratowski, S. & Zhou, H. A suppressor of TBP mutations encodes an RNA polymerase II transcription factor with homology to TFIIB. Cell 71, 221–230 (1992).
    CAS PubMed Google Scholar
  37. Colbert, T. & Hahn, S. A yeast TFIIB-related factor involved in RNA polymerase III transcription. Genes Dev. 6, 1940–1949 (1992).
    CAS PubMed Google Scholar
  38. Dahmus, M.E. & Kedinger, C. Transcription of Adenovirus-2 major late promoter inhibited by monoclonal antibody directed against RNA polymerase IIA and IIO. J. biol. Chem. 258, 2303–2307 (1983).
    CAS PubMed Google Scholar
  39. Usheva, A. et al. Specific interactions between the nonphosphorylated form of RNA polymerase II and the TATA-binding protein. Cell 69, 871–881 (1992).
    CAS PubMed Google Scholar
  40. 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).
    CAS PubMed PubMed Central Google Scholar
  41. Buratowski, S. & Zhou, H. Transcription factor IID mutants defective for interaction with transcription factor IIA. Science 255, 1030–1032 (1992).
    Google Scholar
  42. Ranish, J.A., Lane, W.S. & Hahn, S. Isolation of two genes that encode subunits of the yeast transcription factor IIA. Science 255, 1127–1129 (1992).
    CAS PubMed Google Scholar
  43. Greenblatt, J. Protein-protein interactions as critical determinants of regulated initiation and termination of transcription. in Transcriptional Regulation (eds McKnight, S. & Yamamoto, K.R.) 203–226 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1992).
    Google Scholar
  44. Kim, T.K. et al. Effects of activation-defective TBP mutations on transcription inhibition in yeast. Nature, 369, 252–255 (1994).
    CAS PubMed Google Scholar
  45. Zhou, Q., Boyer, T.G. & Berk, A.J. Factors (TAFs) required for activated transcription interact with TATA box-binding protein conserved core domain. Genes Dev. 7, 180–187 (1993).
    CAS PubMed Google Scholar
  46. Yokomori, K., Chen, J.-L., Admon, A., Zhou, S. & Tjian, R. Molecular cloning and characterization of dTAFII30α and dTAFII30β: two small subunits of Drosophila TFIID. Genes Dev. 7, 2587–2597 (1993).
    CAS PubMed Google Scholar
  47. Kokubo, T., Gong, D.-W., Wootton, J.C., Horikoshi, M. & Roeder, R.G. Molecular cloning of Drosophila TFIID subunits. Nature 367, 484–487 (1993).
    Google Scholar
  48. Weinzierl, R., Ruppert, S., Dynlacht, B., Tanese, N. & Tjian, R. Cloning and expression of Drosophila TAFII60 and human TAFII70 reveal conserved interactions with other subunits of TFIID. EMBO J. 12, 5303–5309 (1993).
    CAS PubMed PubMed Central Google Scholar
  49. Kokubo, T., Yamashita, S., Horikoshi, M., Roeder, R.G. & Nakatani, Y. Interaction between the N-terminal domain of the 230kDa subunit and the TATA box-binding subunit of TFIID negatively regulates TATA box binding. Proc. natn. Acad. Sci. U.S.A. 91, 3520–3524 (1994).
    CAS Google Scholar
  50. Lee, W.S., Kao, C.C., Bryant, G.O., Liu, X. & Berk, A.J. Adenovirus E1A activation domain binds the basic repeat in the TATA box transcription factor. Cell 67, 365–376 (1991).
    CAS PubMed Google Scholar
  51. Winston, F. & Minehart, P.L. Analysis of the yeast SPT3 gene and identification of its product, a positive regulator of Ty transcription. Nucl. Acids Res. 14, 6885–6900 (1986).
    CAS PubMed PubMed Central Google Scholar
  52. Winston, F. Analysis of SPT Genes: A genetic approach toward analysis of TFIID, histones, and other transcription factors of yeast. in Transcriptional Regulation (eds McKnight, S. & Yamamoto, K.R.) 1271–1293 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1992).
    Google Scholar
  53. Eisenmann, D.M., Arndt, K.M., Ricupero, S.L., Rooney, J.W. & Winston, F. SPT3 interacts with TFIID to allow normal transcription in Saccharomyces cerevisiae. Genes Dev. 6, 1319–1331 (1992).
    CAS PubMed Google Scholar
  54. 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).
    CAS PubMed Google Scholar
  55. Felsenfeld, G. Chromatin as an essential part of the transcriptional mechanism. Nature 355, 219–224 (1992).
    CAS PubMed Google Scholar
  56. Meisterernst, M. & Roeder, R.G. Family of proteins that interact with TFIID and regulate promoter activity. Cell 67, 557–567 (1991).
    CAS PubMed Google Scholar
  57. Inostroza, J.A., Mermelstein, F.H., Ha, I., Lane, W.S. & Reinberg, D. Dr1, a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription. Cell 70, 477–489 (1992).
    CAS PubMed Google Scholar
  58. Meisterernst, M., Roy, A.L., Lieu, H.M. & Roeder, R.G. Activation of class II gene transcription by regulatory factors is potentiated by a novel activity. Cell 66, 981–993 (1991).
    CAS PubMed Google Scholar
  59. Cortes, P., Flores, O. & Reinberg, D. Factors involved in specific transcription by mammalian RNA polymerase II: purification and analysis of transcription factor IIA and identification of transcription factor IIJ. Molec. Cell. Biol. 12, 413–421 (1992).
    CAS PubMed PubMed Central Google Scholar
  60. Drapkin, R., Merino, A. & Reinberg, D. Regulation of RNA polymerase II transcription. Curr. Opin. Cell Biol. 5, 469–476 (1993).
    CAS PubMed Google Scholar
  61. Kelleher, III, R.J. et al. Yeast and human TFIIDs are interchangeable for the response to acidic transcriptional activators in vitro. Genes Dev. 6, 296–303 (1992).
    CAS PubMed Google Scholar
  62. Berk, A.J. Adenovirus E1A trans-activation: Understanding it Will Require learning how the general transcription factors function. in Transcriptional Regulation (eds McKnight, S. & Yamamoto, K.R.) 727–742 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1992).
    Google Scholar
  63. Horikoshi, N., et al. Direct interactions between Adenovirus E1A protein and the TATA box binding transcription factor IID. Proc. natn. Acad. Sci. U.S.A. 88, 5124–5128 (1991).
    CAS Google Scholar
  64. Kerr, L.D. et al. Association between proto-oncoprotein rel and TATA-binding protein mediates transcriptional activation by NF-kB. Nature 356, 412–419 (1993).
    Google Scholar
  65. Keaveney, M., Berkenstam, A., Feigenbutz, M., Vriend, G. & Stunnenberg, H.G. Residues in the TATA-binding protein required to mediate a transcriptional response to retinoic acid in EC cells. Nature 365, 562–566 (1993).
    CAS PubMed Google Scholar
  66. Caron, C. et al. Functional and biochemical interaction of the THLV-1 TAX1 transcactivatorwith TBP. EMBO J. 12, 4269–4278 (1993).
    CAS PubMed PubMed Central Google Scholar
  67. Hagemeier, C., Walker, S., Caswell, R., Kouzarides, T. & Sinclair, J. The human cytomegalovirus 80-kilodalton but not the 72-kilodalton immediate-early protein transcactivates heterologous promoters in a TATA box-dependent mechanism and interacts directly with TFIID. J. Virol. 66, 4452–4456 (1992).
    CAS PubMed PubMed Central Google Scholar
  68. Lieberman, P.M. & Berk, A.J. The Zta trans-activator protein stabilizes TFIID association with promoter DMA by direct protein-protein interaction. Genes Dev. 5, 2441–2454 (1991).
    CAS PubMed Google Scholar
  69. Stringer, K.F., Ingles, C.J. & Greenblatt, J. Direct and selective binding of an acidic transcriptional activation domain to the TATA-box factor TFIID. Nature 345, 783–786 (1990).
    CAS PubMed Google Scholar
  70. Martin, D.W., Munoz, R.M., Subler, M.A. & Deb, S. p53 binds to the TATA-binding protein-TATA complex. J. biol. Chem. 268, 13062–13067 (1993).
    CAS PubMed Google Scholar
  71. Seto, E. et al. Wild-type p53 binds to the TATA-binding protein and represses transcription. Proc. natn. Acad. Sci. U.S.A. 89, 12028–12032 (1992).
    CAS Google Scholar
  72. Truant, R., Xiao, H., Ingles, C.J. & Greenblatt, J. Direct interaction between the transcriptional activation domain of human p53 and the TATA box-binding protein. J. biol. Chem. 268, 2284–2287 (1993).
    CAS PubMed Google Scholar
  73. Ragimov, N. et al. Wild-type but not mutant p53 can repress transcription initiation in vitro by interfering with the binding of basal transcription factors to the TATA motif. Oncogene 8, 1183–1193 (1993).
    CAS PubMed Google Scholar
  74. Liu, X., Miller, C.W., Koeffler, P.H. & Berk, A.J. p53 activation domain binds TATA-box-binding polypeptide and a neighboring p53 domain inhibits transcription. Molec. Cell. Biol. 13, 3291–3300 (1993).
    CAS PubMed PubMed Central Google Scholar
  75. Chen, X., Farmer, G., Zhu, H., Praywes, R. & Prives, C. Cooperative DNA binding of p53 with TFIID (TBP): a possible mechanism for transcriptional activation. Genes Dev. 7, 1837–1849 (1993).
    CAS PubMed Google Scholar
  76. Katagiri, F. & Chua, N.-H. Plant transcription factors: present knowledge and future challenges. Trends Genet. 8, 22–27 (1992).
    CAS PubMed Google Scholar
  77. Brunger, A.T. XPLOR Manual (Yale University, New Haven, 1992).
    Google Scholar
  78. Luzzati, P.V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta. crystallogr. 5, 802–810 (1952).
    Google Scholar
  79. Ramachandran, G.N. & Sasisekharan, V. Conformation of polypeptides and proteins. Advan. Prot. Chem. 23, 283–437 (1968).
    CAS Google Scholar
  80. Luthy, R., Bowie, J.U. & Eisenberg, D. Assessment of protein models with three-dimensional profiles. Nature 356, 83–85 (1992).
    CAS PubMed Google Scholar
  81. Kraulis, P.J. Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).
    Google Scholar
  82. Nicholls, A., Sharp, K. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281–296 (1991).
    CAS PubMed Google Scholar
  83. 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).
    CAS Google Scholar
  84. Kim, S.S., Hong, Y. & Kang, C. Effects of multiple mutations at the conserved TATA sequence of bacteriophage SP6 promoter on transcription efficiency. Biochem. molec. Biol. Internatl. 31, 153–159 (1993).
    CAS Google Scholar
  85. Xu, X. et al. Functional interaction of the v-rel and c-rel oncoproteins with the TATA-binding protein and association with TFIIB. Molec. Cell. Biol. 13, 6733–6741 (1993).
    CAS PubMed PubMed Central Google Scholar
  86. Gasch, A., Hoffmann, A., Horikoshi, M., Roeder, R.G. & Chua, N.-H. Arabidopsis thaliana contains two genes for TFIID. Nature 346, 390–394 (1990).
    CAS PubMed Google Scholar
  87. Haass, M.M. & Feix, G. Two different cDNA encoding TFIID proteins of maize. FEBS Lett. 301, 294–298 (1992).
    CAS PubMed Google Scholar
  88. Holdsworth, M.J., Grierson, C., Schuch, W. & Bevan, M. DNA-binding properties of cloned TATA-binding protein from potato tubers. Plant molec. Biol. 19, 455–464 (1992).
    CAS Google Scholar
  89. Kawata, T., Minami, M., Tamura, T.-a., Sumita, K. & Iwabuchi, M. Isolation and characterization of a cDNA clone encoding the TATA•box-binding protein (TFIID) from wheat. Plant molec. Biol. 19, 867–872 (1992).
    CAS Google Scholar
  90. Apsit, V., Freeberg, J.A., Chase, M.R., Davis, E.A. & Ackerman, S. Wheat TFIID TATA binding protein. Nucl. Acids Res. 21, 1494 (1993).
    CAS PubMed PubMed Central Google Scholar
  91. Fikes, J.D., Becker, D.M., Winston, F. & Guarente, L. Striking conservation of TFIID in Schizosaccharomyces pombe and Saccharomyces cerevisiae. Nature 346, 291–294 (1990).
    CAS PubMed Google Scholar
  92. Hoffmann, A. et al. Cloning of the Schizosaccharomyces pombe TFIID gene reveals a strong conservation of functional domains present in Saccharomyces cerevisiae TFIID. Genes Dev. 4, 1141–1148 (1990).
    CAS PubMed Google Scholar
  93. Horikoshi, M. et al. Cloning and structure of a yeast gene encoding a general transcription initiation factor TFIID that binds to the TATA box. Nature 341, 299–303 (1989).
    CAS PubMed Google Scholar
  94. Cavallini, B. et al. Cloning of the gene encoding the yeast protein BTF1Y, which can substitute for the human TATA box-binding factor. Proc. natn. Acad. Sci. U.S.A. 86, 9803–9807 (1989).
    CAS Google Scholar
  95. Hahn, S., Buratowski, S., Sharp, P.A. & Guarente, L. Isolation of the gene encoding the yeast TATA binding protein TFIID: A gene identical to the SPT15 suppressor of Ty element insertions. Cell 58, 1173–1181 (1989).
    CAS PubMed Google Scholar
  96. Schmidt, M.C., Kao, C.C., Pei, R. & Berk, A.J. Yeast TATA-box transcription factor gene. Proc. natn. Acad. Sci. U.S.A. 86, 7785–7789 (1989).
    CAS Google Scholar
  97. Hoey, T., Dynlacht, B.D., Peterson, M.G., Pugh, B.F. & Tjian, R. Isolation and characterization of the Drosophila gene encoding the TATA box binding protein, TFIID. Cell 61, 1179–1186 (1990).
    CAS PubMed Google Scholar
  98. Muhich, M.L., Iida, C.T., Horikoshi, M., Roeder, R.G. & Parker, C.S. cDNA clone encoding Drosophila transcription factor TFIID. Proc. natn. Acad. Sci. U.S.A. 87, 9148–9152 (1990).
    CAS Google Scholar
  99. Kao, C.C. et al. Cloning of a transcriptionally active human TATA binding factor. Science 248, 1646–1650 (1990).
    CAS PubMed Google Scholar
  100. Peterson, M.G., Tanese, N., Pugh, B.F. & Tjian, R. Functional domains and upstream activation properties of cloned human TATA binding protein. Science 248, 1625–1630 (1990).
    CAS PubMed Google Scholar
  101. Wong, J., Liu, F. & Bateman, E. Cloning and expression of the Acanthamoeba castellanii gene encoding transcription factor TFIID. Gene 117, 91–97 (1992).
    CAS PubMed Google Scholar
  102. Li, S. & Donelson, J.E. The gene for the TATA box-binding protein of Onchocerca volvulus. Molec. Biochem. Parasitol. 61, 321–324 (1993).
    CAS Google Scholar
  103. Lichtsteiner, S. & Tjian, R. Cloning and properties of the Caenorhabditis elegans TATA-box binding protein. Proc. natn. Acad. Sci. U.S.A. 90, 9673–9677 (1993).
    CAS Google Scholar
  104. Stargell, L.A. & Gorovsky, M.A. TATA-binding protein and nuclear differentiation in Tetrahymena thermophila. Molec. cell. Biol. 14, 723–734 (1994).
    CAS PubMed PubMed Central Google Scholar

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