Nature Structural Biology
1, 638 - 653 (1994)
doi:10.1038/nsb0994-638
1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAGJoseph L. Kim1
& Stephen K. Burley1
1Laboratories of Molecular Biophysics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue New York, NY 10021, USA 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 / 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. REFERENCES
- Sawadogo, M. & Sentenac, A. RNA polymerase B (II) and general transcription factors. Rev. Biochem. 59, 711−754 (1990). | Article | ChemPort |
- Zawel, L. & Reinberg, D. Advances in RNA polymerase II transcription. Curr. Opin. Cell Biol. 4, 488−495 (1992). | Article | PubMed | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- Roeder, R.G. The complexities of eukaryotic transcription initiation: regulation of preinitiation complex assembly. Trends biochem. Sci. 16, 402−408 (1991). | Article | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- Buratowski, S. & Zhow, H. Transcription factor IID mutants defective for interaction with transcription factor IIA. Science 255, 1030−1032 (1992).
- 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). | PubMed | ISI | ChemPort |
- 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).
- 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 | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- Hernandez, N. TBP, a universal transcription factor? Genes Dev. 7, 1291−1308 (1993). | PubMed | ISI | ChemPort |
- 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). | ChemPort |
- 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). | ChemPort |
- Starr, D.B. & Hawley, D.K. TFIID binds in the minor groove of the TATA box. Cell 67, 1231−1240 (1991). | Article | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- Nikolov, D.B. et al. Crystal structure of TFIID TATA-box binding protein. Nature 360, 40−46 (1992). | Article | PubMed | ISI | ChemPort |
- 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). | ChemPort |
- 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).
- 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 | PubMed | ISI | ChemPort |
- 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 |
- 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). | ChemPort |
- Luzzati, P.V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta. crystallogr. 5, 802−810 (1952). | Article | ISI |
- Lorch, Y. & Kornberg, R.D. Near-zero linking difference upon transcription factor IId binding to promoter DNA. Molec. Cell. Biol. 13, 1872−1875 (1993). | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- 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). | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- Hodel, A., Kim, S.-H. & Brunger, A.T. Model bias in macromolecular crystal structures. Acta crystallogr. A48, 851−858 (1992). | ChemPort |
- 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). | ChemPort |
- Lilley, D.M.J. HMG has DNA wrapped up. Nature 357, 282−283 (1992). | Article | PubMed | ISI | ChemPort |
- Crothers, D.M. Architectural elements in nucleoprotein complexes. Curr. Biol. 3, 675−676 (1993). | ISI | ChemPort |
- Yang, C.-C. & Nash, H.A. The interaction of E. coli IHF protein with its specific binding sites. Cell 57, 869−880 (1989). | Article | PubMed | ISI | ChemPort |
- 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). | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- Weir, H.M. et al. Structure of the HMG box motif in the B-domain of HMG-1. EMBO J. 12, 1311−1319 (1993). | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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). | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- Steitz, T.A. Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q. Rev. Biophys. 23, 205−280 (1990). | PubMed | ISI | ChemPort |
- Harrison, S.C. A structural taxonomy of DNA-binding domains. Nature 353, 715−719 (1991). | Article | PubMed | ISI | ChemPort |
- Wolberger, C. Transcription Factor Structure and DNA Binding. Curr. Opin. struct. Biol. 3, 3−10 (1993). | Article | ISI | ChemPort |
- Burley, S.K. DNA-binding motifs from eukaryotic transcription factors. Curr. Opin. struct. Biol. 4, 3−11 (1994). | ISI | ChemPort |
- Spolar, R. & Record, M.T., Jr Science 263, 777−784 (1994). | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- Livingston, J., Spolar, R. & Record, M.T., Jr. Biochemistry 30, 4237−4244 (1991). | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- Shakked, Z. et al. Sequence-dependent conformation of an A-DNA double helix. J. molec. Biol. 166, 183−201 (1983). | PubMed | ISI | ChemPort |
- 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). | ISI | ChemPort |
- 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). | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- Poon, D. et al. Genetic and biochemical analyses of yeast TATA-binding protein mutants. J. biol. Chem. 268, 5005−5013 (1993). | PubMed | ISI | ChemPort |
- Strubin, M. & Struhl, K. Yeast and human TFIID with altered DNA-binding specificity for TATA elements. Cell 68, 721−730 (1992). | Article | PubMed | ISI | ChemPort |
- Roy, A., Malik, S., Meisterernst, M. & Roeder, R. An alternative pathway for transcription initiation involving TFII-I. Nature 365, 355−359 (1993). | Article | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- Drew, H.R. & Travers, A.A. DNA bending and its relation to nucleosome positioning. J. molec. Biol. 186, 773−790 (1985). | PubMed | ISI | ChemPort |
- Satchwell, S.C., Drew, H.R. & Travers, A.A. Sequence periodicities in chicken nucleosome core DNA. J. molec. Biol. 191, 659−675 (1986). | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- 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). | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- Brunger, A.T. XPLOR Manual (Yale University, New Haven, 1992).
- 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). | ChemPort |
- Brunger, A.T. The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472−474 (1992). | Article | ISI |
- Ramachandran, G.N. & Sasisekharan, V. Conformation of polypeptides and proteins. Advan. prot. Chem. 23, 283−437 (1968). | ChemPort |
- Kraulis, P.J. Molscript: a program to produce both detailed and schematic plots of protein structures. J. appl. Crystallogr. 24, 946−950 (1991). | Article | ISI |
- Nicholls, A., Sharp, K. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281−296 (1991). | PubMed | ISI | ChemPort |
- 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). | ISI | ChemPort |
- Lavery, R. & Sklenar, H. Defining the structure of irregular nucleic acids: conventions and principles. J. biomolec. Struct. Dynamics 6, 655−667 (1989). | ISI | ChemPort |
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