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Volumn 261, Issue 2, 1996, Pages 239-254

How proteins recognize the TATA box

Author keywords

A tract bending; DNA bending; DNA sequence recognition; TATA box; TATA binding proteins

Indexed keywords

DNA BINDING PROTEIN;

EID: 0030590260     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0456     Document Type: Article
Times cited : (299)

References (61)
  • 1
    • 0025278259 scopus 로고
    • Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences
    • Bucher, P. (1990). Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212, 563-578.
    • (1990) J. Mol. Biol. , vol.212 , pp. 563-578
    • Bucher, P.1
  • 2
    • 0020385863 scopus 로고
    • Mechanics of sequence-dependent stacking of bases in B-DNA
    • Calladine, C. R. (1982). Mechanics of sequence-dependent stacking of bases in B-DNA. J. Mol. Biol. 161, 343-352.
    • (1982) J. Mol. Biol. , vol.161 , pp. 343-352
    • Calladine, C.R.1
  • 3
    • 0022914418 scopus 로고
    • Principles of sequence-dependent flexure of DNA
    • Calladine, C. R. & Drew, H. R. (1986). Principles of sequence-dependent flexure of DNA. J. Mol. Biol. 192, 907-918.
    • (1986) J. Mol. Biol. , vol.192 , pp. 907-918
    • Calladine, C.R.1    Drew, H.R.2
  • 4
    • 0024278548 scopus 로고
    • The intrinsic curvature of DNA in solution
    • Calladine, C. R., Drew, H. R. & McCall, M. J. (1988). The intrinsic curvature of DNA in solution. J. Mol. Biol. 201, 127-137.
    • (1988) J. Mol. Biol. , vol.201 , pp. 127-137
    • Calladine, C.R.1    Drew, H.R.2    McCall, M.J.3
  • 5
    • 0023992215 scopus 로고
    • Saturation mutagenesis of a yeast his3 "TATA element": Genetic evidence for a specific TATA-binding protein
    • Chen, W. & Struhl, K. (1988). Saturation mutagenesis of a yeast his3 "TATA element": Genetic evidence for a specific TATA-binding protein. Proc. Natl Acad. Sci. USA, 85, 2691-2695.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2691-2695
    • Chen, W.1    Struhl, K.2
  • 6
    • 0028402160 scopus 로고
    • Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex
    • Chen, X., Ramakrishnan, B., Rao, S. T. & Sundaralingam, M. (1994). Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex. Struct. Biol. 1, 169-175.
    • (1994) Struct. Biol. , vol.1 , pp. 169-175
    • Chen, X.1    Ramakrishnan, B.2    Rao, S.T.3    Sundaralingam, M.4
  • 7
    • 0023494886 scopus 로고
    • A bifurcated hydrogen-bonded conformation in the d(A·T) base-pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin
    • Coll, M., Frederick, C. A., Wang, A. H.-J. & Rich, A. (1987). A bifurcated hydrogen-bonded conformation in the d(A·T) base-pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc. Natl Acad. Sci. USA, 84, 8385-8389.
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 8385-8389
    • Coll, M.1    Frederick, C.A.2    Wang, A.H.-J.3    Rich, A.4
  • 9
    • 0020619672 scopus 로고
    • Base sequence and helix structure variation in B and A-DNA
    • Dickerson, R. E. (1983). Base sequence and helix structure variation in B and A-DNA. J. Mol. Biol. 166, 419-441.
    • (1983) J. Mol. Biol. , vol.166 , pp. 419-441
    • Dickerson, R.E.1
  • 10
    • 0019387686 scopus 로고
    • Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure
    • Dickerson, R. E. & Drew, H. R. (1981). Structure of a B-DNA dodecamer. II. influence of base sequence on helix structure. J. Mol. Biol. 149, 761-786.
    • (1981) J. Mol. Biol. , vol.149 , pp. 761-786
    • Dickerson, R.E.1    Drew, H.R.2
  • 12
    • 0029978007 scopus 로고    scopus 로고
    • MPD and DNA bending in crystals and in solution
    • Dickerson, R. E., Goodsell, D. & Kopka, M. L. (1996). MPD and DNA bending in crystals and in solution. J. Mol. Biol. 256, 108-125.
    • (1996) J. Mol. Biol. , vol.256 , pp. 108-125
    • Dickerson, R.E.1    Goodsell, D.2    Kopka, M.L.3
  • 13
    • 0026809001 scopus 로고
    • Analyzing DNA curvature in polyacrylamide gels
    • Diekmann, S. (1992). Analyzing DNA curvature in polyacrylamide gels. Methods Enzymol. 212, 30-46.
    • (1992) Methods Enzymol. , vol.212 , pp. 30-46
    • Diekmann, S.1
  • 15
    • 0028171224 scopus 로고
    • Design of a G·C-specific DNA minor groove-binding peptide
    • Geierstanger, B. H., Mrksich, M., Dervan, P. B. & Wemmer, D. E. (1994). Design of a G·C-specific DNA minor groove-binding peptide. Science, 266, 646-650.
    • (1994) Science , vol.266 , pp. 646-650
    • Geierstanger, B.H.1    Mrksich, M.2    Dervan, P.B.3    Wemmer, D.E.4
  • 16
    • 0028624664 scopus 로고
    • Bending and curvature calculations in B-DNA
    • Goodsell, D. S. & Dickerson, R. E. (1994). Bending and curvature calculations in B-DNA. Nucl. Acids Res. 22, 5497-5503.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 5497-5503
    • Goodsell, D.S.1    Dickerson, R.E.2
  • 17
    • 0027536101 scopus 로고
    • Crystal structure of C-A-T-G-G-C-C-A-T-G and its implications for A-tract bending models
    • Goodsell, D. S., Kopka, M. L., Cascio, D. & Dickerson, R. E. (1993). Crystal structure of C-A-T-G-G-C-C-A-T-G and its implications for A-tract bending models. Proc. Natl Acad. Sci. USA, 90, 2930-2934.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 2930-2934
    • Goodsell, D.S.1    Kopka, M.L.2    Cascio, D.3    Dickerson, R.E.4
  • 18
    • 0028225644 scopus 로고
    • The crystal structure of C-C-A-T-T-A-A-T-G-G: Implications for bending of B-DNA at T-A steps
    • Goodsell, D. S., Kaczor-Grzeskowiak, M. & Dickerson, R. E. (1994). The crystal structure of C-C-A-T-T-A-A-T-G-G: implications for bending of B-DNA at T-A steps. J. Mol. Biol. 239, 79-96.
    • (1994) J. Mol. Biol. , vol.239 , pp. 79-96
    • Goodsell, D.S.1    Kaczor-Grzeskowiak, M.2    Dickerson, R.E.3
  • 19
    • 0028956354 scopus 로고
    • Refinement of netropsin bound to DNA: Bias and feedback in electron density map iterpretation
    • Goodsell, D. S., Kopka, M. L. & Dickerson, R. E. (1995). Refinement of netropsin bound to DNA: Bias and feedback in electron density map iterpretation. Biochemistry, 34, 4983-4993.
    • (1995) Biochemistry , vol.34 , pp. 4983-4993
    • Goodsell, D.S.1    Kopka, M.L.2    Dickerson, R.E.3
  • 21
    • 0000935665 scopus 로고
    • Evidence for the existence of stable curvature of DNA in solution
    • Hagerman, P. J. (1984). Evidence for the existence of stable curvature of DNA in solution. Proc. Natl Acad. Sci. USA, 81, 4632-4636.
    • (1984) Proc. Natl Acad. Sci. USA , vol.81 , pp. 4632-4636
    • Hagerman, P.J.1
  • 22
  • 24
    • 0027974851 scopus 로고
    • 1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAG
    • Kim, J. L. & Burley, S. K. (1994). 1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAG. Nature Struct. Biol. 1, 638-651.
    • (1994) Nature Struct. Biol. , vol.1 , pp. 638-651
    • Kim, J.L.1    Burley, S.K.2
  • 25
    • 0027483012 scopus 로고
    • Co-crystal structure of TBP recognizing the minor groove of a TATA element
    • Kim, J. L., Nikolov, D. B. & Burley, S. K. (1993). Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature, 365, 520-527.
    • (1993) Nature , vol.365 , pp. 520-527
    • Kim, J.L.1    Nikolov, D.B.2    Burley, S.K.3
  • 26
    • 0027504913 scopus 로고
    • Crystal structure of a yeast TBP/TATA-box complex
    • Kim, Y., Geiger, J. H., Hahn, S. & Sigler, P. B. (1993). Crystal structure of a yeast TBP/TATA-box complex. Nature, 365, 512-520.
    • (1993) Nature , vol.365 , pp. 512-520
    • Kim, Y.1    Geiger, J.H.2    Hahn, S.3    Sigler, P.B.4
  • 27
    • 0027518094 scopus 로고
    • Opening the gateway
    • Klug, A. (1993). Opening the gateway. Nature, 365, 486-487.
    • (1993) Nature , vol.365 , pp. 486-487
    • Klug, A.1
  • 28
    • 0018791736 scopus 로고
    • A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein
    • Klug, A., Jack, A., Viswamitra, M. A., Kennard, O., Shakked, Z. & Steitz, T. A. (1979). A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. J. Mol. Biol. 131, 669-680.
    • (1979) J. Mol. Biol. , vol.131 , pp. 669-680
    • Klug, A.1    Jack, A.2    Viswamitra, M.A.3    Kennard, O.4    Shakked, Z.5    Steitz, T.A.6
  • 31
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P. J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24, 946-950.
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 32
    • 0024058085 scopus 로고
    • The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
    • Lavery, R. & Sklenar, H. (1988). The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynam. 6, 63-91.
    • (1988) J. Biomol. Struct. Dynam. , vol.6 , pp. 63-91
    • Lavery, R.1    Sklenar, H.2
  • 34
    • 0029116757 scopus 로고
    • An inverted TATA box directs downstream transcription of the bone sialoprotein gene
    • Li, J. J., Kim, R. H. & Sodek, J. (1995). An inverted TATA box directs downstream transcription of the bone sialoprotein gene. Biochem. J. 310, 33-40.
    • (1995) Biochem. J. , vol.310 , pp. 33-40
    • Li, J.J.1    Kim, R.H.2    Sodek, J.3
  • 35
    • 0022858456 scopus 로고
    • Molecular recognition between oligopeptides and nucleic acids: Novel imidazole-containing oligopeptides related to netropsin that exhibit altered DNA sequence specificity
    • Lown, J. W., Krowicki, K., Bhat, U. G., Skorobogaty, A., Ward, B. & Dabrowiak, J. C. (1986). Molecular recognition between oligopeptides and nucleic acids: novel imidazole-containing oligopeptides related to netropsin that exhibit altered DNA sequence specificity. Biochemistry, 25, 7408-7416.
    • (1986) Biochemistry , vol.25 , pp. 7408-7416
    • Lown, J.W.1    Krowicki, K.2    Bhat, U.G.3    Skorobogaty, A.4    Ward, B.5    Dabrowiak, J.C.6
  • 37
    • 0026661689 scopus 로고
    • Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin
    • Mrksich, M., Wade, W. S., Dwyer, T. J., Geierstanger, B. H., Wemmer, D. E. & Dervan, P. B. (1992). Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin. Proc. Natl Acad. Sci. USA, 89, 7586-7590.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 7586-7590
    • Mrksich, M.1    Wade, W.S.2    Dwyer, T.J.3    Geierstanger, B.H.4    Wemmer, D.E.5    Dervan, P.B.6
  • 38
    • 84920325457 scopus 로고
    • AMoRe: An automated package for molecular replacement
    • Navaza, J. (1994). AMoRe: an automated package for molecular replacement. Acta Crystallog. 50, 157-163.
    • (1994) Acta Crystallog. , vol.50 , pp. 157-163
    • Navaza, J.1
  • 39
    • 0023513912 scopus 로고
    • The structure of an oligo(dA)·oligo(dT) tract and its biological implications
    • Nelson, H. C. M., Finch, J. T., Luisi, B. F. & Klug, A. (1987). The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature, 330, 221-226.
    • (1987) Nature , vol.330 , pp. 221-226
    • Nelson, H.C.M.1    Finch, J.T.2    Luisi, B.F.3    Klug, A.4
  • 40
    • 0028056035 scopus 로고
    • 2.1 Å resolution refined structure of a TATA box-binding protein (TBP)
    • Nikolov, D. B. & Burley, S. K. (1994). 2.1 Å resolution refined structure of a TATA box-binding protein (TBP). Nature Struct. Biol. 1, 621-637.
    • (1994) Nature Struct. Biol. , vol.1 , pp. 621-637
    • Nikolov, D.B.1    Burley, S.K.2
  • 41
    • 0026515868 scopus 로고
    • Roles of TATA and initiator elements in determining the start site location and direction of RNA polymerase II transcription
    • O'Shea-Greenfield, A. & Smale, S. T. (1992). Roles of TATA and initiator elements in determining the start site location and direction of RNA polymerase II transcription. J. Biol. Chem. 267, 1891-1402.
    • (1992) J. Biol. Chem. , vol.267 , pp. 1891-11402
    • O'Shea-Greenfield, A.1    Smale, S.T.2
  • 42
    • 0024323434 scopus 로고
    • Multiple transcription factor binding sites mediate adenovirus E1A transactivation
    • Pei, R. & Berk, A. J. (1989). Multiple transcription factor binding sites mediate adenovirus E1A transactivation. J. Virol. 63, 3499-3506.
    • (1989) J. Virol. , vol.63 , pp. 3499-3506
    • Pei, R.1    Berk, A.J.2
  • 43
    • 0025885778 scopus 로고
    • Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G
    • Quintana, J. R., Lipanov, A. A. & Dickerson, R. E. (1991). Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G. Biochemistry, 30, 10294-10306.
    • (1991) Biochemistry , vol.30 , pp. 10294-10306
    • Quintana, J.R.1    Lipanov, A.A.2    Dickerson, R.E.3
  • 44
    • 0026624859 scopus 로고
    • Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G
    • Quintana J. R., Grzeskowiak, K., Yanagi, K. & Dickerson, R. E. (1992). Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G. J. Mol. Biol. 225, 379-395.
    • (1992) J. Mol. Biol. , vol.225 , pp. 379-395
    • Quintana, J.R.1    Grzeskowiak, K.2    Yanagi, K.3    Dickerson, R.E.4
  • 45
    • 0028173030 scopus 로고
    • Crystal structure of LacI member, PurR, bound to DNA: Minor groove binding by α helices
    • Schumacher, M. A., Choi, K. Y., Zalkin, H. & Brennan, R. G. (1994). Crystal structure of LacI member, PurR, bound to DNA: Minor groove binding by α helices. Science, 266, 763-770.
    • (1994) Science , vol.266 , pp. 763-770
    • Schumacher, M.A.1    Choi, K.Y.2    Zalkin, H.3    Brennan, R.G.4
  • 46
    • 0025228931 scopus 로고
    • A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation
    • Singer, V. L., Wobbe, C. R. & Struhl, K. (1990). A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation. Genes Dev. 4, 636-645.
    • (1990) Genes Dev. , vol.4 , pp. 636-645
    • Singer, V.L.1    Wobbe, C.R.2    Struhl, K.3
  • 47
    • 0026566106 scopus 로고
    • Yeast and human TFIID with altered DNA-binding specificity for TATA elements
    • Strubin, M. & Struhl, K. (1992). Yeast and human TFIID with altered DNA-binding specificity for TATA elements. Cell, 68, 721-730.
    • (1992) Cell , vol.68 , pp. 721-730
    • Strubin, M.1    Struhl, K.2
  • 48
    • 0029041940 scopus 로고
    • Stereochemical basis of DNA bending by transcription factors
    • Suzuki, M. & Yagi, N. (1995). Stereochemical basis of DNA bending by transcription factors. Nucl. Acids Res. 23, 2083-2091.
    • (1995) Nucl. Acids Res. , vol.23 , pp. 2083-2091
    • Suzuki, M.1    Yagi, N.2
  • 49
    • 0030048596 scopus 로고    scopus 로고
    • Role of base-backbone and base-base interactions in alternating DNA conformations
    • Suzuki, M., Yagi, N. & Finch, J. T. (1996). Role of base-backbone and base-base interactions in alternating DNA conformations. FEBS Letters, 379, 148-152.
    • (1996) FEBS Letters , vol.379 , pp. 148-152
    • Suzuki, M.1    Yagi, N.2    Finch, J.T.3
  • 50
    • 0002524447 scopus 로고
    • Bending of DNA in nucleoprotein complexes
    • (Cozzarelli, N. R. & Wang, J. C., eds), Cold Spring Harbor Laboratory Press, Cold Spring Habor, NY
    • Travers, A. A. & Klug, A. (1990). Bending of DNA in nucleoprotein complexes. In DNA Topology and its Biological Effects (Cozzarelli, N. R. & Wang, J. C., eds), pp. 57-106, Cold Spring Harbor Laboratory Press, Cold Spring Habor, NY.
    • (1990) DNA Topology and its Biological Effects , pp. 57-106
    • Travers, A.A.1    Klug, A.2
  • 51
    • 0027138615 scopus 로고
    • Spurring on transcription?
    • Travers, A. A. & Schwabe, J. W. R. (1993). Spurring on transcription? Curr. Biol. 3, 898-900.
    • (1993) Curr. Biol. , vol.3 , pp. 898-900
    • Travers, A.A.1    Schwabe, J.W.R.2
  • 54
    • 0029068497 scopus 로고
    • RNA polymerase II/III transcription specificity determined by TATA box orientation
    • Wang, Y. & Stumph, W. E. (1995). RNA polymerase II/III transcription specificity determined by TATA box orientation. Proc. Natl Acad. Sci. USA, 92, 8606-8610.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 8606-8610
    • Wang, Y.1    Stumph, W.E.2
  • 56
    • 0030046809 scopus 로고    scopus 로고
    • Intercalation, DNA kinking, and the control of transcription
    • Werner, M. H., Gronenborn, A. M. & Clore, G. M. (1996). Intercalation, DNA kinking, and the control of transcription. Science, 271, 778-784.
    • (1996) Science , vol.271 , pp. 778-784
    • Werner, M.H.1    Gronenborn, A.M.2    Clore, G.M.3
  • 58
    • 0025309524 scopus 로고
    • Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro
    • Wobbe, C. R. & Struhl, K. (1990). Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro. Mol. Cell. Biol. 10, 3859-3867.
    • (1990) Mol. Cell. Biol. , vol.10 , pp. 3859-3867
    • Wobbe, C.R.1    Struhl, K.2
  • 59
    • 0021268779 scopus 로고
    • The locus of sequence-directed and protein-induced DNA bending
    • Wu, H.-M. & Crothers, D. M. (1984). The locus of sequence-directed and protein-induced DNA bending. Nature, 308, 509-513.
    • (1984) Nature , vol.308 , pp. 509-513
    • Wu, H.-M.1    Crothers, D.M.2
  • 60
    • 0025966606 scopus 로고
    • An analysis of local helix geometry in three B-DNA decamers and eight dodecamers
    • Yanagi, K., Privé, G. D. & Dickerson, R. E. (1991). An analysis of local helix geometry in three B-DNA decamers and eight dodecamers. J. Mol. Biol. 217, 201-214.
    • (1991) J. Mol. Biol. , vol.217 , pp. 201-214
    • Yanagi, K.1    Privé, G.D.2    Dickerson, R.E.3
  • 61
    • 0018447932 scopus 로고
    • Anisotropic flexibility of DNA and the nucleosomal structure
    • Zhurkin, V. B., Lysov, Y. P. & Ivanov, V. I. (1979). Anisotropic flexibility of DNA and the nucleosomal structure. Nucl. Acids Res. 6, 1081-1096.
    • (1979) Nucl. Acids Res. , vol.6 , pp. 1081-1096
    • Zhurkin, V.B.1    Lysov, Y.P.2    Ivanov, V.I.3


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