A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein

Nature Structural Biology

Volumn 3, Issue 1, 1996, Pages 32-37

  Guzikevich Guerstein, Gali ^a   Shakked, Zippora ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

TATA BINDING PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BASE PAIRING; CRYSTAL STRUCTURE; DNA CONFORMATION; DNA HELIX; DNA PROTEIN COMPLEX; DNA STRUCTURE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN CONFORMATION; PROTEIN STRUCTURE; TATA BOX;

ANIMALS; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DNA; DNA-BINDING PROTEINS; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; TATA BOX; TATA-BOX BINDING PROTEIN; TRANSCRIPTION FACTORS;

EID: 0030040722     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb0196-32     Document Type: Article

References (28)

1. Shakked, Z. et al. Crystalline A-DNA: the X-ray analysis of the fragment d(G-G-T-A-T-A-C-C). Proc. R. Soc. Lond. B213, 479-487 (1981).
2. Shakked, Z. et al. Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C). J. molec. Biol. 166, 183-201 (1983).
3. Dickerson, R.E. DNA structure from A to Z. In Methods in Enzymology, vol. 211, part A, DNA Structures (eds Lilley, D.M.J. & Dahlberg, J.E.) 67-111 (Academic Press, Inc., 1992).
4. Bingman, C., Jain, S., Zon, G. & Sundaralingam, M. Crystal and molecular structure of the alternating dodecamer d(GCGTACGTACGC) in the A-DNA form: comparison with the isomorphous non-alternating dodecamer d(CCGTACGTACGG). Nucleic Acids Res. 20, 6637-6647 (1992).
5. Weston, S.A., Lahm, A. & Suck, D. X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 Å resolution. J. molec. Biol. 226, 1237-1256 (1992).
6. Lahm, A. & Suck, D. DNase l-induced DNA conformation. A structure of a DNase I-ortamer complex. J. molec. Biol. 222, 645-667 (1991).
7. Kim, Y., Geiger, J.H., Hahn, S. & Sigler, P.B. Crystal structure of a yeast TBP/TATA-box complex. Nature 365, 512-520 (1993)
8. Kim, J.L., Nikolov, D. B. and Burley, S.K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365, 520-527 (1993).
9. Klug, A. Transcription. Opening the gateway. Nature 365, 486-487 (1993).
10. Shakked, Z. & Rabinovich, D. The effect of the base sequence on the fine structure of the DNA double helix. Prog. Biophys. molec. Biol. 47, 159-195 (1986).
11. Kim, J.L. & Burley, S.K. 1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAG. Nature struct. Biol. 1, 638-653 (1994).
12. Selsing, E., Wells, R.D., Alden C.J. & Arnott. S. Bent DNA: visualization of a base-paired and stacked A-B conformational junction. J. biol. Chem. 254, 5417-5422 (1979).
13. Hegde, R.H., Grossman, S.R., Laimins L.A. & Sigler, P.B. Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. Nature, 359, 505-512 (1992).
14. 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).
15. Wu, H.-M. & Crothers, D.M. The locus of sequence-directed and protein-induced DNA binding. Nature, 308, 509-513 (1984).
16. Crothers, D.M., Haran, T.E. and Nadeau, J.G. Intrinsically bent DNA. J. biol. Chem. 256, 7093-7096 (1990).
17. Travers, A.A. and Klug, A. in DNA Topology and its Biological Effects (eds Cozzarelli, N.R. & Wang, J.C.) 57-106 (Cold Spring Harbor Laboratory Press, New York, 1990)
18. Shakked, Z. et al. Determinants of represser/operator recognition from the structure of the trp operator binding site. Nature 368, 469-473 (1994).
19. Shakked, Z. et al. Sequence-specific gene regulatory interactions: the role played by the structure and hydration of the DNA target, in Structural Biology: the State of the Art, vol. 1, (eds Sarma, R.H. & Sarma, M.H.)199-216 (Adenine Press, New York, 1994).
20. Guzikevich-Guerstein, G., Ph. D. thesis (Submitted to the Feinberg Graduate School of the Weizmann Institute of Science, 1995).
21. 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).
22. Hunter, C.A. Sequence-dependent DNA structure. The role of base-stacking interactions. J. molec. Biol. 248, 662-678 (1995).
23. Travers, A.A. Reading the minor groove. Nature struct. Biol. 2, 615-617 (1995).
24. Eisenstein, M. & Shakked, Z. Hydration patterns and intermodular interactions in A-DNA crystal structures. Implications for DNA recognition. J. molec. Biol. 248, 662-678 (1995).
25. Chandrasekaran, R. & Arnott, S. The structure of DNA and RNA helices in oriented fibers. In Landolt-Bornstein, New Series, Croup VII, Vol. 1b (Saenger, W., Ed.)31-170(Springer-Verlag, Berlin; 1989).
26. Lavery, R. & Sklenar, H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. biomol. Struct. Dyn. 6, 63-91 (1988).
27. Fratini, A.V., Kopka, M.L., Drew, H.R. & Dickerson, R.E. Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTbrCGCG. J. biol. Chem. 257, 14686-14707 (1982).
28. Dickerson, R.E. et al. Definitions and nomenclature of nucleic acid structure parameters. EMBO J. 8, 1-4 (1989).