Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: Insights into DNA sequence discrimination by Ets proteins

Molecular Cell

Volumn 2, Issue 2, 1998, Pages 201-212

  Mo, Yi ^a,b   Vaessen, Benjamin ^a,b   Johnston, Karen ^a   Marmorstein, Ronen ^a,b  

^a WISTAR INSTITUTE   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN; E74 PROTEIN, DROSOPHILA; ELK4 PROTEIN, HUMAN; ELK4 PROTEIN, MOUSE; ONCOPROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ELK 4; TRANSCRIPTION FACTOR ETS;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BINDING SITE; CHEMISTRY; COMPARATIVE STUDY; CONFORMATION; ELECTRICITY; GENETICS; HUMAN; MACROMOLECULE; METABOLISM; MOLECULAR GENETICS; MOUSE; NUCLEOTIDE SEQUENCE; ONCOGENE; PROMOTER REGION; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA; DNA-BINDING PROTEINS; ELECTROSTATICS; ETS-DOMAIN PROTEIN ELK-4; GENES, FOS; HUMANS; MACROMOLECULAR SUBSTANCES; MICE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS (GENETICS); PROTEIN CONFORMATION; PROTO-ONCOGENE PROTEINS; PROTO-ONCOGENE PROTEINS C-ETS; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS;

EID: 0032135105     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(00)80130-6     Document Type: Article

References (68)

1. Aggarwal, A.K. (1990). Crystallization of DNA binding proteins with oligonucleotides. Methods 1, 83-90.
2. Bassuk, A.G., and Leiden, J.M. (1997). The roles of Ets transcription factors in the development and function of the mammalian immune system. Adv. Immunol. 64, 65-104.
3. Batchelor, A.H., Piper, D.E., de la Brousse, F.C., McKnight, S.L., and Wolberger, C. (1998). The structure of GABPα/β: an ETS domain-ankyrin repeat heterodimer bound to DNA. Science 279, 1037-1041.
4. Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.H., Srinivasan, A.R., and Schneider, B. (1992). The nucleic-acid database - a comprehensive relational database of 3-dimensional structures of nucleic-acids. Biophys. J. 63, 751-759.
5. Brennan, R.G. (1993). The winged-helix DNA-binding motif: another helix-turn-helix takeoff. Cell 74, 773-776.
6. Brown, T.A., and McKnight, S.L. (1992). Specificities of protein-protein and protein-DNA interaction of GABPα and two newly defined ETS-related proteins. Genes Dev. 6, 2502-2512.
7. Brown, L.A., Amores, A., Schilling, T.F., Jowett, T., Baert, J.-L., de-Launoit, Y., and Sharrocks, A.D. (1998). Molecular characterization of the zebrafish PEA3 ETS-domain transcription factor. Oncogene, in press.
8. Brünger, A.T. (1992a). X-PLOR 3.1, A System for X-Ray Crystallography and NMR. (New Haven, CT: Yale Univ. Press).
9. Brünger, A.T. (1992b). The free R value: a novel statistical quantity assessing the accuracy of crystal structures. Nature 335, 472-474.
10. Brünger, A.T., and Krukowski, A. (1990). Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallogr. A 46, 585-593.
11. Brünger, AT., Kuriyan, J., and Karplus, M. (1987). Crystallographic R factor refinement by molecular dynamics. Science 235, 458-460.
12. Cahill, M.A., Janknecht, R., and Nordheim, A. (1996). Signalling pathways: jack of all cascades. Curr. Biol. 6, 16-19.
13. Clark, K.L., Halay, E.D., Lai, E., and Burley, S.K. (1993). Cocrystal structure of the HNF-3/forkhead DNA-recognition motif resembles histone H5. Nature 364, 412-420.
14. Dalton, S., and Treisman, R. (1992). Characterization of SAP-1, a protein recruited by serum response factor to the c-fos serum response element. Cell 68, 597-612.
15. Dickerson, R.E. (1992). DNAstructurefrom A to Z. Methods Enzymol. 211, 67-111.
16. Dodson, E.J., Winn, M., and Ralph, A. (1997). Collaborative Computational Project, Number 4: providing programs for X-ray crystallography. Methods Enzymol. 277, 620-633.
17. Donaldson, L.W., Petersen, J.M., Graves, B.J., and McIntosh, L.P. (1996). Solution structure of the ETS domain from murine Ets-1: a winged helix-turn-helix DNA binding motif. EMBO J. 15, 125-134.
18. Ellenberger, T.E., Brandi, C.J., Struhl, K., and Harrison, S.C. (1992). The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted a helices: crystal structure of the protein-DNA complex. Cell 71, 1223-1237.
19. Escalante, C.R., Yie, J., Thanos, D., and Aggarwal, A.K. (1998). Structure of IRF-1 with bound DNA reveals determinants of interferon regulation. Nature 391, 103-106.
20. Evans, S.V. (1993). SETOR: hardware lighted three-dimensional solid model representation of macromolecules. J. Mol. Graph. 11, 134-138.
21. Fisher, R.J., Koizumi, S., Kondoh, A., Mariano, J.M., Mavrothalassitis, G., Bhat, N.K., and Papas, T.S. (1992). Human Ets-1-oncoprotein - purification, isoforms, SH modification, and DNA sequence-specific binding. Biol. Chem. 267, 17957-17965.
22. Furey, W., and Swaminathan, S. (1997). PHASES-95: a program package for the processing and analysis of diffraction data from macromolecules. In Methods in Enzymology, C.W. Carter and R.M. Sweet, eds. (Orlando, FL: Academic Press), pp. 590-620.
23. Giovane, A., Pintzas, A., Maira, S.M., Sobieszczuk, P., and Wasylyk, B. (1994). Net, a new ETS transcription factor that is activated by Ras. Genes Dev. 8, 1502-1513.
24. Harrison, S.C., and Aggarwal, A.K. (1990). DNA recognition by proteins with the helix-turn-helix motif. Annu. Rev. Biochem. 59, 933-969.
25. Harrison, C.J., Bohm, A.A., and Nelson, H.C.M. (1994). Crystal structure of the DNA binding domain of the heat shock transcription factor. Science 364, 224-227.
26. Hutchinson, E.G., and Thornton, J.M. (1996). PROMOTIF - a program to identify and analyze structural motifs in proteins. Protein Sci. 5, 212-220.
27. Jiang, J.S., and Brünger, A.T. (1994). Protein hydration observed by X-ray diffraction: solvation properties of penicillopepsin and neuraminidase crystal structures. J. Mol. Biol. 243, 100-115.
28. Jones, T.A., Zou, J.Y., and Cowen, S.W. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119.
29. Kabsch, W. (1988a). Automatic indexing of rotation diffraction patterns. J. Appl. Crystallogr. 21, 67-71.
30. Kabsch, W. (1988b). Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector. J. Appl. Crystallogr. 21, 916-924.
31. Kleywegt, G.J., and Jones, T.A. (1996a). Efficient rebuilding of protein structures. Acta Crystallogr. D 52, 829-832.
32. Kleywegt, G.J., and Jones, T.A. (1996b). Phi/Psi-chology: Ramachandran revisted. Curr. Biol. 4, 1395-1400.
33. Kodandapani, R., Rio, F., Ni, C.-Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R.A., and Ely, K.R. (1996). A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex. Nature 380, 456-460.
34. Kodandapani, R., Pio, F., Ni, C.-Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R.A., and Ely, K.R. (1998). Erratum: A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex. Nature 392 (6676).
35. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
36. Lavery, R., and Sklenar, H. (1989). Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dyn. 6, 655-667.
37. Liang, H., Mao, X., Olejniczak, E.T., Nettesheim, D.G., Yu, L., Meadows, R.P., Thompson, G.B., and Fesik, S.W. (1994). Solution structure of the ets domain of Fli-1 when bound to DNA. Nature Struct. Biol. 1, 871-876.
38. Ling, Y., Lakey, J.H., Roberts, C.E., and Sharrocks, A.D. (1997). Molecular characterization of the B-box protein-protein interaction motif of the ETS-domain transcription factor Elk-1. EMBO J. 16, 2431-2440.
39. Lopez, M., Oettgen, P., Akbarali, Y., Dendorfer, U., and Libermann, T.A. (1994). ERP, a new member of the ETS transcription factor oncoprotein family - cloning, characterization, and differential expression during B-lymphocyte development. Mol. Cell. Biol. 14, 3292-3309.
40. Mao, X.H., Miesfeldt, S., Yang, H.D., Leiden, J.M., and Thompson, C.B. (1994). The Fli-1 chimeric Ews-Fli-1 oncoproteins display similar DNA-binding specificities. J. Biol. Chem. 268, 18216-18222.
41. Marmorstein, R., Carey, M., Ptashne, M., and Harrison, S.C. (1992). DNA recognition by GAL4: structure of a protein-DNA complex. Nature 356, 408-414.
42. Merritt, E.A., and Murphy, M.E.P. (1994). RASTER3D version 2.0: a program for photorealistic molecular graphics. Acta Crystallogr. D 50, 869-873.
43. Navaza, J. (1994). AMoRe: an automated package for molecular replacement. Acta. Crystallogr. A 50, 157-163.
44. Nekludova, L., and Pabo, C.O. (1994). Distinctive DNA conformation with enlarged major groove is found in Zn-finger DNA and other protein-DNA complexes. Proc. Natl. Acad. Sci. USA 91, 6948-6952.
45. Nelson, H.C. (1995). Structure and function of DNA binding proteins. Curr. Opin. Genet. Dev. 5, 180-189.
46. Nye, J.A., Petersen, J.M., Gunther, C.V., Jonsen, M.D., and Graves, B.J. (1992). Interaction of murine ETS-1 with GGA-binding sites establishes the ets domain as a new DNA-binding motif. Genes Dev. 6, 975-990.
47. Otwinowski, Z. (1993). Oscillation data reduction program. In Proceedings of the CCP4 Study Weekend: Data Collection and Processing., L. Sawyer, N. Isaacs, and S. Bailey, eds. (Warrington, UK: SERC Daresbury Laboratory), pp. 56-62.
48. Pellegrini, L., Tan, S., and Richmond, T.J. (1995). Structure of serum response factor core bound to DNA. Nature 376, 490-498.
49. Pio, F., Kodandapani, R., Ni, C.-Z., Shepard, W., Klemsz, M., McKercher, S.R., Maki, R.A., and Ely, K.R. (1996). New insights on DNA recognition by ets proteins from the crystal structure of the PU.1 ETS domain-DNA complex. J. Biol. Chem. 271, 23329-23337.
50. Price, M.A., Rogers, A.E., and Treisman, R. (1995). Comparative analysis of the ternary complex factors Elk-1. SAP-1a and SAP-2 (ERP/NET). EMBO J. 14, 2589-2601.
51. Ramakrishnan, V., Finch, J.T., Graviano, V., Lee, P.L., and Sweet, R.M. (1993). Crystal structure of the globular domain of histone H5 and its implications for nucleosomal binding. Nature 362, 219-223.
52. Rao, U.N., Huebner, K., Isobe, M., Ar-Rushdi, A., Croce, C.M., and Reddy, E.S. (1989). Elk-1, tissue-specific ets related genes on chromosome X and 14 near translocation breakpoints. Science 244, 66-70.
53. Ray-Gallet, D., Mao, C., Tavitian, A., and Moreau-Gachelin, F. (1995). DNA binding specificities of Spi-1/PU.1 and Spi-B transcription factors and identification of a Spi-1/Spi-B binding site in the c-fes/ c-fps promoter. Oncogene 11, 303-313.
54. Rice, L.M., and Brünger, A.T. (1994). Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 19, 277-290.
55. Sharrocks, A.D., Brown, A.L., Ling, Y., and Yates, P.R. (1997). The ETS-domain transcription factor family. Int. J. Biochem. Cell Biol. 29, 1371-1387.
56. Shore, P., and Sharrocks, A.D. (1994). The transcription factors Elk-1 and serum response factor interact by direct protein-protein contacts mediated by a short region of Elk-1. Mol. Cell. Biol. 14, 3283-3291.
57. Shore, P., and Sharrocks, A.D. (1995a). The MADS-box family of transcription factors. Eur. J. Biochem. 229, 1-13.
58. Shore, P., and Sharrocks, A.D. (1995b). The ETS-domain transcription factors ELK-1 and SAP-1 exhibit differential DNA binding specificities. Nucleic Acids Res. 23, 4698-4706.
59. Shore, P., Bisset, L., Lakey, J., Waltho, J.P., Virden, R., and Sharrocks, A.D. (1995). Characterization of the Elk-1 ETS DNA-binding domain. J. Biol. Chem. 270, 5805-5811.
60. Shore, P., Whitmarsh, A.J., Bhaskaran, R., Davis, R.J., Waltho, J.P., and Sharrocks, A.D. (1996). Determinants of DNA-binding specificity of ETS-domain transcription factors. Mol. Cell. Biol. 16, 3338-3349.
61. 6 binuclear cluster. Nature Struct. Biol. 4, 751-759.
62. Treisman, R. (1994). Ternary complex factors: growth factor regulated transcriptional activators. Curr. Opin. Genet. Dev. 4, 96-101.
63. Urness, L.D., and Thummel, C.S. (1990). Molecular interactions within the ecdysone regulatory hierarchy - DNA-binding properties of the Drosophilia ecdysone-inducible E74A protein. Cell 63, 47-61.
64. Wahl, M.C., and Sundaralingam, M. (1997). Crystal structures of A-DNA duplexes. Biopolymers 44, 45-63.
65. Werner, M.H., Clore, G.M., Fisher, C.L., Fisher, R.J., Trinh, L., Shiloach, J., and Gronenborn, A.M. (1995). The solution structure of the human ETS1-DNA complex reveals a novel mode of binding and true side chain intercalation. Cell 83, 761-771.
66. Werner, M.H., Clore, G.M., Fisher, C.L., Fisher, R.J., Trinh, L., Shiloach, J., and Gronenborn, A.M. (1996). Erratum: The solution structure of the human ETS1-DNA complex reveals a novel mode of binding and true side chain intercalation. Cell 87 (2).
67. Werner, M.H., Clore, G.M., Fisher, C.L., Fisher, R.J., Trinh, L., Shiloach, J., and Gronenborn, A.M. (1997). Correction of the NMR structure of the ETS1/DNA complex. J. Biomolecular NMR 10, 317-328.
68. Woods, D.B., Ghysdeal, J., and Owen, M.J. (1992). Identification of nucleotide preferences in DNA-sequences recognized specifically by c-Ets-1 protein. Nucleic Acids Res. 20, 699-704.