Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis

Structure

Volumn 5, Issue 3, 1997, Pages 349-358

  Xu, Rui Ming ^a   Koch, Christian ^b,c   Liu, Yu ^a   Horton, John R ^a   Knapp, Dunja ^b   Nasmyth, Kim ^b   Cheng, Xiaodong ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^b RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

^c UNIVERSITY OF MUNICH   (Germany)

Author keywords

cell cycle; cyclins; DNA synthesis; helix turn helix DNA binding domain; multiwavelength anomalous diffraction; transcription factor

Indexed keywords

EID: 0031569324     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(97)00192-5     Document Type: Article

References (59)

1. Koch, C. & Nasmyth, K. (1994). Cell cycle regulated transcription in yeast. Curr. Opin. Cell Biol. 6, 451-459.
2. Breeden, L. & Nasmyth, K. (1987). Similarity between cell-cycle genes of budding yeast and fission yeast and the Notch gene of Drosophila. Nature 329, 651-654.
3. Andrews, B.J. & Herskowiz, I. (1989). Identification of a DNA-binding factor involved in cell-cycle control of the yeast HO gene. Cell 57, 21-29.
4. Andrews, B.J. & Herskowiz, I. (1989). The yeast SWI4 protein contains a motif present in developmental regulators and is part of a complex involved in cell-cycle-dependent transcription. Nature 342, 830-833.
5. Espinoza, F.H., Ogas, J., Herskowitz, I. & Morgan, D.O. (1994). Cell cycle control by a complex of the cyclin HCS26 (PCL1) and the kinase PHO85. Science 266, 1388-1391.
6. Measday, V., Moore, L., Ogas, J., Tyers, M. & Andrews, B. (1994). The PCL2 (ORFD)-PHO85 cyclin-dependent kinase complex: a cell cycle regulator in yeast. Science 266, 1391-1395.
7. Dirick, L., Moll, T., Auer, H. & Nasmyth, K. (1992). A central role for SWI6 in modulating cell cycle start-specific transcription in yeast. Nature 357, 508-513.
8. +. Nature 355, 449-453.
9. Johnston, L.H. & Lowndes, N.F. (1992). Cell cycle control of DNA synthesis in budding yeast. Nucleic Acids Res. 20, 2403-2410.
10. Koch, C., Moll, T., Neuberg, M., Ahorn, H. & Nasmyth, K. (1993). A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science 261, 1551-1557.
11. McIntosh, E.M. (1993). MCB elements and the regulation of DNA replication genes in yeast. Curr. Genet. 24, 185-192.
12. Tyers, M., Tokiwa, G. & Futcher, B. (1993). Comparison of the Saccharomyces cerevisiae G1 cyclins: Cln3 may be an upstream activator of Cln1, Cln2 and other cyclins. EMBO J. 12, 1955-1968.
13. Dirick, L., Böhm, T. & Nasmyth, K. (1995). Roles and regulation of Cln/Cdc28 kinases at the start of the cell cycle of Saccharomyces cerevisiae. EMBO J. 14, 4803-4813.
14. Stuart, D. & Wittenberg, C. (1995). CLN3, not positive feedback, determines the timing of CLN2 transcription in cycling cells. Genes Dev. 9, 2780-2794.
15. Primig, M., Sockanathan, S., Auer, H. & Nasmyth, K. (1992). Anatomy of a transcription factor important for the cell cycle in Saccharomyces cerevisiae. Nature 358, 593-597.
16. Nurse, P., Thuriauk, P. & Nasmyth, K. (1976). Genetic control of the cell division cycle in the fission yeast Schizosaccharomyces pombe. Mol. Gen. Genet. 146, 167-178.
17. + and SWI4 gene products. EMBO J. 11, 4923-4932.
18. Marks, J., Fankhauser, C., Reymond, A. & Simanis, V. (1992). Cytoskeletal and DNA structure abnormalities result from bypass of requirement for the cdc10 start gene in the fission yeast Schizosaccharomyces pombe. J. Cell Sci. 101, 517-528.
19. Caligiuri, M. & Beach, D. (1993). Sct1 functions in partnership with Cdc10 in a transcription complex that activates cell cycle START and inhibits differentiation. Cell 72, 607-619.
20. +/SWI4 family, controls the start of mitotic and meiotic cycle in fission yeast. EMBO J. 13, 1873-1880.
21. cdc10, is required for meiosis in the fission yeast Schizosaccharomyces pombe. Genes Dev. 8, 885-898.
22. Sanchez, I. & Dynlacht, B.D. (1996). Transcriptional control of the cell cycle. Curr. Opin. Cell Biol. 8, 318-324.
23. Miller, K.Y., Wu, J. & Miller, B.L. (1992). StuA is required for cell pattern formation in Aspergillus. Genes Dev. 6, 1770-1782.
24. Gimeno, C.J. & Fink, G.R. (1994). Induction of pseudohyphal growth by overexpression of PHD1, a Saccharomyces cerevisiae gene related to transcriptional regulators of fungal development. Mol. Cell. Biol. 14, 2100-2112.
25. Ward, M.P., Gimeno, C.J., Fink, G.R. & Garrett, S. (1995). SOK2 may regulate cyclic AMP-dependent protein kinase-stimulated growth and pseudohyphal development by repressing transcription. Mol. Cell. Biol. 15, 6854-6863.
26. Hendrickson, W.A. (1991). Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 254, 51-58.
27. Ramakrishnan, V., Finch, J.T., Graziano, V., Lee, P.L. & Sweet, R.M. (1993). Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature 362, 219-223.
28. Ramakrishnan, V. & Biou, V. (1997). Treatment of MAD data as a specific case of MIR. Methods Enzymol., in press.
29. Schultz, S.C., Schields, G.C. & Steitz, T.A. (1991). Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253, 1001-1007.
30. Wilson, K.P., Shewchuk, L.M., Brennan, R.G., Otsuka, A.J. & Matthews, B.W. (1992). Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. Proc. Natl. Acad. Sci. USA 89, 9257-9261.
31. Clark., K.L., Halay, E.D., Lai, E. & Burley, S.K. (1993). Co-crystal structure of the HNF-3/fork head DNA recognition motif resembles histone H5. Nature 364, 412-420.
32. Harrison, C.J., Bohm, A.A. & Nelson, H.C.M. (1994). Crystal structure of the DNA-binding domain of the heat shock transcription factor. Science 263, 224-227.
33. Vuister, G.W., Kim, S.-J., Orosz, A., Marquardt, J., Wu, C. & Bax, A. (1994). Solution structure of the DNA-binding domain of Drosophila heat shock transcription factor. Nat. Struct. Biol. 1, 605-613.
34. Liang, H., et al., & Fesik, S.W. (1994). Solution structure of the ets domain of Fli-1 when bound to DNA. Nat. Struct. Biol. 1, 871-875.
35. Werner, M.H., et al., & 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. (Erratum Cell 87, No. 2, October 18, 1996).
36. Donaldson, L.W., Petersen, J.M., Graves, B.J. & 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.
37. Kodandapani, R., et al., & 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.
38. Brennan, R.G. & Matthews, B.W. (1989). The helix-turn-helix DNA-binding motif. J. Biol. Chem. 264, 1903-1906.
39. Harrison, S.C. & Aggarwal, A.K. (1990). DNA recognition by proteins with the helix-turn-helix motifs. Annu. Rev. Biochem. 59, 933-969.
40. Kissinger, C.R., Liu, B., Martin-Blanco, E., Kornberg, T.B. & Pabo, C.O. (1990). Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions. Cell 63, 579-590.
41. Jordan, S.R. & Pabo, C.O. (1988). Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions. Science 242, 893-899.
42. Aggarwal, A.K., Rodgers, D.W., Drottar, M., Ptashne, M. & Harrison, S.C. (1988). Recognition of a DNA operator by the repressor of phage 434, a view at high resolution. Science 242, 899-907.
43. Wolberger, C., Dong, Y.C., Ptashne, M. & Harrison, S.C. (1988). Structure of a phage 434 Cro/DNA complex. Nature 335, 789-795.
44. Klemm, J.D., Rould, M.A., Aurora, R., Herr, W. & Pabo, C.O. (1994). Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell 77, 21-32.
45. Clubb, R.T., Omichinski, J.G., Savilahti, H., Mizuuchi, K., Gronenborn, A.M. & Clore, G.M. (1994). A novel class of winged helix-turn-helix protein: the DNA-binding domain of Mu transposase. Structure 2, 1041-1048.
46. Brennan, R.G. (1993). The winged-helix DNA-binding motif: another helix-turn-helix takeoff. Cell 74, 773-776.
47. Lai, E., Clark, K.L., Burley, S.K. & Darnell, J.E., Jr. (1993). Hepatocyte nuclear factor 3/fork head or 'winged helix' proteins: a family of transcription factors of diverse biologic function. Proc. Natl. Acad. Sci. USA 90, 10421-10423.
48. Studier, F.W., Rosenberg, A.H., Dünn, J.J. & Dubendorff, J.W. (1990). Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 185, 60-89.
49. Smith, M.C., Furman, T.C., Ingolia, T.D. & Pidgeon, C. (1988). Chelating peptide-immobilized metal ion affinity chromatography. A new concept in affinity chromatography for recombinant proteins. J. Biol. Chem. 263, 7211-7215.
50. Otwinowski, Z. (1993). Oscillation data reduction program. In Proceedings of the CCP4 Study Weekend: Data Collection and Processing. (Sawyer, L., Issacs, N. & Bailey, S., eds), pp. 56-62, SERC Daresbury Laboratory, Warrington, UK.
51. Matthews, B.W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491-497.
52. Hendrickson, W.A., Horton, J.R. & LeMaster, D.M. (1990). Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9, 1665-1672.
53. Furey, W. & Swaminathan, S. (1997). PHASES - a program package for the processing and analysis of diffraction data from macromolecules. Methods Enzymol., in press.
54. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A 47, 110-119.
55. Brünger, AT. (1992). X-PLOR, Version 3.7. A system for X-ray Crystallography and NMR. Yale University Press, New Haven, CT.
56. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291.
57. Collaborative Computing Project, No. 4. (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D 50, 760-763.
58. Carson, M. (1991). Ribbons 2.0. J. Appl. Cryst. 24, 958-961.
59. Nicholls, A., Sharp, K.A. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.