Structural basis of DNA recognition by PCG2 reveals a novel DNA binding mode for winged helix-turn-helix domains

Nucleic Acids Research

Volumn 43, Issue 2, 2015, Pages 1231-1240

  Liu, Junfeng ^a   Huang, Jinguang ^a,b   Zhao, Yanxiang ^a   Liu, Huaian ^a   Wang, Dawei ^a   Yang, Jun ^a   Zhao, Wensheng ^a   Taylor, Ian A ^c   Peng, You Liang ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b QINGDAO AGRICULTURAL UNIVERSITY   (China)

^c NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN; HELIX LOOP HELIX PROTEIN; PROTEIN BINDING;

CHEMICAL STRUCTURE; CHEMISTRY; MAGNAPORTHE; METABOLISM;

DNA; DNA-BINDING PROTEINS; HELIX-TURN-HELIX MOTIFS; MAGNAPORTHE; MODELS, MOLECULAR; PROTEIN BINDING;

EID: 84941076765     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1351     Document Type: Article

References (39)

1. 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.
2. Bahler, J. (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu. Rev. Genet., 39, 69-94.
3. McInerny, C.J. (2011) Cell cycle regulated gene expression in yeasts. Adv. Genet., 73, 51-85.
4. Zheng, N., Fraenkel, E., Pabo, C.O., Pavletich, N.P. (1999) Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP. Genes Dev., 13, 666-674.
5. Miyamoto, M., Tanaka, K., Okayama, H. (1994) res2+, a new member of the cdc10+/SWI4 family, controls the 'start' of mitotic and meiotic cycles in fission yeast. EMBO J., 13, 1873-1880.
6. Zhu, Y., Takeda, T., Nasmyth, K., Jones, N. (1994) pct1+, which encodes a new DNA-binding partner of p85cdc10, is required for meiosis in the fission yeast Schizosaccharomyces pombe. Genes Dev., 8, 885-898.
7. Ayte, J., Leis, J.F., Herrera, A., Tang, E., Yang, H., DeCaprio, J.A. (1995) The Schizosaccharomyces pombe MBF complex requires heterodimerization for entry into S phase. Mol. Cell. Biol., 15, 2589-2599.
8. Sturm, S., Okayama, H. (1996) Domains determining the functional distinction of the fission yeast cell cycle 'start' molecules Res1 and Res2. Mol. Biol. Cell., 7, 1967-1976.
9. Zhu, Y., Takeda, T., Whitehall, S., Peat, N., Jones, N. (1997) Functional characterization of the fission yeast Start-specific transcription factor Res2. EMBO J., 16, 1023-1034.
10. Sedgwick, S.G., Taylor, I.A., Adam, A.C., Spanos, A., Howell, S., Morgan, B.A., Treiber, M.K., Kanuga, N., Banks, G.R., Foord, R. et al. (1998) Structural and functional architecture of the yeast cell-cycle transcription factor swi6. J. Mol. Biol., 281, 763-775.
11. Foord, R., Taylor, I.A., Sedgwick, S.G., Smerdon, S.J. (1999) X-ray structural analysis of the yeast cell cycle regulator Swi6 reveals variations of the ankyrin fold and has implications for Swi6 function. Nat. Struct. Biol., 6, 157-165.
12. Taylor, I.A., Treiber, M.K., Olivi, L., Smerdon, S.J. (1997) The X-ray structure of the DNA-binding domain from the Saccharomyces cerevisiae cell-cycle transcription factor Mbp1 at 2.1 A resolution. J. Mol. Biol., 272, 1-8.
13. Xu, R.M., Koch, C., Liu, Y., Horton, J.R., Knapp, D., Nasmyth, K., Cheng, X. (1997) Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis. Structure, 5, 349-358.
14. McIntosh, P.B., Taylor, I.A., Smerdon, S.J., Frenkiel, T.A., Lane, A.N. (1999) 1H, 15N and 13C assignments of the DNA binding domain of transcription factor Mbp1 from S. cerevisiae in both its free and the DNA bound forms, and 1H assignments of the free DNA. J. Biomol. NMR, 13, 397-398.
15. Taylor, I.A., McIntosh, P.B., Pala, P., Treiber, M.K., Howell, S., Lane, A.N., Smerdon, S.J. (2000) Characterization of the DNA-binding domains from the yeast cell-cycle transcription factors Mbp1 and Swi4. Biochemistry, 39, 3943-3954.
16. Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M., Brown, P.O. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature, 409, 533-538.
17. Nair, M., McIntosh, P.B., Frenkiel, T.A., Kelly, G., Taylor, I.A., Smerdon, S.J., Lane, A.N. (2003) NMR structure of the DNA-binding domain of the cell cycle protein Mbp1 from Saccharomyces cerevisiae. Biochemistry, 42, 1266-1273.
18. Bean, J.M., Siggia, E.D., Cross, F.R. (2005) High functional overlap between MluI cell-cycle box binding factor and Swi4/6 cell-cycle box binding factor in the G1/S transcriptional program in Saccharomyces cerevisiae. Genetics, 171, 49-61.
19. Deleeuw, L., Tchernatynskaia, A.V., Lane, A.N. (2008) Thermodynamics and specificity of the Mbp1-DNA interaction. Biochemistry, 47, 6378-6385.
20. Chernatynskaya, A.V., Deleeuw, L., Trent, J.O., Brown, T., Lane, A.N. (2009) Structural analysis of the DNA target site and its interaction with Mbp1. Org. Biomol. Chem., 7, 4981-4991.
21. Schultz, S.C., Shields, G.C., Steitz, T.A. (1991) Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science, 253, 1001-1007.
22. 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.
23. Kodandapani, R., Pio, F., Ni, C.Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R.A., 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.
24. Gajiwala, K.S., Chen, H., Cornille, F., Roques, B.P., Reith, W., Mach, B., Burley, S.K. (2000) Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Nature, 403, 916-921.
25. Zhang, A.P., Pigli, Y.Z., Rice, P.A. (2010) Structure of the LexA-DNA complex and implications for SOS box measurement. Nature, 466, 883-886.
26. Wang, D., Ma, X., Yang, J., Xue, M., Chen, X., Zhao, W., Peng, Y. (2011) Pcg2, a novel pathogenicity gene in Magnaporthe oryzae encodes a transcription factor that activates and represses expression of distinct genes. Phytopathology., 101, S187-S187.
27. Brown, P.H., Schuck, P. (2006) Macromolecular size-and-shape distributions by sedimentation velocity analytical ultracentrifugation. Biophys. J., 90, 4651-4661.
28. Winn, M.D., Ballard, C.C., Cowtan, K.D., Dodson, E.J., Emsley, P., Evans, P.R., Keegan, R.M., Krissinel, E.B., Leslie, A.G., McCoy, A. et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr. D. Biol. Crystallogr., 67, 235-242.
29. Winter, G. (2010) xia2: an expert system for macromolecular crystallography data reduction. J. Appl. Crystallogr., 43, 186-190.
30. Mccoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C., Read, R.J. (2007) Phaser crystallographic software. J. Appl. Crystallogr., 40, 658-674.
31. Emsley, P., Lohkamp, B., Scott, W.G., Cowtan, K. (2010) Features and development of Coot. Acta Crystallogr. D., 66, 486-501.
32. Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W. et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D., 66, 213-221.
33. Afonine, P.V., Grosse-Kunstleve, R.W., Echols, N., Headd, J.J., Moriarty, N.W., Mustyakimov, M., Terwilliger, T.C., Urzhumtsev, A., Zwart, P.H., Adams, P.D. (2012) Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D., 68, 352-367.
34. Chen, V.B., Arendall, W.B., Headd, J.J., Keedy, D.A., Immormino, R.M., Kapral, G.J., Murray, L.W., Richardson, J.S., Richardson, D.C. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D., 66, 12-21.
35. Krissinel, E., Henrick, K. (2007) Inference of macromolecular assemblies from crystalline state. J. Mol. Biol., 372, 774-797.
36. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
37. Taylor, I.A., Goldstone, D.C., Pala, P., Haire, L.F., Smerdon, S.J. (2010) Structure of the amino-terminal domain from the cell-cycle regulator Swi6. Proteins, 78, 2861-2865.
38. Harami, G.M., Gyimesi, M., Kovacs, M. (2013) From keys to bulldozers: expanding roles for winged helix domains in nucleic-acid-binding proteins. Trends Biochem. Sci., 38, 364-371.
39. Gajiwala, K.S., Burley, S.K. (2000) Winged helix proteins. Curr. Opin. Struct. Biol., 10, 110-116.