Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding

Nature

Volumn 403, Issue 6772, 2000, Pages 916-921

  Gajiwala, Ketan S ^a   Chen, Hua ^a   Cornille, Fabrice ^b   Roques, Bernard P ^b   Reith, Walter ^c   Mach, Bernard ^c   Burley, Stephen K ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b INSERM   (France)

^c UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; ESTROGEN RECEPTOR; GENE PRODUCT; HELIX LOOP HELIX PROTEIN; HISTONE; LINK PROTEIN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2;

ARTICLE; BARE LYMPHOCYTE SYNDROME; BREAST TUMOR; DNA HISTONE INTERACTION; GENE EXPRESSION REGULATION; GENE FUSION; HUMAN; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA; DNA-BINDING PROTEINS; ELECTROCHEMISTRY; HELIX-TURN-HELIX MOTIFS; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; TRANSCRIPTION FACTORS;

EID: 0034708205     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/35002634     Document Type: Article

References (25)

1. Mach, B., Steimle, V., Martinez-Soria, E. & Reith, W. Regulation of MHC class 11 genes: lessons from a disease. Annu. Rev. Immunol. 14, 301-331 (1996).
2. Iwama, A. et al. Dimeric RFX proteins contribute to the activity and lineage specificity of the interleukin-5 receptor alpha promoter through activation and repression domains. Mol. Cell Biol. 19, 3940-3950 (1999).
3. Dotzlaw, H., Alkhalaf, M. & Murphy, L. C. Characterization of estrogen receptor variant mRNAs from human breast cancers. Mol. Endocrinol. 6, 773-785 (1992).
4. Reith, W. et al. MHC class II regulatory factor RFX has a novel DNA-binding domain and a functionally independent dimerization domain. Genes Dev. 4, 1528-1540 (1990).
5. Cornille, F. et al. DNA binding properties of a chemically synthesized DNA binding domain of hRFX1. Nucleic Acids Res. 26, 2143-2149 (1998).
6. Clark, K. L., Halay, E. D., Lai, E. & Burley, S. K. Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5. Nature 364, 412-420 (1993).
7. Lai, E., Clark, K. L., Burley, S. & James E. Darnell, J. Hepatocyte nuclear factor 3/fork head or "winged helix" proteins: A family of transcription factors of diverse biological function. Proc. Natl Acad. Sci. USA 90, 10421-10423 (1993).
8. Emery, P. et al. A consensus motif in the RFX DNA binding domain and binding domain mutants with altered specificity. Mol. Cell Biol. 16, 4486-4494 (1996).
9. Ostapchuk, P., Scheirle, G. & Hearing, P. Binding of nuclear factor EF-C to a functional domain of the hepatitis B virus enhancer region. Mol. Cell Biol. 9, 2787-2797 (1989).
10. Jin, C., Marsden, I., Chen, X. & Liao, X. Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex. J. Mol. Biol. 289, 683-690 (1999).
11. Zheng, N., Fraenkel, E., Pabo, C. O. & Pavletich, N. P. Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP. Genes Dev. 13, 666-674 (1999).
12. Janin, J. Principles of protein-protein recognition from structure to thermodynamics. Biochimie 77, 497-505 (1995).
13. Reith, W. et al. RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins. Mol. Cell Biol. 14, 1230-1244 (1994).
14. Lavery, R. & Sklenar, H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynamics 6, 63-91 (1988).
15. Klemm, J. D. & Pabo, C. O. Oct-I POU domain-DNA interactions: cooperative binding of isolated subdomains and effects of covalent linkage. Genes Dev. 10, 27-36 (1996).
16. Ramakrishnan, V., Finch, J., Graziano, V., & Sweet, R. Crystal structure of the globular domain of histone H5 and its implications for nucleosome binding. Nature 362, 219-223 (1993).
17. Thomas, J. O. & Wilson, C. M. Selective radiolabelling and identification of a strong nucleosome binding site on the globular domain of histone H5. EMBO J. 5, 3531-3537 (1986).
18. Buckle, R. S., Maman, I. D. & Allan, J. Site-directed mutagenesis studies on the binding of the globular domain of linker histone H5 to the nucleosome. J. Mol. Biol. 223, 651-659 (1992).
19. Holm, L. & Sander, C. Families of structurally similar proteins, version 1.0. J. Mol. Biol. 233, 123-138 (1993).
20. Goytisolo, F. A. et al. Identification of two DNA-binding sites on the globular domain of histone H5. EMBO J. 15, 3421-3429 (1996).
21. Cirillo, L. A. et al. Binding of the winged-helix transcription factor HNF3 to a linker histone site on the nucleosome. EMBO J. 17, 244-254 (1998).
22. Zhou, Y. B., Gerchman, S. E., Ramakrishnan, V., Travers, A. & Muyldermans, S. Position and orientation of the globular domain of linker histone H5 on the nucleosome. Nature 395, 402-405 (1998).
23. Brunger, A. T. et al. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905-921 (1998).
24. Laskowski, R. J., MacArthur, M. W., Moss, D. S. & Thornton, J. M. PROCHECK: a program to check stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-290 (1993).
25. Nicholls, A., Sharp, K. & Honig, B. Protein folding and association; insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281-296 (1991).