1H,15N resonance assignment and three-dimensional structure of CYP1 (HAP1) DNA-binding domain

Journal of Molecular Biology

Volumn 259, Issue 4, 1996, Pages 792-804

  Timmerman, Johanna ^a   Vuidepot, Anne Lise ^a   Bontems, Francois ^a   Lallemand, Jean Yves ^a   Gervais, Michel ^b   Shechter, Evelyne ^b   Guiard, Bernard ^b  

^a ECOLE POLYTECHNIQUE   (France)

^b CENTRE DE GÉNÉTIQUE MOLÉCULAIRE   (France)

Author keywords

CYP1(HAP1); NMR structure; Protein DNA interactions; Transcription; Zinc cluster

Indexed keywords

CADMIUM; CYSTEINE; DNA; DNA BINDING PROTEIN; TRANSCRIPTION FACTOR; ZINC; FUNGAL PROTEIN; GAL4 PROTEIN, S CEREVISIAE; HAP1 PROTEIN, S CEREVISIAE; PEPTIDE FRAGMENT; PPR1 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSACTIVATOR PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CALCULATION; DIMERIZATION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONSENSUS SEQUENCE; ESCHERICHIA COLI; GENETICS; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

SACCHAROMYCES CEREVISIAE;

AMINO ACID SEQUENCE; BINDING SITES; CADMIUM; CLONING, MOLECULAR; CONSENSUS SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DNA-BINDING PROTEINS; ESCHERICHIA COLI; FUNGAL PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS; ZINC;

EID: 0030596420     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0358     Document Type: Article

References (48)

1. 2-GAL4 from S. cerevisiae. Nature, 356, 450-453.
2. Baleja, J. D., Mau, T. & Wagner, G. (1994). Recognition of DNA by GAL4 in solution: use of monomeric protein-DNA complex for study by NMR. Biochemistry, 33, 3071-3078
3. Bax, A. & Davis, D. G. (1985). MLEV17-based two dimensional homonuclear magnetization transfer spectroscopy. J. Magn. Reson. 65, 355-360.
4. Bax, A., Griffey, R. H. & Hawkins, B. L. (1983). Correlation of proton and nitrogen-15 chemical shifts by multiple quantum NMR. J. Magn. Reson. ?, 301-315.
5. Bontems, F., Gilquin, B., Roumestand, C., Ménez, A. & Toma, F. (1992). Analysis of side-chains organization of a refined model of charybdotoxin: structural and functional implications. Biochemistry, 31, 7756-7764.
6. Braunschweiler, L. & Ernst, R. R. (1983). Coherence transfer by isotropic mixing: application to proton correlation spectroscopy, J. Magn. Reson. 53, 521-528.
7. Brooks, B., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S. & Karplus, M. (1983). CHARMM: a program for macromolecular energy minimization and molecular dynamics calculation. J. Comp. Chem. 4, 187-217.
8. 1H NMR spectra in proteins. J. Magn. Reson. 77, 166-169.
9. Brünger, A. T. (1988). X-PLOR Manual, The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.
10. Creusot, F., Verdière, J., Gaisne, M. & Slonimski, P. P. (1988). CYP1 (HAP1). regulator of oxygen-dependent gene expression in yeast. J. Mol. Biol. 204, 263-276.
11. Delsuc, M.-A. (1989). A new maximum entropy processing algorithm, with application to nuclear magnetic resonance experiments. In Maximum Entropy and Bayesian Methods. (Skilling, J., ed.), pp. 285-290, Kluwer. Dordrecht.
12. Defranoux, N., Gaisne, M. & Verdiere, J. (1994). Functional analysis of the zinc cluster domain of CYP1 (HAP1) complex regulator in heme-sufficient and heme-deficient yeast cells. Mol. Gen. Genet. 242, 699-707.
13. Fytlovich, S., Gervais, M., Agrimonti, C. & Guiard, B. (1993). Evidence for an interaction between the CYP1(HAP1) activator and a cellular factor during heme-dependant transcriptional regulation in the yeast Saccharomyces cerevisiae. EMBO J. 12, 1209-1218.
14. 6 DNA-binding domain. Nature Struct. Biol. 2, 898-905
15. Gippert, G. P., Yip, P. F., Wright, P. E. & Case, D. A. (1990). Computational methods for determining protein structures from NMR data. Biochem. Pharmacol. 40, 15-22.
16. Güntert, P. & Wüthrich, K. (1991). Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J. Biomol. NMR, 1, 447-456.
17. Güntert, P., Braun, W. & Wüthrich, K. (1991). Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217, 517-530.
18. Jeener, J., Meier, B. H., Bachmann, P. & Ernst, R. R. (1979). Investigation of exchange process by two-dimensional NMR spectroscopy. J. Chem. Phys. 71, 4546-4553.
19. Johnston, M. (1987). A model fungal gene regulatory mechanism: the GAL4 genes of Saccharomyces cerevisiae. Microbiol. Rev. 51, 458-476.
20. Kraulis, P. J., Raine, A. R. C, Gadhavi, P. L. & Laue, E. D. (1992). Structure of the DNA-binding domain of zinc GAL4. Nature, 356, 448-450.
21. Kumar, A., Ernst, R. R. & Wüthrich, K. (1980). A two-dimensional nuclear Overhauser enhancement (2D NOE). experiment for the elucidation of the complete proton-proton cross-relaxation networks in biological macromolecules. Biochem. Biophys. Res. Commun. 95, 1-6.
22. 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. Crystallog. 26, 283-291.
23. Lefèvre, J. F., Dayie, K. T., Peng, J. W. & Wagner, G. (1996). Internal mobility in the partially folded binding and dimerization domains of GAL4:NMR analysis of the N-H spectral density functions. Biochemistry, 35, 2674-2686.
24. Marion, D. & Bax, A. (1989). Baseline correction of 2D FT NMR spectra using a simple linear prediction extrapolation of the time-domain data. J. Magn. Reson. 83, 205-211.
25. 1H spin-spin coupling constant in proteins. Biochem. Biophys. Res. Commun. 113, 967-974.
26. 15N Hartmann-Hahn multiple quantum coherence and nuclear Overhauser multiple quantum coherence spectroscopy: application to interleukin 1β. Biochemistry, 28, 6150-6156.
27. 15N-labeled proteins. J. Am. Chem. Soc. 111, 1515-1517.
28. Marion, D., Ikura, M., Tschudin, R. & Bax, A. (1989c). Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins, J. Magn. Reson. 85, 393-399.
29. 6 binuclear cluster. Gene. Dev. 8, 2504-2512.
30. Marmorstein, R., Carey, M., Ptashne, M. & Harrison, S. C. (1992). DNA recognition by GAL4: structure of a protein-DNA complex. Nature, 356, 408-414.
31. Morris, A. L., MacArthur, M. W., Hutchinson, E. G. & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. Proteins: Struct. Func. Genet. 12, 345-364.
32. Nilgels, M., Clore, G. M. & Gronenborn, A. M. (1988). Determination of the three-dimensional structures of proteins from interproton distance data by hibrid distance geometry-dynamical simulated annealing calculations. FEBS Letters, 229, 317-324.
33. Pan, T. & Coleman, J. E. (1989). Structure and function of the Zn(II) binding site within the DNA-binding domain of the GAL4 transcription factor. Proc. Natl Acad. Sci. USA, 86, 3145-3149.
34. 6 binuclear cluster. J. Biol. Chem. 265, 21427-21429.
35. Pfeifer, K., Kim, K. S., Kogan, S. & Guarente L. (1989). Functional dissection and sequence of yeast HAP1 activator. Cell, 56, 291-301.
36. 1H spectra of proteins via double quantum filtering. Biochem. Biophys. Res. Commun. 117, 458-479.
37. 6 zinc cluster proteins. Science, 261, 909-911.
38. Rouh, A., Delsuc, M. A., Bertran, G. & Lallemand, J. Y. (1993). The use of classification in baseline correction of FT NMR spectra. J. Magn. Reson. ser. A, 102, 357-359.
39. Shaka, A. J., Lee, C. J. & Pines, A. (1988). Iterative schemes for bilinear operators; application to spin decoupling. J. Magn. Reson. 77, 274-293.
40. 13C resonances, identification of elements of secondary structure and determination of the global fold of the DNA binding domain of GAL4. Biochemistry, 32, 2144-2153.
41. Timmerman, J., Guiard, B., Schechter, E., Delsuc, M.-A., Lallemand, J.-Y. & Gervais, M. (1994). The DNA binding domain of the yeast Saccharomyces cerevisiae CYP1(HAP1) transcription factor possesses two zinc ions which are complexed in a zinc cluster. Eur. J. Biochem. 225, 593-599.
42. Verdière, J., Creusot, F. & Guerineau, M. (1985). Regulation of the expression of iso-2-cytochrome c gene in Saccharomyces cerevisiae: cloning of the positive regulatory gene CYP1 and identification of the region of its target sequence on the structural gene CYP3. Mol. Gen. Genet. 199, 524-526.
43. Verdière, J., Gaisne, M., Guiard, B., Defranoux, N. & Slonimski, P. P. (1988). CYP1 (HAP1) regulator of oxygen-dependant gene expression in yeast. II. Miscence mutation suggests alternative Zn finger as decriminating agent of gene control. J. Mol. Biol. 204, 277-282.
44. Wüthrich, K., Billeter, M. & Brown, W. (1983). Pseudo structure for the 20 common amino-acids for use in studies of protein conformations by measurements of intra-molecular proton-proton distance constraints with nuclear magnetic resonance. J. Mol. Biol. 169, 949-961.
45. Zhang, L. & Guarente, L. (1994). The yeast activator HAP1 - a GAL4 family member - binds DNA in a directly repeated orientation. Gene. Dev. 8, 2110-2119.
46. Zhang, L. & Guarente, L. (1995). Heme binds to a short sequence that serves a regulatory function in diverse proteins. EMBO J. 14, 313-320.
47. Zitomer, R. S. & Lowry, C. V. (1992). Regulation of the gene expression by oxygen in Saccharomices cerevisiae. Microbiol. Rev. 56, 1-11.
48. Zuiderweg, E. R. P. & Fesik, S. W. (1989). Heteronuclear three-dimensional NMR spectroscopy of the inflamatory protein C5a. Biochemistry, 28, 2387-2391.