NMR structure of the amino-terminal domain from the Tfb1 subunit of TFIIH and characterization of its phosphoinositide and VP16 binding sites

Biochemistry

Volumn 44, Issue 21, 2005, Pages 7678-7686

  Di Lello, Paola ^a   Nguyen, Bao D ^b   Jones, Tamara N ^c   Potempa, Krzysztof ^c   Kobor, Michael S ^d   Legault, Pascale ^a,c   Omichinski, James G ^a,c  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO-TERMINAL DOMAINS; CHEMICAL SHIFT MAPPING; PREINITIATION COMPLEX (PIC); PROTOTYPING;

AMINO ACIDS; CHEMICAL BONDS; NUCLEAR MAGNETIC RESONANCE; PROTEINS; STRUCTURE (COMPOSITION);

PHOSPHORUS COMPOUNDS;

ETOPOSIDE; PHOSPHATIDYLINOSITIDE; PROTEIN P62; PROTEIN SUBUNIT; TRANSCRIPTION FACTOR IIH;

AMINO TERMINAL SEQUENCE; ARTICLE; BETA CHAIN; BINDING SITE; NUCLEAR MAGNETIC RESONANCE; PH; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN QUATERNARY STRUCTURE; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; SEQUENCE ANALYSIS; TRANSCRIPTION INITIATION;

BINDING SITES; BLOOD PROTEINS; CRYSTALLOGRAPHY, X-RAY; HERPES SIMPLEX VIRUS PROTEIN VMW65; HUMANS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDE FRAGMENTS; PEPTIDE MAPPING; PHOSPHATIDYLINOSITOLS; PHOSPHOPROTEINS; PHOSPHORYLATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; SACCHAROMYCES CEREVISIAE PROTEINS; SOLUTIONS; STRUCTURAL HOMOLOGY, PROTEIN; TRANSCRIPTION FACTOR TFIIH; TRANSCRIPTION FACTORS, TFII; VIRUS ACTIVATION;

EID: 19644388865     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050099s     Document Type: Article

References (53)

1. Hampsey, M. ( 1998) Molecular genetics of the RNA polymerase II general transcriptional machinery, Microbiol. Mol. Biol. Rev. 62, 465-503.
2. Allison, L. A., Moyle, M., Shales, M., and Ingles, C. J. (1985) Extensive homology among the large subunits of eukaryotic and prokaryotic RNA polymerases, Cell 42, 599-610.
3. Corden, J. L., Cadena, D. L., Ahearn, J. M., and Dahmus, M. E. (1985) A unique structure at the carboxyl terminus of the largest subunit of eukaryotic RNA polymerase II, Proc. Natl. Acad. Sci. U.S.A. 82, 7934-7938.
4. Lu, H., Flores, O., Weinmann, R., and Reinberg, D. (1991) The nonphophorylated form of the RNA polymerase II preferentially associates with the preinitiation complex, Proc. Natl. Acad. Sci. U.S.A. 88, 10004-10008.
5. O'Brien, T. S., Hardin, S., Greenleaf, A., and Lis, J. T. (1994) Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation, Nature 370, 75-77.
6. Lu, H., Zawel, L., Fisher, L., Egly, J. M., and Reinberg, D. (1992) Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase II, Nature 358, 641-645.
7. Schultz, P., Fribourg, S., Poterszman, A., Mallouh, V., Moras, D., and Egly, J. M. (2000) Molecular structure of human TFIIH, Cell 102, 599-607.
8. Chang, W.-H., and Kornberg, R. D. (2000) Electron crystal structure of the transcription factor and DNA repair complex, core TFIIH, Cell 102, 609-613.
9. Conaway, R. C., and Conaway, J. W. (1989) An RNA polymerase II transcription factor has an associated DNA-depenent ATPase (dATPase) activity strongly stimulated by the TATA region of promoters, Proc. Natl. Acad. Sci. U.S.A. 86, 7356-7360.
10. Schaefer, L., Moncollin, V., Roy, R., Staub, A., Mezzina, M., Sarasin, A., Weeda, G., Hoeijmakers, J. H., Chambon, P., and Egly, J. M. (1993) DNA repair helicase: A component of BTF2 (TFIIH) basic transcription factor, Science 260, 58-63.
11. Ohkuma, Y., Hashimoto, S., Wang, C. K., Horikoshi, M., and Roeder, R. G. (1995) Analysis of the role of TFIIE in basal transcription and TFIIH-mediated carboxy-terminal domain phosphorylation through structure-function studies of TFIIEα, Mol. Cell. Biol. 15, 4856-4866.
12. Hengartner, C. J., Thompson, C. M., Zhang, J., Chao, D. M., Liao, S. M., Koleske, A. J., Okamura, S., and Young, R. A. (1995) Association of an activator with an RNA polymerase II holo-enzyme, Genes Dev. 15, 897-910.
13. Blau, J., Xiao, H., McCracken, S., O'Hare, P., Greenblatt, J., and Bentley, D. (1996) Three functional classes of transcriptional activation domains, Mol. Cell. Biol. 16, 2044-2055.
14. Pearson, A., and Greenblatt, J. (1997) Modular organization of the E2F1 activation domain an its interaction with general transcription factors TBP and TFIIH, Oncogene 15, 2643-2658.
15. Gervais, V., Lamour, V., Jawhari, A., Frindel, F., Wasielewski, E., Dubaele, S., Egly, J.-M., Thierry, J.-C., Kieffer, B., and Poterszman, A. (2004) TFIIH contains a PH domain involved in DNA nucleotide excision repair, Nat. Struct. Mol. Biol. 11, 616-622.
16. Nguyen, B. D., Chen, H.-T., Kobor, M. S., Greenblatt, J., Legault, P., and Omichinski, J. G. (2003) Solution structure of the carboxyl-terminal domain of RAP74 and NMR characterization of the FCP1-binding sites of RAP74 and human TFIIB, Biochemistry 42, 1460-1469.
17. Bax, A., Sparks, S. W., and Torchia, D. A. (1989) Detection of insensitive nuclei, Methods Enzymol. 176, 134-150.
18. 15N-labeled proteins, J. Am. Chem. Soc. 111, 1515-1517.
19. 2O, J. Magn. Reson. 103, 197-201.
20. Zuiderweg, E. R. P., McIntosh, L. P., Dahlquist, F. W., and Fesik, S. W. (1990) Three-dimensional carbon-13-resolved proton NOE spectroscopy of uniformly carbon-13-labeled proteins for the NMR assignment and structure determination of larger molecules, J. Magn. Reson. 86, 210-216.
21. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes, J. Biomol. NMR 6, 277-293.
22. Johnson, B. A., and Blevins, R. A. (1994) NMRView: A computer program for the visualization and analysis of NMR data, J. Biomol. NMR 4, 603-614.
23. Morton, C. J., Pugh, D. J. R., Brown, E. L. J., Kahmann, J. D., Renzoni, D. A. C., and Campbell, I. D. (1996) Solution structure and peptide binding of the SH3 domain from human Fyn, Structure 4, 705-714.
24. Fielding, L. (2003) NMR Methods for the Determination of Protein-Ligand Dissociation Constants, Curr. Top. Med. Chem. 3, 39-53.
25. + binding site on the MurB enzyme by NMR, Nat. Struct. Biol. 3, 995-997.
26. Brunger, A. T., Adams, P. D., Clore, G. M., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography and NMR system (CNS): A new software system for macromolecular structure determination, Acta Crystallogr. D54, 905-921.
27. Kuszewski, J., Gronenborn, A. M., and Clore, G. M. (1996) Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases, Protein Sci. 5, 1067-1080.
28. Choy, W.-Y., Tollinger, M., Mueller, G. A., and Kay, L. E. (2001) Direct structure refinement of high molecular weight proteins against residual dipolar couplings and carbonyl chemical shift changes upon alignment: An application to maltose binding protein, J. Biomol. NMR 21, 31-40.
29. Laskowski, R. A., Antoon, J., Rullmann, C., Macarthur, M. W., Kaptein, R., and Thornton, J. M. (1996) AQUA and PROCHECKNMR: Programs for checking the quality of protein structures solved by NMR, J. Biomol. NMR 8, 477-486.
30. Koradi, R., Billeter, M., and Wüthrich, K. (1996) MOLMOL: A program for display and analysis of macromolecular structures, J. Mol. Graphics 14, 51-55.
31. Nicholls, A., Sharp, K. A., and Honig, B. (1991) Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons, Proteins: Struct., Funct., Genet. 11, 281-296.
32. Cornilescu, G., Delaglio, F., and Bax, A. (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology, J. Biomol. NMR 13, 289-302.
33. Blomberg, N., Baraldi, E., Nilges, M., and Saraste, M. (1999) The PH superfold: A structural scaffold for multiple functions, Trends Biochem. Sci. 24, 441-445.
34. Lemmon, M. A., Ferguson, K. M., and Abrams, C. S. (2002) Pleckstrin homology domains and the cytoskeleton, FEBS Lett. 513, 71-76.
35. Haslam, R. J., Koide, H. B., and Hammings, B. A. (1993) Pleckstrin homology domain, Nature 363, 309-310.
36. Lemmon, M. A. (2003) Phosphoinositide recognition domains, Traffic 4, 201-213.
37. Lemmon, M. A., and Ferguson, K. M. (2000) Signal-dependent membrane targeting by pleckstrin homology (PH) domains, Biochem. J. 350, 1-18.
38. Lietzke, S. E., Bose, S., Cronin, T., Klarlund, J., Chawla, A., Czech, M. P., and Lambright, D. G. (2000) Structural basis of 3-phosphoinositide recognition by pleckstrin homology domains, Mol. Cell 6, 385-394.
39. Henikoff, S., and Henikoff, J. G. (1992) Amino acid substitution matrices from protein blocks, Proc. Natl. Acad. Sci. U.S.A. 89, 10915-10919.
40. Kavran, J. M., Klein, D. E., Lee, A., Falasca, M., Isakoff, S. J., Skolnik, E. Y., and Lemmon, M. A. (1998) Specificity and promiscuity in phosphoinositide binding by pleckstrin homology domains, J. Biol. Chem. 273, 30497-30508.
41. Dowler, S., Currie, R. A., Campbell, D. G., Deak, M., Kular, G., Downes, C. P., and Alessi, D. R. (2000) Identification of pleckstrin-homolgy-domain- containing proteins with novel phosphoinositide-binding specificities, Biochem. J. 351, 19-31.
42. Auguin, D., Barthe, P., Auge-Therese, M.-T., Stern, M.-H., Noguchi, M., and Roumestand, C. (2004) Solution structure and backbone dynamics of the pleckstrin homology domain of the human protein kinase B(PKB/Akt). Interaction with inositol phosphates, J. Biomol. NMR 28, 137-155.
43. Isakoff, S. J., Cardozo, T., Andreev, J., Li, Z., Ferguson, K. M., Abagyan, R., Lemmon, M. A., Aronheim, A., and Skolnik, E. Y. (1998) Identification and analysis of PH domain-containing targets of phosphatidylinositol 3-kinase using a novel in vivo assay in yeast, EMBO J. 17, 5374-5387.
44. Xiao, H., Pearson, A., Coulombe, B., Truant, R., Zhang, S., Regier, J. L., Trienzenberg, S. J., Reinberg, D., Flores, O., Ingles, C. J., and Greenblatt, J. (1994) Binding of basal transcription factor TFlIH to the acidic activation domain of VP16 and p53, Mol. Cell. Biol. 14, 7013-7024.
45. Chen, D., Riedl, T., Washbrook, E., Pace, P. E., Coombes, R. C., Egly, J.-M., and Ali, S. (2000) Activation of estrogen receptor a by S118 phosphorylation involves a ligand-dependent interaction with TFIIH and participation of CDK7, Mol. Cell 6, 127-137.
46. Ferguson, K. M., Lemmon, M. A., Schlessinger, J., and Sigler, P. B. (1995) Structure of the high affinity complex of inositol trisphosphate with a phospholipase C pleckstrin homology domain, Cell 83, 1037-1046.
47. Ferguson, K. M., Kavran, J. M., Sankaran, V. G., Fournier, E., Isakoff, S. J., Skolnik, E. Y., and Lemmon, M. A. (2000) Structural basis for discrimination of 3-phosphoinositides by pleckstrin homology domains, Mol. Cell 6, 373-384.
48. Prestwich, G. D. (2004) Phosphoinositide Signaling: From Affinity Probes to Pharmaceutical Targets, Chem. Biol. 11, 619-637.
49. Irvine, R. F. (2003) Twenty years of Ins(1,4,5)P3, and 40 years before, Nat. Rev. Mol. Cell Biol. 4, 586-590.
50. Clarke, J. H. (2003) Lipid Signalling: Picking Out the PIPs, Curr. Biol. 13, R815-R817.
51. Gozani, O., Karuman, P., Jones, D. R., Ivanov, D., Cha, J., Lugovskoy, A. A., Baird, C. L., Zhu, H., Field, S. J., Lessnick, S. L., Villasenor, J., Mehrotra, B., Chen, J., Rao, V. R., Brugge, J. S., Ferguson, C. G., Payrastre, B., Myszka, D. G., Cantley, L. C., Wagner, G., Divecha, N., Prestwich, G. D., and Yuan, J. (2003) The PHD finger of the chromatin-associated protein ING2 functions as a nuclear phosphoinositide receptor, Cell 114, 99-111.
52. Irvine, R. F. (2003) Nuclear lipid signalling, Nat. Rev. Mol. Cell Biol. 4, 349-361.
53. Clarke, J. H., Letcher, A. J., D'Santos, C. S., Halstead, J. R., Irvine, R. F., and Divecha, N. (2001) Inositol lipids are regulated during cell cycle progression in the nuclei of murine erythroleukaemia cells, Biochem. J. 357, 905-910.