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TFIIH contains a PH domain involved in DNA nucleotide excision repair

Nature Structural & Molecular Biology volume 11, pages 616–622 (2004)Cite this article

Abstract

The human general transcription factor TFIIH is involved in both transcription and DNA repair. We have identified a structural domain in the core subunit of TFIIH, p62, which is absolutely required for DNA repair activity through the nucleotide excision repair pathway. Using coimmunoprecipitation experiments, we showed that this activity involves the interaction between the N-terminal domain of p62 and the 3′ endonuclease XPG, a major component of the nucleotide excision repair machinery. Furthermore, we reconstituted a functional TFIIH particle with a mutant of p62 lacking the N-terminal domain, showing that this domain is not required for assembly of the TFIIH complex and basal transcription. We solved its three-dimensional structure and found an unpredicted pleckstrin homology and phosphotyrosine binding (PH/PTB) domain, uncovering a new class of activity for this fold.

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Figure 1: Three-dimensional structure of the N-terminal domain of p62 (residues 1–108).
Figure 2: Structure-guided sequence alignment of the N-terminal domain of human (Homo sapiens) p62 with orthologous sequences and selected PH/PTB domains.
Figure 3: Structural comparison of PH and PTB domains and molecular surface properties of p62(1–108).
Figure 4: Deletion of p62(1–108) impairs the NER activity of TFIIH.
Figure 5: p62(1–108) interacts with the endonuclease XPG.

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References

  1. Coin, F. & Egly, J.M. Ten years of TFIIH. Cold Spring Harb. Symp. Quant. Biol. 63, 105–110 (1998).

    Article  CAS  PubMed  Google Scholar 

  2. Schultz, P. et al. Molecular structure of human TFIIH. Cell 102, 599–607 (2000).

    Article  CAS  PubMed  Google Scholar 

  3. Lehmann, A.R. DNA repair-deficient diseases, xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. Biochimie 85, 1101–1111 (2003).

    Article  CAS  PubMed  Google Scholar 

  4. Fischer, L. et al. Cloning of the 62-kilodalton component of basic transcription factor BTF2. Science 257, 1392–1395 (1992).

    Article  CAS  PubMed  Google Scholar 

  5. Tirode, F., Busso, D., Coin, F. & Egly, J.M. Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7. Mol. Cell 3, 87–95 (1999).

    Article  CAS  PubMed  Google Scholar 

  6. Ohkuma, Y. Multiple functions of general transcription factors TFIIE and TFIIH in transcription: possible points of regulation by trans-acting factors. J. Biochem. 122, 481–489 (1997).

    Article  CAS  PubMed  Google Scholar 

  7. Svejstrup, J.Q., Vichi, P. & Egly, J.M. The multiple roles of transcription/repair factor TFIIH. Trends Biochem. Sci. 21, 346–350 (1996).

    Article  CAS  PubMed  Google Scholar 

  8. Bushnell, D.A., Bamdad, C. & Kornberg, R.D. A minimal set of RNA polymerase II transcription protein interactions. J. Biol. Chem. 271, 20170–20174 (1996).

    Article  CAS  PubMed  Google Scholar 

  9. Lu, H., Zawel, L., Fisher, L., Egly, J.M. & Reinberg, D. Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase II. Nature 358, 641–645 (1992).

    Article  CAS  PubMed  Google Scholar 

  10. Zurita, M. & Merino, C. The transcriptional complexity of the TFIIH complex. Trends Genet. 19, 578–584 (2003).

    Article  CAS  PubMed  Google Scholar 

  11. Xiao, H. et al. Binding of basal transcription factor TFIIH to the acidic activation domains of VP16 and p53. Mol. Cell. Biol. 14, 7013–7024 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Vandel, L. & Kouzarides, T. Residues phosphorylated by TFIIH are required for E2F-1 degradation during S-phase. EMBO J. 18, 4280–4291 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Chen, D. et al. Activation of estrogen receptor alpha by S118 phosphorylation involves a ligand-dependent interaction with TFIIH and participation of CDK7. Mol. Cell 6, 127–137 (2000).

    Article  CAS  PubMed  Google Scholar 

  14. Yokoi, M. et al. The xeroderma pigmentosum group C protein complex XPC-HR23B plays an important role in the recruitment of transcription factor IIH to damaged DNA. J. Biol. Chem. 275, 9870–9875 (2000).

    Article  CAS  PubMed  Google Scholar 

  15. Iyer, N., Reagan, M.S., Wu, K.J., Canagarajah, B. & Friedberg, E.C. Interactions involving the human RNA polymerase II transcription/nucleotide excision repair complex TFIIH, the nucleotide excision repair protein XPG, and Cockayne syndrome group B (CSB) protein. Biochemistry 35, 2157–2167 (1996).

    Article  CAS  PubMed  Google Scholar 

  16. Gervais, V., Lamour, V., Gaudin, F., Thierry, J.C. & Kieffer, B. Assignment of the 1H, 15N, 13C resonances of the N-terminal domain of the human TFIIH p62 subunit. J. Biomol. NMR 19, 281–282 (2001).

    Article  CAS  PubMed  Google Scholar 

  17. Ruckert, M. & Otting, G.J. Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments. J. Am. Chem. Soc. 122, 7793–7797 (2000).

    Article  Google Scholar 

  18. Tjandra, N., Wingfield, P., Stahl, S. & Bax, A. Anisotropic rotational diffusion of perdeuterated HIV protease from 15N NMR relaxation measurements at two magnetic fields. J. Biomol. NMR 8, 273–284 (1996).

    Article  CAS  PubMed  Google Scholar 

  19. Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. J Mol. Biol. 233, 123–138 (1993).

    Article  CAS  PubMed  Google Scholar 

  20. Blomberg, N., Baraldi, E., Nilges, M. & Saraste, M. The PH superfold: a structural scaffold for multiple functions. Trends Biochem. Sci. 24, 441–445 (1999).

    Article  CAS  PubMed  Google Scholar 

  21. Dhe-Paganon, S., Ottinger, E.A., Nolte, R.T., Eck, M.J. & Shoelson, S.E. Crystal structure of the pleckstrin homology-phosphotyrosine binding (PH-PTB) targeting region of insulin receptor substrate 1. Proc. Natl. Acad. Sci. USA 96, 8378–8383 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Pearson, M.A., Reczek, D., Bretscher, A. & Karplus, P.A. Structure of the ERM protein moesin reveals the FERM domain fold masked by an extended actin binding tail domain. Cell 101, 259–270 (2000).

    Article  CAS  PubMed  Google Scholar 

  23. Ferguson, K.M. et al. Structural basis for discrimination of 3-phosphoinositides by pleckstrin homology domains. Mol. Cell 6, 373–384 (2000).

    Article  CAS  PubMed  Google Scholar 

  24. Araujo, S.J. et al. Nucleotide excision repair of DNA with recombinant human proteins: definition of the minimal set of factors, active forms of TFIIH, and modulation by CAK. Genes Dev. 14, 349–359 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Jawhari, A. et al. p52 mediates XPB function within the transcription/repair factor TFIIH. J. Biol. Chem. 277, 31761–31767 (2002).

    Article  CAS  PubMed  Google Scholar 

  26. Coin, F. et al. Mutations in the XPD helicase gene result in XP and TTD phenotypes, preventing interaction between XPD and the p44 subunit of TFIIH. Nat. Genet. 20, 184–188 (1998).

    Article  CAS  PubMed  Google Scholar 

  27. Seroz, T., Perez, C., Bergmann, E., Bradsher, J. & Egly, J.M. p44/SSL1, the regulatory subunit of the XPD/RAD3 helicase, plays a crucial role in the transcriptional activity of TFIIH. J. Biol. Chem. 275, 33260–33266 (2000).

    Article  CAS  PubMed  Google Scholar 

  28. Yan, K.S., Kuti, M. & Zhou, M.M. PTB or not PTB? that is the question. FEBS Lett. 513, 67–70 (2002).

    Article  CAS  PubMed  Google Scholar 

  29. Schmidt, A. & Hall, A. The Rho exchange factor Net1 is regulated by nuclear sequestration. J. Biol. Chem. 277, 14581–14588 (2002).

    Article  CAS  PubMed  Google Scholar 

  30. Tanaka, K. et al. Evidence that a phosphatidylinositol 3,4,5-trisphosphate-binding protein can function in nucleus. J. Biol. Chem. 274, 3919–3922 (1999).

    Article  CAS  PubMed  Google Scholar 

  31. Irvine, R.F. Nuclear lipid signalling. Nat. Rev. Mol. Cell Biol. 4, 349–360 (2003).

    Article  CAS  PubMed  Google Scholar 

  32. Cook, P.R. The organization of replication and transcription. Science 284, 1790–1795 (1999).

    Article  CAS  PubMed  Google Scholar 

  33. Araujo, S.J., Nigg, E.A. & Wood, R.D. Strong functional interactions of TFIIH with XPC and XPG in human DNA nucleotide excision repair, without a preassembled repairosome. Mol. Cell Biol. 21, 2281–2291 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Winkler, G.S., Sugasawa, K., Eker, A.P., de Laat, W.L. & Hoeijmakers, J.H. Novel functional interactions between nucleotide excision DNA repair proteins influencing the enzymatic activities of TFIIH, XPG, and ERCC1-XPF. Biochemistry 40, 160–165 (2001).

    Article  CAS  PubMed  Google Scholar 

  35. Cornilescu, G., Delaglio, F. & Bax, A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13, 289–302 (1999).

    Article  CAS  PubMed  Google Scholar 

  36. Vuister, G.W., Delaglio, F. & Bax, A. The use of 1JCα-Hα coupling constants as a probe for protein backbone conformation. J. Biomol. NMR 3, 67–80 (1993).

    CAS  PubMed  Google Scholar 

  37. Ottiger, M., Delaglio, F. & Bax, A. Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. J. Magn. Reson. 131, 373–378 (1998).

    Article  CAS  PubMed  Google Scholar 

  38. Clore, G.M., Gronenborn, A.M. & Tjandra, N. Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude. J. Magn. Reson. 131, 159–162 (1998).

    Article  CAS  PubMed  Google Scholar 

  39. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998).

    Article  CAS  PubMed  Google Scholar 

  40. Nilges, M., Macias, M.J., O'Donoghue, S.I. & Oschkinat, H. Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J. Mol. Biol. 269, 408–422 (1997).

    Article  CAS  PubMed  Google Scholar 

  41. Schwieters, C.D., Kuszewski, J.J., Tjandra, N. & Clore, G.M. The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 160, 65–73 (2003).

    Article  CAS  PubMed  Google Scholar 

  42. Koradi, R., Billeter, M. & Wuthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51–55 (1996).

    Article  CAS  PubMed  Google Scholar 

  43. Laskowski, R.A., Rullman, J.A., MacArthur, M.W., Kaptein, R. & Thornton, J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477–486 (1996).

    Article  CAS  PubMed  Google Scholar 

  44. Vriend, G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8, 52–56 (1990).

    Article  CAS  PubMed  Google Scholar 

  45. Jawhari, A. et al. Expression of FLAG fusion proteins in insect cells: application to the multi-subunit transcription/DNA repair factor TFIIH. Protein Expr. Purif. 24, 513–523 (2002).

    Article  CAS  PubMed  Google Scholar 

  46. Gerard, M. et al. Purification and interaction properties of the human RNA polymerase B(II) general transcription factor BTF2. J. Biol. Chem. 266, 20940–20945 (1991).

    CAS  PubMed  Google Scholar 

  47. Shivji, M.K., Moggs, J.G., Kuraoka, I. & Wood, R.D. Dual-incision assays for nucleotide excision repair using DNA with a lesion at a specific site. Methods Mol. Biol. 113, 373–392 (1999).

    CAS  PubMed  Google Scholar 

  48. Thompson, J.D., Plewniak, F., Thierry, J.C. & Poch, O. DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res. 28, 2919–2926 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Holm, L. & Sander, C. Alignment of three-dimensional protein structures: network server for database searching. Methods Enzymol. 266, 653–662 (1996).

    Article  CAS  PubMed  Google Scholar 

  50. Clore, G.M. & Garrett, D.S. R-factor, Free R, and complete cross-validation for dipolar coupling refinement of NMR structures. J. Am. Chem. Soc. 121, 9008–9012 (1999).

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by funds from the Université Louis Pasteur de Strasbourg, the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale and SPINE (contract QLG2-CT-2002-00988). V.G. was supported by a grant from ADRERUS/LILLY and by the Ministère de la Recherche et de l'Enseignement Supérieur and A.J. by the Association pour la Recherche contre le Cancer. We express our gratitude to D. Moras for constant support and fruitful discussions. We wish to acknowledge A. Milon at the IPBS in Toulouse for his hospitality during structure calculations. I. Kolb and J.L. Weickert are acknowledged for insect cell production. We are grateful to C. Ling for the management of the computing and NMR facilities and to R.A. Atkinson for critical reading of the manuscript.

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Author notes

  1. Virginie Gervais

    Present address: Institut de Pharmacologie et de Biologie Structurale, 205 Rte de Narbonne, 31077, Toulouse Cedex, France

  2. Valérie Lamour

    Present address: Rockefeller University, 1230 York Avenue, New York, New York, 10021-6399, USA

  3. Virginie Gervais, Valérie Lamour and Anass Jawhari: These authors contributed equally to this work.

Authors and Affiliations

  1. Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104, 1 Rue Laurent Fries, BP 10142, Illkirch, 67404, Cedex, France

    Virginie Gervais, Valérie Lamour, Anass Jawhari, Florent Frindel, Emeric Wasielewski, Sandy Dubaele, Jean-Marc Egly, Jean-Claude Thierry, Bruno Kieffer & Arnaud Poterszman

  2. Institut de Pharmacologie et de Biologie Structurale, 205 Rte de Narbonne, 31077, Toulouse Cedex, France

    Valérie Lamour

  3. Rockefeller University, 1230 York Avenue, New York, New York, 10021-6399, USA

    Virginie Gervais

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Supplementary information

Supplementary Fig. 1

Secondary structure elements of p62(1–108). (PDF 34 kb)

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Gervais, V., Lamour, V., Jawhari, A. et al. TFIIH contains a PH domain involved in DNA nucleotide excision repair. Nat Struct Mol Biol 11, 616–622 (2004). https://doi.org/10.1038/nsmb782

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