Skip to main content
Biochemical Journal logoLink to Biochemical Journal
. 2004 Mar 1;378(Pt 2):317–324. doi: 10.1042/BJ20031706

Probing Zn2+-binding effects on the zinc-ribbon domain of human general transcription factor TFIIB.

Mahua Ghosh 1, Laura M Elsby 1, Tapas K Mal 1, Jane M Gooding 1, Stefan G E Roberts 1, Mitsuhiko Ikura 1
PMCID: PMC1223989  PMID: 14641108

Abstract

The general transcription factor, TFIIB, plays an important role in the assembly of the pre-initiation complex. The N-terminal domain (NTD) of TFIIB contains a zinc-ribbon motif, which is responsible for the recruitment of RNA polymerase II and TFIIF to the core promoter region. Although zinc-ribbon motif structures of eukaryotic and archaeal TFIIBs have been reported previously, the structural role of Zn2 binding to TFIIB remains to be determined. In the present paper, we report NMR and biochemical studies of human TFIIB NTD, which characterize the structure and dynamics of the TFIIB Zn2-binding domain in both Zn2-bound and -free states. The NMR data show that, whereas the backbone fold of NTD is pre-formed in the apo state, Zn2 binding reduces backbone mobility in the b-turn (Arg28-Gly30), induces enhanced structural rigidity of the charged-cluster domain in the central linker region of TFIIB and appends a positive surface charge within the Zn2-binding site. V8 protease-sensitivity assays of full-length TFIIB support the Zn2-dependent structural changes. These structural effects of Zn2 binding on TFIIB may have a critical role in interactions with its binding partners, such as the Rpb1 subunit of RNA polymerase II.

Full Text

The Full Text of this article is available as a PDF (344.6 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Agostini I., Navarro J. M., Bouhamdan M., Willetts K., Rey F., Spire B., Vigne R., Pomerantz R., Sire J. The HIV-1 Vpr co-activator induces a conformational change in TFIIB. FEBS Lett. 1999 May 7;450(3):235–239. doi: 10.1016/s0014-5793(99)00501-3. [DOI] [PubMed] [Google Scholar]
  2. Armache Karim-Jean, Kettenberger Hubert, Cramer Patrick. Architecture of initiation-competent 12-subunit RNA polymerase II. Proc Natl Acad Sci U S A. 2003 May 13;100(12):6964–6968. doi: 10.1073/pnas.1030608100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bagby S., Kim S., Maldonado E., Tong K. I., Reinberg D., Ikura M. Solution structure of the C-terminal core domain of human TFIIB: similarity to cyclin A and interaction with TATA-binding protein. Cell. 1995 Sep 8;82(5):857–867. doi: 10.1016/0092-8674(95)90483-2. [DOI] [PubMed] [Google Scholar]
  4. Bax A., Kontaxis G., Tjandra N. Dipolar couplings in macromolecular structure determination. Methods Enzymol. 2001;339:127–174. doi: 10.1016/s0076-6879(01)39313-8. [DOI] [PubMed] [Google Scholar]
  5. Berg J. M. Zinc finger domains: hypotheses and current knowledge. Annu Rev Biophys Biophys Chem. 1990;19:405–421. doi: 10.1146/annurev.bb.19.060190.002201. [DOI] [PubMed] [Google Scholar]
  6. Brünger A. T., Adams P. D., Clore G. M., DeLano W. L., Gros P., Grosse-Kunstleve R. W., Jiang J. S., Kuszewski J., Nilges M., Pannu N. S. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905–921. doi: 10.1107/s0907444998003254. [DOI] [PubMed] [Google Scholar]
  7. Buratowski S., Hahn S., Guarente L., Sharp P. A. Five intermediate complexes in transcription initiation by RNA polymerase II. Cell. 1989 Feb 24;56(4):549–561. doi: 10.1016/0092-8674(89)90578-3. [DOI] [PubMed] [Google Scholar]
  8. Chen H. T., Legault P., Glushka J., Omichinski J. G., Scott R. A. Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription. Protein Sci. 2000 Sep;9(9):1743–1752. doi: 10.1110/ps.9.9.1743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chen Hung-Ta, Hahn Steven. Binding of TFIIB to RNA polymerase II: Mapping the binding site for the TFIIB zinc ribbon domain within the preinitiation complex. Mol Cell. 2003 Aug;12(2):437–447. doi: 10.1016/s1097-2765(03)00306-x. [DOI] [PubMed] [Google Scholar]
  10. Chou J. J., Li S., Bax A. Study of conformational rearrangement and refinement of structural homology models by the use of heteronuclear dipolar couplings. J Biomol NMR. 2000 Nov;18(3):217–227. doi: 10.1023/a:1026563923774. [DOI] [PubMed] [Google Scholar]
  11. 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. 1998 Mar;131(1):159–162. doi: 10.1006/jmre.1997.1345. [DOI] [PubMed] [Google Scholar]
  12. Cramer P., Bushnell D. A., Fu J., Gnatt A. L., Maier-Davis B., Thompson N. E., Burgess R. R., Edwards A. M., David P. R., Kornberg R. D. Architecture of RNA polymerase II and implications for the transcription mechanism. Science. 2000 Apr 28;288(5466):640–649. doi: 10.1126/science.288.5466.640. [DOI] [PubMed] [Google Scholar]
  13. Cramer P., Bushnell D. A., Kornberg R. D. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science. 2001 Apr 19;292(5523):1863–1876. doi: 10.1126/science.1059493. [DOI] [PubMed] [Google Scholar]
  14. Delaglio F., Grzesiek S., Vuister G. W., Zhu G., Pfeifer J., Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR. 1995 Nov;6(3):277–293. doi: 10.1007/BF00197809. [DOI] [PubMed] [Google Scholar]
  15. Fairley Jennifer A., Evans Rachel, Hawkes Nicola A., Roberts Stefan G. E. Core promoter-dependent TFIIB conformation and a role for TFIIB conformation in transcription start site selection. Mol Cell Biol. 2002 Oct;22(19):6697–6705. doi: 10.1128/MCB.22.19.6697-6705.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Farrow N. A., Muhandiram R., Singer A. U., Pascal S. M., Kay C. M., Gish G., Shoelson S. E., Pawson T., Forman-Kay J. D., Kay L. E. Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry. 1994 May 17;33(19):5984–6003. doi: 10.1021/bi00185a040. [DOI] [PubMed] [Google Scholar]
  17. Foster M. P., Wuttke D. S., Clemens K. R., Jahnke W., Radhakrishnan I., Tennant L., Reymond M., Chung J., Wright P. E. Chemical shift as a probe of molecular interfaces: NMR studies of DNA binding by the three amino-terminal zinc finger domains from transcription factor IIIA. J Biomol NMR. 1998 Jul;12(1):51–71. doi: 10.1023/a:1008290631575. [DOI] [PubMed] [Google Scholar]
  18. Freedman L. P., Luisi B. F., Korszun Z. R., Basavappa R., Sigler P. B., Yamamoto K. R. The function and structure of the metal coordination sites within the glucocorticoid receptor DNA binding domain. Nature. 1988 Aug 11;334(6182):543–546. doi: 10.1038/334543a0. [DOI] [PubMed] [Google Scholar]
  19. Gnatt A. L., Cramer P., Fu J., Bushnell D. A., Kornberg R. D. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science. 2001 Apr 19;292(5523):1876–1882. doi: 10.1126/science.1059495. [DOI] [PubMed] [Google Scholar]
  20. Ha I., Roberts S., Maldonado E., Sun X., Kim L. U., Green M., Reinberg D. Multiple functional domains of human transcription factor IIB: distinct interactions with two general transcription factors and RNA polymerase II. Genes Dev. 1993 Jun;7(6):1021–1032. doi: 10.1101/gad.7.6.1021. [DOI] [PubMed] [Google Scholar]
  21. Hahn S., Roberts S. The zinc ribbon domains of the general transcription factors TFIIB and Brf: conserved functional surfaces but different roles in transcription initiation. Genes Dev. 2000 Mar 15;14(6):719–730. [PMC free article] [PubMed] [Google Scholar]
  22. Hawkes N. A., Evans R., Roberts S. G. The conformation of the transcription factor TFIIB modulates the response to transcriptional activators in vivo. Curr Biol. 2000 Mar 9;10(5):273–276. doi: 10.1016/s0960-9822(00)00363-8. [DOI] [PubMed] [Google Scholar]
  23. Hayashi F., Ishima R., Liu D., Tong K. I., Kim S., Reinberg D., Bagby S., Ikura M. Human general transcription factor TFIIB: conformational variability and interaction with VP16 activation domain. Biochemistry. 1998 Jun 2;37(22):7941–7951. doi: 10.1021/bi9801098. [DOI] [PubMed] [Google Scholar]
  24. Knaus R., Pollock R., Guarente L. Yeast SUB1 is a suppressor of TFIIB mutations and has homology to the human co-activator PC4. EMBO J. 1996 Apr 15;15(8):1933–1940. [PMC free article] [PubMed] [Google Scholar]
  25. Koradi R., Billeter M., Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph. 1996 Feb;14(1):51-5, 29-32. doi: 10.1016/0263-7855(96)00009-4. [DOI] [PubMed] [Google Scholar]
  26. Laity J. H., Lee B. M., Wright P. E. Zinc finger proteins: new insights into structural and functional diversity. Curr Opin Struct Biol. 2001 Feb;11(1):39–46. doi: 10.1016/s0959-440x(00)00167-6. [DOI] [PubMed] [Google Scholar]
  27. Nicholls A., Sharp K. A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 1991;11(4):281–296. doi: 10.1002/prot.340110407. [DOI] [PubMed] [Google Scholar]
  28. Nikolov D. B., Chen H., Halay E. D., Usheva A. A., Hisatake K., Lee D. K., Roeder R. G., Burley S. K. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature. 1995 Sep 14;377(6545):119–128. doi: 10.1038/377119a0. [DOI] [PubMed] [Google Scholar]
  29. Ohkuma Y., Sumimoto H., Hoffmann A., Shimasaki S., Horikoshi M., Roeder R. G. Structural motifs and potential sigma homologies in the large subunit of human general transcription factor TFIIE. Nature. 1991 Dec 5;354(6352):398–401. doi: 10.1038/354398a0. [DOI] [PubMed] [Google Scholar]
  30. Olmsted V. K., Awrey D. E., Koth C., Shan X., Morin P. E., Kazanis S., Edwards A. M., Arrowsmith C. H. Yeast transcript elongation factor (TFIIS), structure and function. I: NMR structural analysis of the minimal transcriptionally active region. J Biol Chem. 1998 Aug 28;273(35):22589–22594. doi: 10.1074/jbc.273.35.22589. [DOI] [PubMed] [Google Scholar]
  31. Orphanides G., Lagrange T., Reinberg D. The general transcription factors of RNA polymerase II. Genes Dev. 1996 Nov 1;10(21):2657–2683. doi: 10.1101/gad.10.21.2657. [DOI] [PubMed] [Google Scholar]
  32. Ottiger M., Delaglio F., Bax A. Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. J Magn Reson. 1998 Apr;131(2):373–378. doi: 10.1006/jmre.1998.1361. [DOI] [PubMed] [Google Scholar]
  33. Pardee T. S., Bangur C. S., Ponticelli A. S. The N-terminal region of yeast TFIIB contains two adjacent functional domains involved in stable RNA polymerase II binding and transcription start site selection. J Biol Chem. 1998 Jul 10;273(28):17859–17864. doi: 10.1074/jbc.273.28.17859. [DOI] [PubMed] [Google Scholar]
  34. Peterson M. G., Inostroza J., Maxon M. E., Flores O., Admon A., Reinberg D., Tjian R. Structure and functional properties of human general transcription factor IIE. Nature. 1991 Dec 5;354(6352):369–373. doi: 10.1038/354369a0. [DOI] [PubMed] [Google Scholar]
  35. Qian X., Gozani S. N., Yoon H., Jeon C. J., Agarwal K., Weiss M. A. Novel zinc finger motif in the basal transcriptional machinery: three-dimensional NMR studies of the nucleic acid binding domain of transcriptional elongation factor TFIIS. Biochemistry. 1993 Sep 28;32(38):9944–9959. doi: 10.1021/bi00089a010. [DOI] [PubMed] [Google Scholar]
  36. Roberts S. G., Green M. R. Activator-induced conformational change in general transcription factor TFIIB. Nature. 1994 Oct 20;371(6499):717–720. doi: 10.1038/371717a0. [DOI] [PubMed] [Google Scholar]
  37. Roeder R. G. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci. 1996 Sep;21(9):327–335. [PubMed] [Google Scholar]
  38. Schwabe J. W., Klug A. Zinc mining for protein domains. Nat Struct Biol. 1994 Jun;1(6):345–349. doi: 10.1038/nsb0694-345. [DOI] [PubMed] [Google Scholar]
  39. Tjandra N., Bax A. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science. 1997 Nov 7;278(5340):1111–1114. doi: 10.1126/science.278.5340.1111. [DOI] [PubMed] [Google Scholar]
  40. Tolman J. R., Flanagan J. M., Kennedy M. A., Prestegard J. H. Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution. Proc Natl Acad Sci U S A. 1995 Sep 26;92(20):9279–9283. doi: 10.1073/pnas.92.20.9279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Vorherr T., James P., Krebs J., Enyedi A., McCormick D. J., Penniston J. T., Carafoli E. Interaction of calmodulin with the calmodulin binding domain of the plasma membrane Ca2+ pump. Biochemistry. 1990 Jan 16;29(2):355–365. doi: 10.1021/bi00454a008. [DOI] [PubMed] [Google Scholar]
  42. Wang B., Jones D. N., Kaine B. P., Weiss M. A. High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases. Structure. 1998 May 15;6(5):555–569. doi: 10.1016/s0969-2126(98)00058-6. [DOI] [PubMed] [Google Scholar]
  43. Wishart D. S., Sykes B. D., Richards F. M. The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry. 1992 Feb 18;31(6):1647–1651. doi: 10.1021/bi00121a010. [DOI] [PubMed] [Google Scholar]
  44. Xiao H., Friesen J. D., Lis J. T. A highly conserved domain of RNA polymerase II shares a functional element with acidic activation domains of upstream transcription factors. Mol Cell Biol. 1994 Nov;14(11):7507–7516. doi: 10.1128/mcb.14.11.7507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Zawel L., Reinberg D. Common themes in assembly and function of eukaryotic transcription complexes. Annu Rev Biochem. 1995;64:533–561. doi: 10.1146/annurev.bi.64.070195.002533. [DOI] [PubMed] [Google Scholar]
  46. Zhang Dong-Yi, Carson Daniel J., Ma Jun. The role of TFIIB-RNA polymerase II interaction in start site selection in yeast cells. Nucleic Acids Res. 2002 Jul 15;30(14):3078–3085. doi: 10.1093/nar/gkf422. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Biochemical Journal are provided here courtesy of The Biochemical Society

RESOURCES