Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20

Nature Structural and Molecular Biology

Volumn 13, Issue 10, 2006, Pages 895-901

  Larivière, Laurent ^a   Geiger, Sebastian ^a   Hoeppner, Sabine ^a   Röther, Susanne ^a   Sträßer, Katja ^a   Cramer, Patrick ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MEDIATOR HEAD SUBCOMPLEX PROTEIN; PROTEIN MED18; PROTEIN MED20; PROTEIN MED8; PROTEIN SUBUNIT; TATA BINDING PROTEIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; ESCHERICHIA COLI; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; X RAY ANALYSIS;

AMINO ACID SEQUENCE; BINDING SITES; DIMERIZATION; MEDIATOR COMPLEX; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; RNA POLYMERASE II; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURE-ACTIVITY RELATIONSHIP; TATA-BOX BINDING PROTEIN; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 33749514827     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb1143     Document Type: Article

References (49)

1. Malik, S. & Roeder, R.G. Transcriptional regulation through Mediator-like coactivators in yeast and metazoan cells. Trends Biochem. Sci. 25, 277-283 (2000).
2. Bjorklund, S. & Gustafsson, C.M. The mediator complex. Adv. Protein Chem. 67, 43-65 (2004).
3. Naar, A.M., Lemon, B.D. & Tjian, R. Transcriptional coactivator complexes. Annu. Rev. Biochem. 70, 475-501 (2001).
4. Kornberg, R.D. Mediator and the mechanism of transcriptional activation. Trends Biochem. Sci. 30, 235-239 (2005).
5. Bourbon, H.M. et al. A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol. Cell 14, 553-557 (2004).
6. Boube, M., Joulia, L., Cribbs, D.L. & Bourbon, H.M. Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man. Cell 110, 143-151 (2002).
7. Nonet, M.L. & Young, R.A. Intragenic and extragenic suppressors of mutations in the heptapeptide repeat domain of Saccharomyces cerevisiae RNA polymerase II. Genetics 123, 715-725 (1989).
8. Thompson, C.M., Koleske, A.J., Chao, D.M. & Young, R.A. A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast. Cell 73, 1361-1375 (1993).
9. Guglielmi, B. et al. A high resolution protein interaction map of the yeast Mediator complex. Nucleic Acids Res. 32, 5379-5391 (2004).
10. Kang, J.S. et al. The structural and functional organization of the yeast mediator complex. J. Biol. Chem. 276, 42003-42010 (2001).
11. Dotson, M.R. et al. Structural organization of yeast and mammalian mediator complexes. Proc. Natl. Acad. Sci. USA 97, 14307-14310 (2000).
12. Cantin, G.T., Stevens, J.L. & Berk, A.J. Activation domain-mediator interactions promote transcription preinitiation complex assembly on promoter DNA. Proc. Natl. Acad. Sci. USA 100, 12003-12008 (2003).
13. Ranish, J.A., Yudkovsky, N. & Hahn, S. Intermediates in formation and activity of the RNA polymerase II preinitiation complex: holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB. Genes Dev. 13, 49-63 (1999).
14. Holstege, F.C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717-728 (1998).
15. Takagi, Y. & Kornberg, R.D. Mediator as a general transcription factor. J. Biol. Chem. 281, 80-89 (2006).
16. Lee, Y.C., Park, J.M., Min, S., Han, S.J. & Kim, Y.J. An activator binding module of yeast RNA polymerase II holoenzyme. Mol. Cell. Biol. 19, 2967-2976 (1999).
17. Koleske, A.J., Buratowski, S., Nonet, M. & Young, R.A. A novel transcription factor reveals a functional link between the RNA polymerase II CTD and TFIID. Cell 69, 883-894 (1992).
18. Koh, S.S., Ansari, A.Z., Ptashne, M. & Young, R.A. An activator target in the RNA polymerase II holoenzyme. Mol. Cell 1, 895-904 (1998).
19. Lee, T.I. et al. Interplay of positive and negative regulators in transcription initiation by RNA polymerase II holoenzyme. Mol. Cell. Biol. 18, 4455-4462 (1998).
20. Holm, L. & Sander, C. Dali: a network tool for protein structure comparison. Trends Biochem. Sci. 20, 478-480 (1995).
21. Lima, C.D., Wang, L.K. & Shuman, S. Structure and mechanism of yeast RNA triphosphatase: an essential component of the mRNA capping apparatus. Cell 99, 533-543 (1999).
22. Sismeiro, O., Trotot, P., Biville, F., Vivares, C. & Danchin, A. Aeromonas hydrophila adenylyl cyclase 2: a new class of adenylyl cyclases with thermophilic properties and sequence similarities to proteins from hyperthermophilic archaebacteria. J. Bacteriol. 180, 3339-3344 (1998).
23. Iyer, L.M. & Aravind, L. The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclase define a novel superfamily of domains that bind organic phosphates. BMC Genomics 3, 33 (2002).
24. Brower, C.S. et al. Mammalian mediator subunit mMED8 is an Elongin BC-interacting protein that can assemble with Cul2 and Rbx1 to reconstitute a ubiquitin ligase. Proc. Natl. Acad. Sci. USA 99, 10353-10358 (2002).
25. Baumli, S., Hoeppner, S. & Cramer, P. A conserved mediator hinge revealed in the structure of the MED7/MED21 (Med7/Srb7) heterodimer. J. Biol. Chem. 280, 18171-18178 (2005).
26. Hoeppner, S., Baumli, S. & Cramer, P. Structure of the mediator subunit cyclin C and its implications for CDK8 function. J. Mol. Biol. 350, 833-842 (2005).
27. van de Peppel, J. et al. Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets. Mol. Cell 19, 511-522 (2005).
28. Yudkovsky, N., Ranish, J.A. & Hahn, S. A transcription reinitiation intermediate that is stabilized by activator. Nature 408, 225-229 (2000).
29. Zhu, X. et al. Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions. Mol. Cell 22, 169-178 (2006).
30. Andrau, J.C. et al. Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA. Mol. Cell 22, 179-192 (2006).
31. Johnson, K.M. & Carey, M. Assembly of a mediator/TFIID/TFIIA complex bypasses the need for an activator. Curr. Biol. 13, 772-777 (2003).
32. Wu, S.Y., Zhou, T. & Chiang, C.M. Human mediator enhances activator-facilitated recruitment of RNA polymerase II and promoter recognition by TATA-binding protein (TBP) independently of TBP-associated factors. Mol. Cell. Biol. 23, 6229-6242 (2003).
33. Taatjes, D.J., Naar, A.M., Andel, F., III, Nogales, E. & Tjian, R. Structure, function, and activator-induced conformations of the CRSP coactivator. Science 295, 1058-1062 (2002).
34. Liu, Y., Ranish, J.A., Aebersold, R. & Hahn, S. Yeast nuclear extract contains two major forms of RNA polymerase II mediator complexes. J. Biol. Chem. 276, 7169-7175 (2001).
35. Budisa, N. et al. High-level biosynthetic substitution of methionine in proteins by its analogs 2-aminohexanoic acid, selenomethionine, telluromethionine and ethionine in Escherichia coli. Eur. J. Biochem. 230, 788-796 (1995).
36. Meinhart, A., Blobel, J. & Cramer, P. An extended winged helix domain in general transcription factor E/IIEalpha. J. Biol. Chem. 278, 48267-48274 (2003).
37. Juo, Z.S., Kassavetis, G.A., Wang, J., Geiduschek, E.P. & Sigler, P.B. Crystal structure of a transcription factor IIIB core interface ternary complex. Nature 422, 534-539 (2003).
38. Armache, K.-J., Kettenberger, H. & Cramer, P. Architecture of the initiation-competent 12-subunit RNA polymerase II. Proc. Natl. Acad. Sci. USA 100, 6964-6968 (2003).
39. Leslie, A. in Joint CCP4 and ESF-EACMB Newsletter on Protein Crystallography No. 26 (Daresbury Laboratory, Warrington, UK, 1992).
40. Terwilliger, T.C. Automated structure solution, density modification and model building. Acta Crystallogr. D Biol. Crystallogr. 58, 1937-1940 (2002).
41. Roussel, A. & Cambillau, C. Turbo-FRODO. in Silicon Graphics Geometry, Partners Directory 77-78 (Silicon Graphics, Mountain View, California, USA, 1989).
42. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905-921 (1998).
43. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Meth. Enzym. 276, 307-326 (1996).
44. McCoy, A.J., Grosse-Kunstleve, R.W., Storoni, L.C. & Read, R.J. Likelihood-enhanced fast translation functions. Acta Crystallogr. D Biol. Crystallogr. 61, 458-464 (2005).
45. Collaborative Computational Project, Number 4. The CCP4 Suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr 50, 760-763 (1994).
46. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291 (1993).
47. Thompson, J.D., Higgins, D.G. & Gibson, T.J. CLUSTAL W: improving the sensibility of progressive multiple sequence alignment through sequence weighing, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994).
48. Gouet, P., Courcelle, E., Stuart, D.I. & Metoz, F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15, 305-308 (1999).
49. DeLano, W.L. The PyMOL Molecular Graphics System (DeLano Scientific, San Carlos, California, USA, 2002).