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Solution NMR structure of MED25(391–543) comprising the activator-interacting domain (ACID) of human mediator subunit 25

  • Alexander Eletsky
  • William T. Ruyechan
  • Rong Xiao
  • Thomas B. Acton
  • Gaetano T. Montelione
  • Thomas Szyperski
Article

Abstract

The solution NMR structure of protein MED25(391–543), comprising the activator interacting domain (ACID) of subunit 25 of the human mediator, is presented along with the measurement of polypeptide backbone heteronuclear 15N-{1H} NOEs to identify fast internal motional modes. This domain interacts with the acidic transactivation domains of Herpes simplex type 1 (HSV-1) protein VP16 and the Varicella-zoster virus (VZV) major transactivator protein IE62, which initiate transcription of viral genes. The structure is similar to the β-barrel domains of the human protein Ku and the SPOC domain of human protein SHARP, and provides a starting point to understand the structural biology of initiation of HSV-1 and VZV gene activation. Homology models built for the two ACID domains of the prostate tumor overexpressed (PTOV1) protein using the structure of MED25(391–543) as a template suggest that differential biological activities of the ACID domains in MED25 and PTOV1 arise from modulation of quite similar protein–protein interactions by variable residues grouped around highly conserved charged surface areas.

Keywords

ACID MED25 Mediator complex PTOV Structural genomics 

Abbreviations

ACID

Activator-interacting domain

CBP

CREB-binding protein

HDAC

Histone deacetylase complex

HSV-1

Herpes simplex virus type 1

NESG

Northeast Structural Genomics Consortium

MED25

Subunit 25 of the human mediator complex

NOE

Nuclear Overhauser effect

PDB

Protein Data Bank

PTOV

Prostate tumor overexpressed

RMSD

Root mean square deviation

SHARP

SMRT/HDAC1-associated repressor protein

SPOC

Spen paralog and ortholog C-terminal domain

TAD

Transactivation domain

VBD

VP16-binding domain

VZV

Varicella-zoster virus

Notes

Acknowledgments

We thank R. Shastry, C. Ciccosanti, H. Janjua, and G.V.T. Swapna for contributions in sample preparation, and J. K. Everett and S. Bhattacharya for helpful discussions. This work was supported by the National Institutes of Health, grant numbers: U54 GM094597 (T.S. and G.T.M.) and R01 AI18449 (W.T.R.). Prof. T. Szyperski is a member of the New York Structural Biology Center. The Center is a STAR center supported by the New York State Office of Science, Technology, and Academic Research. 900 MHz spectrometer was purchased with funds from NIH, USA, the Keck Foundation, New York State, and the NYC Economic Development Corporation. Support was also obtained from the University at Buffalo’s Center for Computational Research.

Supplementary material

10969_2011_9115_MOESM1_ESM.doc (1.1 mb)
Supplementary material 1 (DOC 1170 kb)

References

  1. 1.
    Kim YJ, Bjorklund S, Li Y, Sayre MH, Kornberg RD (1994) A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA-polymerase-II. Cell 77:599–608PubMedCrossRefGoogle Scholar
  2. 2.
    Malik S, Roeder RG (2005) Dynamic regulation of pol II transcription by the mammalian Mediator complex. Trends Biochem Sci 30:256–263PubMedCrossRefGoogle Scholar
  3. 3.
    Casamassimi A, Napoli C (2007) Mediator complexes and eukaryotic transcription regulation: an overview. Biochimie 89:1439–1446PubMedCrossRefGoogle Scholar
  4. 4.
    Conaway RC, Sato S, Tomomori-Sato C, Yao TT, Conaway JW (2005) The mammalian Mediator complex and its role in transcriptional regulation. Trends Biochem Sci 30:250–255PubMedCrossRefGoogle Scholar
  5. 5.
    Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, Bjorklund S, Blackwell TK, Borggrefe T, Carey M, Carlson M, Conaway JW, Conaway RC, Emmons SW, Fondell JD, Freedman LP, Fukasawa T, Gustafsson CM, Han M, He X, Herman PK, Hinnebusch AG, Holmberg S, Holstege FC, Jaehning JA, Kim YJ, Kuras L, Leutz A, Lis JT, Meisterernest M, Naar AM, Nasmyth K, Parvin JD, Ptashne M, Reinberg D, Ronne H, Sadowski I, Sakurai H, Sipiczki M, Sternberg PW, Stillman DJ, Strich R, Struhl K, Svejstrup JQ, Tuck S, Winston F, Roeder RG, Kornberg RD (2004) A unified nomenclature for protein subunits of Mediator complexes linking transcriptional regulators to RNA polymerase II. Mol Cell 14:553–557PubMedCrossRefGoogle Scholar
  6. 6.
    Mittler G, Stuhler T, Santolin L, Uhlmann T, Kremmer E, Lottspeich F, Berti L, Meisterernst M (2003) A novel docking site on Mediator is critical for activation by VP16 in mammalian cells. EMBO J 22:6494–6504PubMedCrossRefGoogle Scholar
  7. 7.
    Yang FJ, DeBeaumont R, Zhou S, Naar AM (2004) The activator-recruited cofactor/Mediator coactivator subunit ARC92 is a functionally important target of the VP16 transcriptional activator. Proc Natl Acad Sci USA 101:2339–2344PubMedCrossRefGoogle Scholar
  8. 8.
    Yang M, Hay J, Ruyechan WT (2008) Varicella-zoster virus IE62 protein utilizes the human mediator complex in promoter activation. J Virol 82:12154–12163PubMedCrossRefGoogle Scholar
  9. 9.
    Yamamoto S, Eletsky A, Szyperski T, Hay J, Ruyechan WT (2009) Analysis of the varicella-zoster virus IE62N-terminal acidic transactivating domain and its interaction with the human mediator complex. J Virol 83:6300–6305PubMedCrossRefGoogle Scholar
  10. 10.
    Taatjes DJ (2010) The human mediator complex: a versatile, genome-wide regulator of transcription. Trends Biochem Sci 35:315–322PubMedCrossRefGoogle Scholar
  11. 11.
    Perera LP, Mosca JD, Ruyechan WT, Hayward GS, Straus SE, Hay J (1993) A major transactivator of varicella-zoster virus, the immediate-early protein IE62, contains a potent N-terminal activation domain. J Virol 67:4474–4483PubMedGoogle Scholar
  12. 12.
    Jonker HRA, Wechselberger RW, Boelens R, Folkers GE, Kaptein R (2005) Structural properties of the promiscuous VP16 activation domain. Biochemistry 44:827–839PubMedCrossRefGoogle Scholar
  13. 13.
    Lee HK, Park UH, Kim EJ, Um SJ (2007) MED25 is distinct from TRAP220/MED1 in cooperating with CBP for retinoid receptor activation. EMBO J 26:3545–3557PubMedCrossRefGoogle Scholar
  14. 14.
    Cress WD, Triezenberg SJ (1991) Critical structural elements of the VP16 transcriptional activation domain. Science 251:87–90PubMedCrossRefGoogle Scholar
  15. 15.
    Hermann S, Berndt KD, Wright AP (2001) How transcriptional activators bind target proteins. J Biol Chem 276:40127–40132PubMedCrossRefGoogle Scholar
  16. 16.
    Ferreira ME, Hermann S, Prochasson P, Workman JL, Berndt KD, Wright APH (2005) Mechanism of transcription factor recruitment by acidic activators. J Biol Chem 280:21779–21784PubMedCrossRefGoogle Scholar
  17. 17.
    Langlois C, Mas C, Di Lello P, Jenkins LMM, Legault P, Omichinski JG (2008) NMR structure of the complex between the Tfb1 subunit of TFIIH and the activation domain of VP16: structural similarities between VP16 and p53. J Am Chem Soc 130:10596–10604PubMedCrossRefGoogle Scholar
  18. 18.
    Rana R, Surapureddi S, Kam W, Ferguson S, Goldstein JA (2011) Med25 is required for RNA Pol II recruitment to specific promoters thus regulating xenobiotic and lipid metabolism in human liver. Mol Cell Biol 31:466–481PubMedCrossRefGoogle Scholar
  19. 19.
    Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer ELL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucleic Acids Res 38:D211–D222PubMedCrossRefGoogle Scholar
  20. 20.
    Benedit P, Paciucci R, Thomson TM, Valeri M, Nadal M, Caceres C, de Torres I, Estivill X, Lozano JJ, Morote J, Reventos J (2001) PTOV1, a novel protein overexpressed in prostate cancer containing a new class of protein homology blocks. Oncogene 20:1455–1464PubMedCrossRefGoogle Scholar
  21. 21.
    Acton TB, Gunsalus KC, Xiao R, Ma LC, Aramini J, Baran MC, Chiang YW, Climent T, Cooper B, Denissova NG, Douglas SM, Everett JK, Ho CK, Macapagal D, Rajan PK, Shastry R, Shih LY, Swapna GVT, Wilson M, Wu M, Gerstein M, Inouye M, Hunt JF, Montelione GT (2005) Robotic cloning and protein production platform of the Northeast Structural Genomics Consortium. In: Nuclear magnetic resonance of biological macromolecules, Part C. Elsevier, San Diego, pp 210–243Google Scholar
  22. 22.
    Xiao R, Anderson S, Aramini J, Belote R, Buchwald WA, Ciccosanti C, Conover K, Everett JK, Hamilton K, Huang YJ, Janjua H, Jiang M, Kornhaber GJ, Lee DY, Locke JY, Ma LC, Maglaqui M, Mao L, Mitra S, Patel D, Rossi P, Sahdev S, Sharma S, Shastry R, Swapna GVT, Tong SN, Wang DY, Wang HA, Zhao L, Montelione GT, Acton TB (2010) The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium. J Struct Biol 172:21–33PubMedCrossRefGoogle Scholar
  23. 23.
    Neri D, Szyperski T, Otting G, Senn H, Wuthrich K (1989) Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling. Biochemistry 28:7510–7516PubMedCrossRefGoogle Scholar
  24. 24.
    Cavanagh J, Fairbrother WJ, Palmer AG III, Rance M, Skelton NJ (2007) Protein NMR spectroscopy: principles and practice. Academic Press, AmsterdamGoogle Scholar
  25. 25.
    Shen Y, Atreya HS, Liu GH, Szyperski T (2005) G-matrix Fourier transform NOESY-based protocol for high-quality protein structure determination. J Am Chem Soc 127:9085–9099PubMedCrossRefGoogle Scholar
  26. 26.
    Yamazaki T, Formankay JD, Kay LE (1993) 2-Dimensional NMR experiments for correlating C-13-beta and H-1-delta/epsilon chemical-shifts of aromatic residues in C-13-labeled proteins via scalar couplings. J Am Chem Soc 115:11054–11055CrossRefGoogle Scholar
  27. 27.
    Renner C, Schleicher M, Moroder L, Holak TA (2002) Practical aspects of the 2D N-15-{H-1}-NOE experiment. J Biomol NMR 23:23–33PubMedCrossRefGoogle Scholar
  28. 28.
    du Penhoat CH, Li Z, Atreya HS, Kim S, Yee A, Xiao R, Murray D, Arrowsmith CH, Szyperski T (2005) NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure. J Struct Funct Genomics 6:51–62CrossRefGoogle Scholar
  29. 29.
    Guntert P, Dotsch V, Wider G, Wuthrich K (1992) Processing of multidimensional NMR data with the new software PROSA. J Biomol NMR 2:619–629CrossRefGoogle Scholar
  30. 30.
    Keller R (2004) The computer aided resonance assignment tutorial. CANTINA Verlag, GoldauGoogle Scholar
  31. 31.
    Bartels C, Xia TH, Billeter M, Guntert P, Wuthrich K (1995) The program Xeasy for computer-supported NMR spectral-analysis of biological macromolecules. J Biomol NMR 6:1–10CrossRefGoogle Scholar
  32. 32.
    Zimmerman DE, Kulikowski CA, Huang YP, Feng WQ, Tashiro M, Shimotakahara S, Chien CY, Powers R, Montelione GT (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol 269:592–610PubMedCrossRefGoogle Scholar
  33. 33.
    Moseley HNB, Monleon D, Montelione GT (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Method Enzymol 339:91–108CrossRefGoogle Scholar
  34. 34.
    Pelton JG, Torchia DA, Meadow ND, Roseman S (1993) Tautomeric states of the active-site histidines of phosphorylated and unphosphorylated III(Glc), a signal-transducing protein from Escherichia coli, using 2-dimensional heteronuclear NMR techniques. Protein Sci 2:543–558PubMedCrossRefGoogle Scholar
  35. 35.
    Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289–302PubMedCrossRefGoogle Scholar
  36. 36.
    Guntert P, Mumenthaler C, Wuthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283–298PubMedCrossRefGoogle Scholar
  37. 37.
    Herrmann T, Guntert P, Wuthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209–227PubMedCrossRefGoogle Scholar
  38. 38.
    Linge JP, Williams MA, Spronk C, Bonvin A, Nilges M (2003) Refinement of protein structures in explicit solvent. Proteins Struct Funct Genet 50:496–506PubMedCrossRefGoogle Scholar
  39. 39.
    Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921PubMedCrossRefGoogle Scholar
  40. 40.
    Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins Struct Funct Bioinf 66:778–795CrossRefGoogle Scholar
  41. 41.
    Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22:195–201PubMedCrossRefGoogle Scholar
  42. 42.
    Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242PubMedCrossRefGoogle Scholar
  43. 43.
    Bontems F, Verger A, Dewitte F, Lens Z, Baert J-L, Ferreira E, Launoit Yd, Sizun C, Guittet E, Villeret V, Monté D (2011) NMR structure of the human mediator MED25 ACID domain. J Struct Biol 174:245–251PubMedCrossRefGoogle Scholar
  44. 44.
    Milbradt AG, Kulkarni M, Yi TF, Takeuchi K, Sun ZYJ, Luna RE, Selenko P, Naar AM, Wagner G (2011) Structure of the VP16 transactivator target in the mediator. Nat Struct Mol Biol 18:410–415PubMedCrossRefGoogle Scholar
  45. 45.
    Vojnic E, Mourao A, Seizl M, Simon B, Wenzeck L, Lariviere L, Baumli S, Baumgart K, Meisterernst M, Sattler M, Cramer P (2011) Structure and VP16 binding of the Mediator Med25 activator interaction domain. Nat Struct Mol Biol 18:404–409PubMedCrossRefGoogle Scholar
  46. 46.
    Holm L, Sander C (1995) Dali—a network tool for protein structure comparison. Trends Biochem Sci 20:478–480PubMedCrossRefGoogle Scholar
  47. 47.
    Shi YH, Downes M, Xie W, Kao HY, Ordentlich P, Tsai CC, Hon M, Evans RM (2001) Sharp, an inducible cofactor that integrates nuclear receptor repression and activation. Genes Dev 15:1140–1151PubMedCrossRefGoogle Scholar
  48. 48.
    Oswald F, Kostezka U, Astrahantseff K, Bourteele S, Dillinger K, Zechner U, Ludwig L, Wilda M, Hameister H, Knochel W, Liptay S, Schmid RM (2002) SHARP is a novel component of the Notch/RBP-J kappa signalling pathway. EMBO J 21:5417–5426PubMedCrossRefGoogle Scholar
  49. 49.
    Ariyoshi M, Schwabe JWR (2003) A conserved structural motif reveals the essential transcriptional repression function of Spen proteins and their role in developmental signaling. Genes Dev 17:1909–1920PubMedCrossRefGoogle Scholar
  50. 50.
    Youn H-S, Park U-H, Kim E-J, Um S-J (2011) PTOV1 antagonizes MED25 in RAR transcriptional activation. Biochem Biophys Res Commun 404:239–244PubMedCrossRefGoogle Scholar
  51. 51.
    Koradi R, Billeter M, Wuthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14:51–55PubMedCrossRefGoogle Scholar
  52. 52.
    Huang YJ, Powers R, Montelione GT (2005) Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127:1665–1674PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Alexander Eletsky
    • 1
    • 2
  • William T. Ruyechan
    • 3
    • 4
  • Rong Xiao
    • 5
    • 6
    • 7
  • Thomas B. Acton
    • 5
    • 6
    • 7
  • Gaetano T. Montelione
    • 5
    • 6
    • 7
  • Thomas Szyperski
    • 1
    • 2
  1. 1.Department of ChemistryThe State University of New York at BuffaloBuffaloUSA
  2. 2.Northeast Structural Genomics ConsortiumBuffaloUSA
  3. 3.Department of Microbiology and ImmunologyThe State University of New York at BuffaloBuffaloUSA
  4. 4.Northeast Structural Genomics ConsortiumBuffaloUSA
  5. 5.Center of Advanced Biotechnology and Medicine, Department of Molecular Biology and BiochemistryRutgers, The State University of New JerseyPiscatawayUSA
  6. 6.Department of Biochemistry, Robert Wood Johnson Medical SchoolUniversity of Medicine and Dentistry of New JerseyPiscatawayUSA
  7. 7.Northeast Structural Genomics ConsortiumPiscatawayUSA

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