Structural and functional characterization of a phosphatase domain within yeast general transcription factor IIIC

Journal of Biological Chemistry

Volumn 288, Issue 21, 2013, Pages 15110-15120

  Taylor, Nicholas M I ^a   Glatt, Sebastian ^a   Hennrich, Marco L ^a   Von Scheven, Gudrun ^a   Grötsch, Helga ^a   Fernández Tornero, Carlos ^b   Rybin, Vladimir ^a   Gavin, Anne Claude ^a   Kolb, Peter ^c   Müller, Christoph W ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

^c PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR FUNCTION; DOCKING METHODS; FUNCTIONAL CHARACTERIZATION; N-TERMINALS; PHOSPHOPEPTIDES; PROTEIN PHOSPHATASE; RNA POLYMERASE; SUBSTRATE SPECIFICITY;

AMINO ACIDS; ENZYME ACTIVITY; PHOSPHATASES; RNA; SUBSTRATES; TRANSCRIPTION FACTORS;

YEAST;

HISTIDINE PHOSPHATASE; PHOSPHATASE; PHOSPHOSERINE; PHOSPHOTYROSINE; PROTEIN HUF; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR IIIC; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CELL FUNCTION; COMPUTER ANALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ASSAY; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; IN VITRO STUDY; MOLECULAR DOCKING; NONHUMAN; PARALOGY; PHOSPHOPROTEOMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEOMICS; SACCHAROMYCES CEREVISIAE;

ENZYME STRUCTURE; HISTIDINE PHOSPHATASE FAMILY; MASS SPECTROMETRY (MS); METABOLISM; MOLECULAR DOCKING; PHOSPHOPROTEOMICS; PROTEIN PHOSPHATASE; RNA POLYMERASE III; TRANSCRIPTION REGULATION; X-RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; MOLECULAR DOCKING SIMULATION; PHOSPHORIC MONOESTER HYDROLASES; PROTEIN STRUCTURE, TERTIARY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS, TFIII;

EID: 84878228062     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M112.427856     Document Type: Article

References (42)

1. Schramm, L., and Hernandez, N. (2002) Recruitment of RNA polymerase III to its target promoters. Genes Dev. 16, 2593-2620
2. Stillman, D. J., and Geiduschek, E. P. (1984) Differential binding of a S. cerevisiae RNA polymerase III transcription factor to two promoter segments of a tRNA gene. EMBO J. 3, 847-853
3. Kassavetis, G. A., Braun, B. R., Nguyen, L. H., and Geiduschek, E. P. (1990) S. cerevisiae TFIIIB is the transcription initiation factor proper of RNA polymerase III, while TFIIIA and TFIIIC are assembly factors. Cell 60, 235-245
4. Ducrot, C., Lefebvre, O., Landrieux, E., Guirouilh-Barbat, J., Sentenac, A., and Acker, J. (2006) Reconstitution of the yeast RNA polymerase III transcription system with all recombinant factors. J. Biol. Chem. 281, 11685-11692 (Pubitemid 43855426)
5. Dumay-Odelot, H., Marck, C., Durrieu-Gaillard, S., Lefebvre, O., Jourdain, S., Prochazkova, M., Pflieger, A., and Teichmann, M. (2007) Identification, molecular cloning, and characterization of the sixth subunit of human transcription factor TFIIIC. J. Biol. Chem. 282, 17179-17189 (Pubitemid 47093196)
6. Fothergill, L. A., and Harkins, R. N. (1982) The amino acid sequence of yeast phosphoglycerate mutase. Proc. R, Soc. Lond. B Biol. Sci. 215, 19-44 (Pubitemid 12096609)
7. Fothergill-Gilmore, L. A., and Watson, H. C. (1989) The phosphoglycerate mutases. Adv. Enzymol. Relat. Areas Mol. Biol. 62, 227-313
8. Rigden, D. J. (2008) The histidine phosphatase superfamily. Structure and function. Biochem. J. 409, 333-348
9. Bazan, J. F., Fletterick, R. J., and Pilkis, S. J. (1989) Evolution of a bifunctional enzyme. 6-Phosphofructo-2-kinase/fructose-2,6-bisphosphatase. Proc. Natl. Acad. Sci. U.S.A. 86, 9642-9646
10. Manaud, N., Arrebola, R., Buffin-Meyer, B., Lefebvre, O., Voss, H., Riva, M., Conesa, C., and Sentenac, A. (1998) A chimeric subunit of yeast transcription factor IIIC forms a subcomplex with π95. Mol. Cell Biol. 18, 3191-3200 (Pubitemid 28240492)
11. Kanehisa, M., and Goto, S. (2000) KEGG. Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30
12. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K. F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M. (2006) From genomics to chemical genomics. New developments in KEGG. Nucleic Acids Res. 34, D354-D357
13. Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R., and Ferrin, T. E. (1982) A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161, 269-288
14. Meng, E. C., Shoichet, B. K., and Kuntz, I. D. (1992) Automated docking with grid-based energy evaluation. J. Comp. Chem. 13, 505-524
15. Shoichet, B. K., and Kuntz, I. D. (1993) Matching chemistry and shape in molecular docking. Protein Eng. 6, 723-732 (Pubitemid 23293201)
16. Shoichet, B. K., Leach, A. R., and Kuntz, I. D. (1999) Ligand solvation in molecular docking. Proteins 34, 4-16
17. Boersema, P. J., Raijmakers, R., Lemeer, S., Mohammed, S., and Heck, A. J. (2009) Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat. Protoc. 4, 484-494
18. Zhou, H., Low, T. Y., Hennrich, M. L., van der Toorn, H., Schwend, T., Zou, H., Mohammed, S., and Heck, A. J. (2011) Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment. Mol. Cell. Proteomics, M110.006452
19. Hennrich, M. L., Groenewold, V., Kops, G. J., Heck, A. J., and Mohammed, S. (2011) Improving depth in phosphoproteomics by using a strong cation exchange-weak anion exchange-reversed phase multidimensional separation approach. Anal. Chem. 83, 7137-7143
20. Mikhailik, A., Ford, B., Keller, J., Chen, Y., Nassar, N., and Carpino, N. (2007) A phosphatase activity of Sts-1 contributes to the suppression of TCR signaling. Mol. Cell 27, 486-497 (Pubitemid 47161133)
21. Chen, Y., Jakoncic, J., Carpino, N., and Nassar, N. (2009) Structural and functional characterization of the 2H-phosphatase domain of Sts-2 reveals an acid-dependent phosphatase activity. Biochemistry 48, 1681-1690
22. San Luis, B., Sondgeroth, B., Nassar, N., and Carpino, N. (2011) Sts-2 is a phosphatase that negatively regulates zeta-associated protein (ZAP)-70 and T cell receptor signaling pathways. J. Biol. Chem. 286, 15943-15954
23. Mak, L. H., Vilar, R., and Woscholski, R. (2010) Characterisation of the PTEN inhibitor VO-OHpic. J. Chem. Biol. 3, 157-163
24. Hou, L., Wang, J., Zhou, Y., Li, J., and Zang, Y. (2011) Structural insights into the homology and differences between mouse protein tyrosine phosphatase-sigma and human protein tyrosine phosphatase-sigma. Acta Biochim. Biophys. Sin (Shanghai) 43, 977-988
25. Donze, D. (2012) Extra-transcriptional functions of RNA Polymerase III complexes. TFIIIC as a potential global chromatin bookmark. Gene 493, 169-175
26. Kleinschmidt, R. A., LeBlanc, K. E., and Donze, D. (2011) Autoregulation of an RNA polymerase II promoter by the RNA polymerase III transcription factor III C (TF(III)C) complex. Proc. Natl. Acad. Sci. U.S.A. 108, 8385-8389
27. Moqtaderi, Z., Wang, J., Raha, D., White, R. J., Snyder, M., Weng, Z., and Struhl, K. (2010) Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat. Struct. Mol. Biol. 17, 635-640
28. Oler, A. J., Alla, R. K., Roberts, D. N., Wong, A., Hollenhorst, P. C., Chandler, K. J., Cassiday, P. A., Nelson, C. A., Hagedorn, C. H., Graves, B. J., and Cairns, B. R. (2010) Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat. Struct. Mol. Biol. 17, 620-628
29. Barski, A., Chepelev, I., Liko, D., Cuddapah, S., Fleming, A. B., Birch, J., Cui, K., White, R. J., and Zhao, K. (2010) Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes. Nat. Struct. Mol. Biol. 17, 629-634
30. Albuquerque, C. P., Smolka, M. B., Payne, S. H., Bafna, V., Eng, J., and Zhou, H. (2008) A multidimensional chromatography technology for indepth phosphoproteome analysis. Mol. Cell. Proteomics 7, 1389-1396 (Pubitemid 352038280)
31. Smolka, M. B., Albuquerque, C. P., Chen, S. H., and Zhou, H. (2007) Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc. Natl. Acad. Sci. U.S.A. 104, 10364-10369 (Pubitemid 47185671)
32. Chi, A., Huttenhower, C., Geer, L. Y., Coon, J. J., Syka, J. E., Bai, D. L., Shabanowitz, J., Burke, D. J., Troyanskaya, O. G., and Hunt, D. F. (2007) Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 104, 2193-2198 (Pubitemid 46391374)
33. Li, X., Gerber, S. A., Rudner, A. D., Beausoleil, S. A., Haas, W., Villén, J., Elias, J. E., and Gygi, S. P. (2007) Large-scale phosphorylation analysis of α-factor-arrested Saccharomyces cerevisiae . J. Proteome Res. 6, 1190 -1197
34. Mayer, A., Heidemann, M., Lidschreiber, M., Schreieck, A., Sun, M., Hintermair, C., Kremmer, E., Eick, D., and Cramer, P. (2012) CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II. Science 336, 1723-1725
35. Flores, A., Briand, J. F., Gadal, O., Andrau, J. C., Rubbi, L., Van Mullem, V., Boschiero, C., Goussot, M., Marck, C., Carles, C., Thuriaux, P., Sentenac, A., and Werner, M. (1999) A protein-protein interaction map of yeast RNA polymerase III. Proc. Natl. Acad. Sci. U.S.A. 96, 7815-7820 (Pubitemid 29328364)
36. Capozzo, C., Sartorello, F., Dal Pero, F., D'Angelo, M., Vezzi, A., Campanaro, S., and Valle, G. (2000) Gene disruption and basic phenotypic analysis of nine novel yeast genes from chromosome XIV. Yeast 16, 1089-1097
37. Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., and O'Shea, E. K. (2003) Global analysis of protein localization in budding yeast. Nature 425, 686-691 (Pubitemid 37314307)
38. Bodenmiller, B., Wanka, S., Kraft, C., Urban, J., Campbell, D., Pedrioli, P. G., Gerrits, B., Picotti, P., Lam, H., Vitek, O., Brusniak, M. Y., Roschitzki, B., Zhang, C., Shokat, K. M., Schlapbach, R., Colman-Lerner, A., Nolan, G. P., Nesvizhskii, A. I., Peter, M., Loewith, R., von Mering, C., and Aebersold, R. (2010) Phosphoproteomic analysis reveals interconnected systemwide responses to perturbations of kinases and phosphatases in yeast. Sci. Signal. 3, rs4
39. Herve, M., Buffin-Meyer, B., Bouet, F., and Son, T. D. (2000) Detection of modifications in the glucose metabolism induced by genetic mutations in Saccharomyces cerevisiae by 13C and H NMR spectroscopy. Eur. J. Biochem. 267, 3337-3344 (Pubitemid 30341163)
40. Smith, T. L., and Rutter, J. (2007) Regulation of glucose partitioning by PAS kinase and Ugp1 phosphorylation. Mol. Cell 26, 491-499 (Pubitemid 46765181)
41. Conesa, C., Ruotolo, R., Soularue, P., Simms, T. A., Donze, D., Sentenac, A., and Dieci, G. (2005) Modulation of yeast genome expression in response to defective RNA polymerase III-dependent transcription. Mol. Cell Biol. 25, 8631-8642 (Pubitemid 41369182)
42. Gille, C., and Frömmel, C. (2001) STRAP. Editor for STRuctural Alignments of Proteins. Bioinformatics 17, 377-378 (Pubitemid 32421936)