Structure and mechanism of RNA polymerase II CTD phosphatases

Molecular Cell

Volumn 15, Issue 3, 2004, Pages 399-407

  Kamenski, Tomislav ^a   Heilmeier, Susanna ^a   Meinhart, Anton ^a   Cramer, Patrick ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; FLUORIDE; PHOSPHATASE; PHOSPHOTRANSFERASE; RNA POLYMERASE II;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; ENZYME ACTIVE SITE; HYDROPHOBICITY; MOLECULAR MECHANICS; NONHUMAN; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; X RAY ANALYSIS;

AMINO ACID SEQUENCE; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; HUMANS; MOLECULAR SEQUENCE DATA; PHOSPHOPROTEIN PHOSPHATASE; PROTEIN STRUCTURE, TERTIARY; RNA POLYMERASE II; SACCHAROMYCES CEREVISIAE;

INSERTION SEQUENCES;

EID: 4143117908     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2004.06.035     Document Type: Article

References (41)

1. Archambault J., Chambers R.S., Kobor M.S., Ho Y., Cartier M., Bolotin D., Andrews B., Kane C.M., Greenblatt J. An essential component of a C-terminal domain phosphatase that interacts with transcription factor IIF in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA. 94:1997;14300-14305
2. Archambault J., Pan G., Dahmus G.K., Cartier M., Marshall N., Zhang S., Dahmus M.E., Greenblatt J. FCP1, the RAP74-interacting subunit of a human protein phosphatase that dephosphorylates the carboxyl-terminal domain of RNA polymerase IIO. J. Biol. Chem. 273:1998;27593-27601
3. Armache K.-J., Kettenberger H., Cramer P. Architecture of the initiation-competent 12-subunit RNA polymerase II. Proc. Natl. Acad. Sci. USA. 100:2003;6964-6968
4. Brunger 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., et al. Crystallography & NMR system. a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921
5. Bushnell D.A., Kornberg R.D. Complete RNA polymerase II at 4.1 Å resolution. implications for the initiation of transcription Proc. Natl. Acad. Sci. USA. 100:2003;6969-6972
6. Chabre M. Aluminofluoride and beryllofluoride complexes. a new phosphate analogs in enzymology Trends Biochem. Sci. 15:1990;6-10
7. Chambers R.S., Dahmus M.E. Purification and characterization of a phosphatase from HeLa cells which dephosphorylates the C-terminal domain of RNA polymerase II. J. Biol. Chem. 269:1994;26243-26248
8. Chambers R.S., Kane C.M. Purification and characterization of an RNA polymerase II phosphatase from yeast. J. Biol. Chem. 271:1996;24498-24504
9. Chambers R.S., Wang B.Q., Burton Z.F., Dahmus M.E. The activity of COOH-terminal domain phosphatase is regulated by a docking site on RNA polymerase II and the by the general transcription factors IIF and IIB. J. Biol. Chem. 270:1995;14962-14969
10. Cho H., Kim T.K., Mancebo H., Lane W.S., Flores O., Reinberg D. A protein phosphatase functions to recycle RNA polymerase II. Genes Dev. 13:1999;1540-1552
11. Cho H., Wang W., Kim R., Yokota H., Damo S., Kim S.H., Wemmer D., Kustu S., Yan D. BeF(3)(-) acts as a phosphate analog in proteins phosphorylated on aspartate. structure of a BeF(3)(-) complex with phosphoserine phosphatase Proc. Natl. Acad. Sci. USA. 98:2001;8525-8530
12. Collet J.F., Stroobant V., Pirard M., Delpierre G., Van Schaftingen E. A new class of phosphotransferases phosphorylated on an aspartate residue in an amino-terminal DXDX(T/V) motif. J. Biol. Chem. 273:1998;14107-14112
13. Cramer P., Bushnell D.A., Kornberg R.D. Structural basis of transcription. RNA polymerase II at 2.8 Å resolution Science. 292:2001;1863-1876
14. Fabrega C., Shen V., Shuman S., Lima C.D. Structure of an mRNA capping enzyme bound to the phosphorylated carboxy-terminal domain of RNA polymerase II. Mol. Cell. 11:2003;1549-1561
15. Hausmann S., Shuman S. Characterization of the CTD phosphatase Fcp1 from fission yeast. Preferential dephosphorylation of serine 2 versus serine 5. J. Biol. Chem. 277:2002;21213-21220
16. Hausmann S., Shuman S. Defining the active site of Schizosaccharomyces pombe C-terminal domain phosphatase Fcp1. J. Biol. Chem. 278:2003;13627-13632
17. Hausmann S., Erdjument-Bromage H., Shuman S. Schizosaccharomyces pombe CTD phosphatase Fcp1. distributive mechanism, minimal CTD substrate, and active site mapping J. Biol. Chem. 279:2004;10892-10900
18. Hirose Y., Manley J.L. RNA polymerase II and the integration of nuclear events. Genes Dev. 14:2000;1415-1429
19. Holm L., Sander C. Dali. a network tool for protein structure comparison Trends Biochem. Sci. 20:1995;478-480
20. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26:1993;795-800
21. Kamada K., Roeder R.G., Burley S.K. Molecular mechanism of recruitment of TFIIF-associating RNA polymerase C-terminal domain phosphatase (FCP1) by transcription factor IIF. Proc. Natl. Acad. Sci. USA. 100:2003;2296-2299
22. Kobor M.S., Archambault J., Lester W., Holstege F.C., Gileadi O., Jansma D.B., Jennings E.G., Kouyoumdjian F., Davidson A.R., Young R.A., et al. An unusual eukaryotic protein phosphatase required for transcription by RNA polymerase II and CTD dephosphorylation in S. cerevisiae. Mol. Cell. 4:1999;55-62
23. La Fortelle E.D., Bricogne G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276:1997;472-494
24. Lahiri S.D., Zhang G., Dunaway-Mariano D., Allen K.N. The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction. Science. 299:2003;2067-2071
25. Lehmann A.L., Dahmus M.E. The sensitivity of RNA polymerase II in elongation complexes to C-terminal domain phosphatase. J. Biol. Chem. 275:2000;14923-14932
26. Lin P.S., Dubois M.F., Dahmus M.E. TFIIF-associating carboxyl-terminal domain phosphatase dephosphorylates phosphoserines 2 and 5 of RNA polymerase II. J. Biol. Chem. 277:2002;45949-45956. a
27. Lin P.S., Marshall N.F., Dahmus M.E. CTD phosphatase. role in RNA polymerase II cycling and the regulation of transcript elongation Prog. Nucleic Acid Res. Mol. Biol. 72:2002;333-365. b
28. Meinhart A., Blobel J., Cramer P. An extended winged helix domain in general transcription factor E/IIEalpha. J. Biol. Chem. 278:2003;48267-48274
29. Nguyen B.D., Abbott K.L., Potempa K., Kobor M.S., Archambault J., Greenblatt J., Legault P., Omichinski J.G. NMR structure of a complex containing the TFIIF subunit RAP74 and the RNA polymerase II carboxyl-terminal domain phosphatase FCP1. Proc. Natl. Acad. Sci. USA. 100:2003;5688-5693
30. Orphanides G., Reinberg D. A unified theory of gene expression. Cell. 108:2002;439-451
31. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Meth. Enzym. 276:1996;307-326
32. Proudfoot N.J., Furger A., Dye M.J. Integrating mRNA processing with transcription. Cell. 108:2002;501-512
33. Ridder I.S., Rozeboom H.J., Kalk K.H., Dijkstra B.W. Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase. J. Biol. Chem. 274:1999;30672-30678
34. Terwilliger T.C. Automated structure solution, density modification and model building. Acta Crystallogr. D Biol. Crystallogr. 58:2002;1937-1940
35. Verdecia M.A., Bowman M.E., Lu K.P., Hunter T., Noel J.P. Structural basis for phosphoserine-proline recognition by group IV WW domains. Nat. Struct. Biol. 7:2000;639-643
36. Wang W., Kim R., Jancarik J., Yokota H., Kim S.H. Crystal structure of phosphoserine phosphatase from Methanococcus jannaschii, a hyperthermophile, at 1.8 Å resolution. Structure. 9:2001;65-71
37. Williams R.S., Green R., Glover J.N. Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1. Nat. Struct. Biol. 8:2001;838-842
38. Xu Y.X., Hirose Y., Zhou X.Z., Lu K.P., Manley J.L. Pin1 modulates the structure and function of human RNA polymerase II. Genes Dev. 17:2003;2765-2776
39. Yan D., Cho H.S., Hastings C.A., Igo M.M., Lee S.Y., Pelton J.G., Stewart V., Wemmer D.E., Kustu S. Beryllofluoride mimics phosphorylation of NtrC and other bacterial response regulators. Proc. Natl. Acad. Sci. USA. 96:1999;14789-14794
40. Yeo M., Lin P.S., Dahmus M.E., Gill G.N. A novel RNA polymerase II C-terminal domain phosphatase that preferentially dephosphorylates serine 5. J. Biol. Chem. 278:2003;26078-26085
41. Yu X., Chini C.C., He M., Mer G., Chen J. The BRCT domain is a phospho-protein binding domain. Science. 302:2003;639-642