Structural Basis of Site-Specific Histone Recognition by the Bromodomains of Human Coactivators PCAF and CBP/p300

Structure

Volumn 16, Issue 4, 2008, Pages 643-652

  Zeng, Lei ^a   Zhang, Qiang ^a   Gerona Navarro, Guillermo ^a   Moshkina, Natalia ^a   Zhou, Ming Ming ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

DNA; PROTEINS

Indexed keywords

CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN BINDING PROTEIN; HISTONE ACETYLTRANSFERASE PCAF; HISTONE H3; HISTONE H4; LYSINE;

ACETYLATION; ARTICLE; HYDROPHOBICITY; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

AMINO ACID SEQUENCE; CREB-BINDING PROTEIN; HISTONES; HUMANS; LYSINE; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; P300-CBP TRANSCRIPTION FACTORS; PEPTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY;

EID: 41449114497     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2008.01.010     Document Type: Article

References (48)

1. Agalioti T., Chen G., and Thanos D. Deciphering the transcriptional histone acetylation code for a human gene. Cell 111 (2002) 381-392
2. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., and Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410 (2001) 120-124
3. Berger S.L. Histone modifications in transcriptional regulation. Curr. Opin. Genet. Dev. 12 (2002) 142-148
4. Bernstein E., Duncan E., Masui O., Gil J., Heard E., and Allis C. Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol. Cell. Biol. 26 (2006) 2560-2569
5. Brown C.E., Howe L., Sousa K., Alley S.C., Carrozza M.J., Tan S., and Workman J.L. Recruitment of HAT complexes by direct activator interactions with the ATM-related Tra1 subunit. Science 292 (2001) 2333-2337
6. 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
7. Cairns B.R., Schlichter A., Erdjument-Bromage H., Tempst P., Kornberg R.D., and Winston F. Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. Mol. Cell 4 (1999) 715-723
8. Chua P., and Roeder G. Bdf1, a yeast chromosomal protein required for sporulation. Mol. Cell. Biol. 15 (1995) 3685-3696
9. Clore G.M., and Gronenborn A.M. Multidimensional heteronuclear nuclear magnetic resonance of proteins. Methods Enzymol. 239 (1994) 349-363
10. Dhalluin C., Carlson J., Zeng L., He C., Aggarwal K., and Zhou M. Structure and ligand of a histone acetyltransferase bromodomain. Nature 399 (1999) 491-496
11. Du J., Nasir I., Benton B.K., Kladde M.P., and Laurent B.C. Sth1p, a Saccharomyces cerevisiae Snf2p/Swi2p homolog, is an essential ATPase in RSC and differs from Snf/Swi in its interactions with histones and chromatin-associated proteins. Genetics 150 (1998) 987-1005
12. Fischle W., Wang Y., and Allis C. Histone and chromatin cross-talk. Curr. Opin. Cell Biol. 15 (2003) 172-183
13. Garcia B.A., Hake S.B., Diaz R.L., Kauer M., Morris S.A., Recht J., Shabanowitz J., Mishra N., Strahl B.D., Allis C.C., et al. Organismal differences in post-translational modifications in histones H3 and H4. J. Biol. Chem. 282 (2007) 7641-7655
14. Georgakopoulos T., Gounalaki N., and Thireos G. Genetic evidence for the interaction of the yeast transcriptional co-activator proteins GCN5 and ADA2. Mol. Gen. Genet. 246 (1995) 723-728
15. Greenwald R.J., Tumang J.R., Sinha A., Currier N., Cardiff R.D., Rothstein T.L., Faller D.V., and Denis G.V. E mu-BRD2 transgenic mice develop B-cell lymphoma and leukemia. Blood 103 (2004) 1475-1484
16. Hassan A.H., Prochasson P., Neely K.E., Galasinski S.C., Chandy M., Carrozza M.J., and Workman J.L. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111 (2002) 369-379
17. Jacobson R.R., Ladurner A.G., King D.S., and Tjian R. Structure and function of a human TAFII250 double bromodomain module. Science 288 (2000) 1422-1425
18. Jeanmougin F., Wurtz J.M., Le Douarin B., Chambon P., and Losson R. The bromodomain revisited. Trends Biochem. Sci. 22 (1997) 151-153
19. Jenuwein T., and Allis C. Translating the histone code. Science 293 (2001) 1074-1080
20. Lachner M., O'Carroll D., Rea S., Mechtler K., and Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410 (2001) 116-120
21. Laskowski R.A., Rullmannn J.A., MacArthur M.W., Kaptein R., and Thornton J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8 (1996) 477-486
22. Li H., Ilin S., Wang W., Duncan E., Wysocka J., Allis C., and Patel D. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442 (2006) 91-95
23. Manning E.T., Ikehara T., Ito T., Kadonaga J.T., and Kraus W.L. p300 forms a stable, template-committed complex with chromatin: role for the bromodomain. Mol. Cell. Biol. 21 (2001) 3876-3887
24. Meyer B., and Peters T. NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. Angew. Chem. Int. Ed. Engl. 42 (2003) 864-890
25. Morris C.A., and Moazed D. Centromere assembly and propagation. Cell 128 (2007) 647-650
26. Muchardt C., and Yaniv M. ATP-dependent chromatin remodelling: SWI/SNF and Co. are on the job. J. Mol. Biol. 293 (1999) 187-198
27. Muchardt C., Bourachot B., Reyes J.C., and Yaniv M. ras transformation is associated with decreased expression of the brm/SNF2α ATPase from the mammalian SWI-SNF complex. EMBO J. 17 (1998) 223-231
28. Mujtaba S., He Y., Zeng L., Farooq A., Carlson J., Ott M., Verdin E., and Zhou M. Structural basis of lysine-acetylated HIV-1 Tat recognition by PCAF bromodomain. Mol. Cell 9 (2002) 575-586
29. Mujtaba S., He Y., Zeng L., Yan S., Plotnikova O., Sachchidanand, Sanchez R., Zeleznik-Le N., Ronai Z., and Zhou M. Structural mechanism of the bromodomain of the coactivator CBP in p53 transcriptional activation. Mol. Cell 13 (2004) 251-263
30. Mujtaba S., Zeng L., and Zhou M. Structure and acetyl-lysine recognition of the bromodomain. Oncogene 26 (2007) 5521-5527
31. Nakamura Y., Umehara T., Nakano K., Jang M., Shirouzu M., Morita S., Uda-Tochio H., Hamana H., Terada T., Adachi N., et al. Crystal structure of the human BRD2 bromodomain: insights into dimerization and recognition of acetylated histone H4. J. Biol. Chem. 282 (2007) 4193-4201
32. Neely K.E., and Workman J.L. Histone acetylation and chromatin remodeling: which comes first?. Mol. Genet. Metab. 76 (2002) 1-5
33. Nightingale K.P., O'Neill L.P., and Turner B.M. Histone modifications: signalling receptors and potential elements of a heritable epigenetic code. Curr. Opin. Genet. Dev. 16 (2006) 125-136
34. Nilges M., and O'Donoghue S. Ambiguous NOEs and automated NOE assignment. Prog. Nucl. Magn. Reson. Spectrosc. 32 (1998) 107-139
35. Owen D.J., Ornaghi P., Yang J.C., Lowe N., Evans P.R., Ballario P., Neuhaus D., Filetici P., and Travers A.A. The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p. EMBO J. 19 (2000) 6141-6149
36. Roehrl M.H., Wang J.Y., and Wagner G. A general framework for development and data analysis of competitive high-throughput screens for small-molecule inhibitors of protein-protein interactions by fluorescence polarization. Biochemistry 43 (2004) 16056-16066
37. Ruthenburg A.J., Allis C.D., and Wysocka J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol. Cell 25 (2007) 15-30
38. Schreiber S.L., and Bernstein B.E. Signaling network model of chromatin. Cell 111 (2002) 771-778
39. Seet B.T., Dikic I., Zhou M.M., and Pawson T. Reading protein modifications with interaction domains. Nat. Rev. Mol. Cell Biol. 7 (2006) 473-483
40. Shen W., Xu C., Huang W., Zhang J., Carlson J., Tu X., Wu J., and Shi Y. Solution structure of human Brg1 bromodomain and its specific binding to acetylated histone tails. Biochemistry 46 (2007) 2100-2110
41. Sterner D.E., Grant P.A., Roberts S.M., Duggan L.J., Belotserkovskaya R., Pacella L.A., Winston F., Workman J.L., and Berger S.L. Functional organization of the yeast SAGA complex: distinct components involved in structural integrity, nucleosome acetylation, and TATA-binding protein interaction. Mol. Cell. Biol. 19 (1999) 86-98
42. Strahl B.D., Allis C.D.,. The language of covalent histone modifications. Nature 403 (2000) 41-45
43. Syntichaki P., Topalidou I., and Thireos G. The Gcn5 bromodomain co-ordinates nucleosome remodelling. Nature 404 (2000) 414-417
44. Travers A. Chromatin modification: how to put a HAT on the histones. Curr. Biol. 9 (1999) R23-R25
45. Turner B.M.,. Histone acetylation as an epigenetic determinant of long-term transcriptional competence. Cell. Mol. Life Sci. 54 (1998) 21-31
46. Turner B.M. Cellular memory and the histone code. Cell 111 (2002) 285-291
47. Vandemark A.P., Kasten M.M., Ferris E., Heroux A., Hill C.P., and Cairns B.R. Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. Mol. Cell 27 (2007) 817-828
48. Yap K.L., and Zhou M.M. Structure and function of protein modules in chromatin biology. Results Probl. Cell Differ. 41 (2006) 1-23