Structure of the chromatin binding (chromo) domain from mouse modifier protein 1

EMBO Journal

Volumn 16, Issue 9, 1997, Pages 2473-2481

  Ball, Linda J ^a   Murzina, Natalia V ^a   Broadhurst, R William ^a   Raine, Andrew R C ^a   Archer, Sharon J ^b   Stott, Francesca J ^a   Murzin, Alexey G ^c   Singh, Prim B ^d   Domaille, Peter J ^a   Laue, Ernest D ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b DUPONT COMPANY   (United States)

^c MEDICAL RESEARCH COUNCIL   (United Kingdom)

^d BABRAHAM INSTITUTE   (United Kingdom)

Author keywords

Chromo domain; Homology; NMR spectroscopy; Protein interaction motif; Structure

Indexed keywords

DNA BINDING PROTEIN;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CHROMATIN; CONTROLLED STUDY; MOUSE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; ARCHAEAL PROTEINS; BACTERIAL PROTEINS; BINDING SITES; CARRIER PROTEINS; CHROMATIN; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CHROMOSOMAL PROTEINS, NON-HISTONE; CLONING, MOLECULAR; DNA-BINDING PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SOLUTIONS;

ARCHAEA;

EID: 0030922584     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.9.2473     Document Type: Article

References (65)

1. Aasland, R. and Stewart, A.F. (1995) The chromo shadow domain, a second chromo domain in heterochromatin-binding protein-1, HP-1. Nucleic Acids. Res., 23, 3168-3173.
2. β-resonances in larger proteins. J. Magn. Resonance, 95, 636-641.
3. Baumann, H., Knapp, S., Lundbäck, T., Ladenstein, R. and Härd, T. (1994) Solution structure and DNA-binding properties of a thermostable protein from the archaeon Solfolobus solfataricus. Nature Struct. Biol., 1, 808-819.
4. Baumann, H., Knapp, S., Karshikoff, A., Ladenstein, R. and Härd, T. (1995a) DNA-binding surface of the Sso7d protein from Solfolobus solfataricus. J. Mol. Biol., 247, 840-846.
5. Baumann, P., Qureshi, S.A. and Jackson, S.R (1995b) Transcription - new insights from studies on archaea. Trends Genet., 11, 279-283.
6. 13C enriched proteins. J. Magn. Resonance, 88, 425-431.
7. Bax, A., Ikura, M., Kay, L.E., Torchia, D.A. and Tschudin, R. (1990b) Comparison of different modes of 2-dimensional reverse-correlation NMR for the study of proteins. J. Magn. Resonance, 86, 304-318.
8. 1H-COSY experiments. J. Biomol. NMR, 2, 257-274.
9. Brünger, A. (1992) X-PLOR, Version 3.1, A System for X-Ray Crystallography and NMR. Yale University Press, New Haven, CT.
10. Clark, R.F. and Elgin, S.C.R. (1992) Heterochromatin protein-1, a known suppressor of position-effect variegation, is highly conserved in Drosophila. Nucleic Acids Res., 20, 6067-6074.
11. 15N labeled proteins. J. Biomol. NMR, 3, 349-354.
12. Clowes, R.T., Crawford, A., Raine, A.R.C., Smith, B.O. and Laue, E.D. (1995) Improved methods for structural studies of proteins using NMR spectroscopy. Can: Opin. Biotechnol., 6, 81-88.
13. Delmas, V., Stokes, D.G. and Perry, R.P. (1993) A mammalian DNA-binding protein that contains a chromo domain and an SNF2/SW12-like helicase domain. Proc. Natl Acad. Sci. USA, 90, 2414-2418.
14. Dernburg, A.F., Sedat, J.W. and Hawley, R.S. (1996) Direct evidence of a role for heterochromatin in meiotic chromosome segregation. Cell, 86, 135-146.
15. Dijk, J. and Reinhardt, R. (1986) In Gualerzi, C. and Pon, C. (eds). Bacterial Chromatin. Springer Verlag, Berlin, Germany.
16. Edmondson, S.P., Qui, L. and Shriver, J.W. (1995) Solution structure of the DNA-binding protein Sac7d from the hyperthermophile Sulfolobus acidocaldarius. Biochemistry, 34, 13289-13304.
17. Eissenherg, J.C., James, T.C., Foster-Hartnett, D.M., Hartnett, T., Ngan, V. and Elgin, S.C.R. (1990) Mutation in a heterochromatin-specific chromosomal protein is associated with suppression of position-effect variegation in Drosophila melanogaster. Proc. Natl Acad. Sci. USA, 87, 9923-9927.
18. Eissenberg, J.C., Morris, G.D., Reuter, G. and Hartnett, T. (1992) The heterochromatin-associated protein HP-1 is an essential protein in Drosophila with dosage-dependent effects on position-effect variegation. Genetics, 131, 345-352.
19. Ekwall, K., Javerzat, J-P., Lorentz, A., Schmidt, H., Cranston, G. and Allshire, R.C. (1995) The chromodomain protein Swi6: a key component at fission yeast centromeres. Science, 269, 1429-1431.
20. Epstein, H., James, T.C. and Singh, P.B. (1992) Cloning and expression of Drosophila HP1 homologs from a mealybug, Planococcus citri. J. Cell Sci., 101, 463-174.
21. Gartler, S.M. and Riggs, A.D. (1983) Mammalian X-chromosome inactivation. Annu. Rev. Genet., 17, 155-190.
22. Gilson, M.K., Sharp, K.A and Honig, B. (1988) Calculation of the total electrostatic energy of a macromolecular system - solvation energies, binding energies and conformational analysis. J. Comput. Chem., 9, 327-335.
23. Grzesiek, S. and Bax, A. (1992a) Correlating backbone amide and sidechain resonances in larger proteins by multiple relayed triple resonance NMR. J. Am. Chem. Soc., 114, 6291.
24. Grzesiek, S. and Bax, A. (1992b) An efficient experiment for sequential backbone assignment of medium-sized isotopically enriched proteins. J. Magn. Resonance, 99, 201-207.
25. CC couplings between backbone carbonyl and methyl carbons in isotopically enriched proteins. J. Biomol. NMR, 3, 487-493.
26. Holm, L. and Sander, C. (1993) Protein-structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
27. 15N spectra of larger proteins -heteronuclear triple-resonance 3-dimensional NMR-spectroscopy -application to calmodulin. Biochemistry, 29, 4659-1667.
28. Karpen, G.H., Le,M.-H. and Le.H. (1996) Centric heterochromatin and the efficiency of achiasmate disjunction in Drosophila female meiosis. Science, 273, 118-122.
29. Kay, L.E., Clore, G.M., Bax, A. and Gronenborn, A.M. (1990) 4-Dimensional heteronuclear triple-resonance NMR spectroscopy of interleukin-1β in solution. Science, 249, 411-414.
30. Koonin, E.V., Zhou, S.B. and Lucchesi, J.C. (1995) The chromo superfamily - new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin. Nucleic Acids. Res., 23, 4229-4233.
31. Kraulis, P.J. (1991) Molscript - a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, 946-950.
32. Kraulis, P.J., Domaille, P.J., Campbell-Burk, S.L., Van Aken, T. and Laue, E.D. (1994) Solution structure and dynamics of Ras p21·GDP determined by heteronuclear three- and four-dimensional NMR spectroscopy. Biochemistry, 33, 3515-3531.
33. Kumar, A., Ernst, R.R. and Wüthrich, K. (1980) A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem. Biophys. Res. Commun., 95, 1-6.
34. Laskowski, R.A., Macarthur, M.W., Moss, D.S. and Thornton, J.M. (1993) Procheck - a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.
35. Laurenson, P. and Rine, J. (1992) Silencers, silencing and heritable transcriptional states. Microbiol. Rev., 56, 543-560.
36. Leonard, E.J. and Yoshimura, T. (1990) Human monocyte chemoattractant protein-1 (MCP-1). Immunol. Today, 11, 97-101.
37. Le Douarin, B., Nielsen, A.L., Garnier, J.-M., Ichinose, H., Jeanmougin, F., Losson, R. and Chambon, P. (1996) A possible involvement of TIF1α and TIF1β in the epigenetic control of transcription by nuclear receptors. EMBO J., 15, 6701-6715.
38. Lorentz, A., Ostermann, K., Fleck, O. and Schmidt, H. (1994) Switching gene Swi6, involved in repression of silent mating-type loci in fission yeast, encodes a homologue of chromatin-associated proteins from Drosophila and mammals. Gene, 143, 139-143.
39. Madireddi, M.T, Coyne, R.S., Smothers, J.F., Mickey, K.M., Yao, M.-C. and Allis, C.D. (1996) PDD1P, a novel chromo domain-containing protein, links heterochromatin assembly and DNA elimination in tetrahymena. Cell, 87, 75-84.
40. Marion, D., Ikura, M., Tschudin, R. and Bax, A. (1989a) Rapid recording of 2D NMR-spectra without phase cycling - application to the study of hydrogen exchange in proteins. J. Magn. Resonance, 85, 393-399.
41. 15N Hartmann-Hahn multiple quantum coherence and nuclear Overhauser multiple quantum coherence spectroscopy - application to interleukin-1β. Biochemistry, 28, 6150-6156.
42. Messmer, S., Franke, A. and Paro, R. (1992) Analysis of the functional role of the Polycomb chromo domain in Drosophila melanogaster. Genes Dev., 6, 1241-1254.
43. Nicholls, A., Sharp, K.A. and Honig, B. (1991) Protein folding and association - insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins, 11, 281-296.
44. Nilges, M. (1995) Calculation of protein structures with ambiguous distance restraints - automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. J. Mol. Biol., 245, 645-660.
45. Nilges, M., Clore, G.M. and Gronenborn, A.M. (1988) Determination of three-dimensional structures of protons from interproton distance data by dynamical simulated annealing from a random array of atoms. FEBS Lett., 239, 129-136.
46. Nilges, M., Kuszewski, J. and Brünger A.T. (1991) In Hoch, J.C. (ed.), Computational Aspects of the Study of Biological Macromolecules by NMR. Plenum Press, New York, NY.
47. 15N spectroscopy. J. Magn. Resonance, 87, 488-501.
48. HNα for identification of helical secondary structure. J. Mol. Biol., 180, 741-751.
49. Paro, R. (1990) Imprinting a determined state into the chromatin of Drosophila. Trends Genet., 6, 416-421.
50. Paro, R. (1993) Mechanisms of heritable gene repression during development in Drosophila. Curr. Opin. Cell Biol., 5, 999-1005.
51. Paro, R. and Hogness, D. (1991) The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila. Proc. Natl Acad. Sci. USA. 88, 263-267.
52. Platero, J.S., Hartnett, T. and Eissenberg, J.C. (1995) Functional analysis of the chromo domain of HP1. EMBO J., 14, 3977-3986.
53. Powers, J.A. and Eissenberg, J.C. (1993) Overlapping domains of the heterochromatin-associated protein HP1 mediate nuclear localization and heterochromatin binding. J. Cell Biol., 120, 291-299.
54. Powers, R., Garrett, D.S., March, C.J., Frieden, E.A., Gronenborn, A.M. and Clore, G.M. (1993) The high-resolution, 3-dimensional solution structure of human interleukin-4 determined by multidimensional heteronuclear magnetic resonance spectroscopy. Biochemistry, 32, 6744-6762.
55. 1H-NMR spectra of proteins via double quantum filtering. Biochem. Biophys. Res. Commun., 117, 479-485.
56. Reuter, G. and Spierer, P. (1992) Position effect variegation and chromatin proteins. BioEssays, 14, 605-612.
57. Schagger, H. and von Jagow, G. (1987) Tricine sodium dodecyl sulfate polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 kDa to 100 kDa. Anal. Biochem., 166, 368-379.
58. Singh, P.B., Miller, J.R., Pearce, J., Kothary, R., Burton, R.D., Paro, R., James, T.C. and Gaunt, S.J. (1991) A sequence motif found in a Drosophila heterochromatin protein is conserved in plants and animals. Nucleic Acids. Res., 19, 789-794.
59. Solter, D. (1988) Differential imprinting and expression of maternal and paternal genomes. Annu. Rev. Genet., 22, 127-146.
60. Szekely, L., Uzvolgyi, E., Jiang, W.-Q., Durko, M. Wiman, K.G., Klein, G. and Sumegi, J. (1991) Subcellular localization of the retinoblastoma protein. Cell Growth Differentiation, 2, 287-295.
61. 13C. J. Am. Chem. Soc., 115, 5334-5335.
62. Wishart, D.S. and Sykes, B.D. (1994) Chemical shifts as a tool for structure determination. Methods Enzymol., 239, 363-392.
63. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids. Wiley, New York, NY.
64. 13C-labeled proteins via scalar couplings. J. Am. Chem. Soc., 115, 11054-11055.
65. 13C-labeled proteins for the NMR assignment and structure determination of larger molecules. J. Magn. Resonance, 86, 210-216.