Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase

Cell

Volumn 111, Issue 1, 2002, Pages 117-127

  Zhang, Xing ^a   Tamaru, Hisashi ^b   Khan, Seema I ^a   Horton, John R ^a   Keefe, Lisa J ^c   Selker, Eric U ^b   Cheng, Xiaodong ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF OREGON   (United States)

^c ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; LYSINE; METHYLTRANSFERASE; PROTEIN; PROTEIN DIM 5; UNCLASSIFIED DRUG; ZINC;

ARTICLE; BINDING SITE; BIOCHEMISTRY; CHEMICAL REACTION; CRYSTAL STRUCTURE; ENZYME ANALYSIS; METHYLATION; NEUROSPORA; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN STRUCTURE; SITE DIRECTED MUTAGENESIS; STRUCTURE ANALYSIS;

NEUROSPORA;

EID: 0037020217     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(02)00999-6     Document Type: Article

References (54)

1. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature. 410:2001;120-124.
2. Baumbusch L.O., Thorstensen T., Krauss V., Fischer A., Naumann K., Assalkhou R., Schulz I., Reuter G., Aalen R.B. The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. Nucleic Acids Res. 29:2001;4319-4333.
3. Blumenthal R.M., Cheng X. A Taq attack displaces bases. Nat. Struct. Biol. 8:2001;101-103.
4. Boggs B.A., Cheung P., Heard E., Spector D.L., Chinault A.C., Allis C.D. Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes. Nat. Genet. 30:2002;73-76.
5. Briggs S.D., Bryk M., Strahl B.D., Cheung W.L., Davie J.K., Dent S.Y., Winston F., Allis C.D. Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev. 15:2001;3286-3295.
6. Brünger A.T. X-PLOR. A System for X-Ray Crystallography and NMR, 3.1 edn. 1992;Yale University, New Haven, CT.
7. Carson M. Ribbons. Methods Enzymol. 227:1997;493-505.
8. Cheng X., Roberts R.J. AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res. 29:2001;3784-3795.
9. Duerre J.A., Chakrabarty S. Methylated basic amino acid composition of histones from the various organs from the rat. J. Biol. Chem. 250:1975;8457-8461.
10. Fang J., Feng Q., Ketel C.S., Wang H., Cao R., Xia L., Erdjument-Bromage H., Tempst P., Simon J.A., Zhang Y. Purification and functional characterization of SET8, a nucleosomal histone H4-lysine 20-specific methyltransferase. Curr. Biol. 12:2002;1086-1099.
11. Fauman E.B., Blumenthal R.M., Cheng X. Structure and evolution of Adomet-dependent methyltransferases. Cheng X., Blumenthal R.M. S-Adenosylmethionine-Dependent Methyltransferases. Structures and Functions:1999;1-38 World Scientific, River Edge, NJ.
12. Feng Q., Wang H., Ng H.H., Erdjument-Bromage H., Tempst P., Struhl K., Zhang Y. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr. Biol. 12:2002;1052-1058.
13. Fu Z., Hu Y., Konishi K., Takata Y., Ogawa H., Gomi T., Fujioka M., Takusagawa F. Crystal structure of glycine N-methyltransferase from rat liver. Biochemistry. 35:1996;11985-11993.
14. Goedecke K., Pignot M., Goody R.S., Scheidig A.J., Weinhold E. Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog. Nat. Struct. Biol. 8:2001;121-125.
15. Gong W., O'Gara M., Blumenthal R.M., Cheng X. Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res. 25:1997;2702-2715.
16. Heurgue-Hamard V., Champ S., Engstrom A., Ehrenberg M., Buckingham R.H. The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors. EMBO J. 21:2002;769-778.
17. Jackson J.P., Lindroth A.M., Cao X., Jacobsen S.E. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature. 416:2002;556-560.
18. Jacobs S.A., Khorasanizadeh S. Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science. 295:2002;2080-2083.
19. Jacobs S.A., Taverna S.D., Zhang Y., Briggs S.D., Li J., Eissenberg J.C., Allis C.D., Khorasanizadeh S. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J. 20:2001;5232-5241.
20. Jenuwein T., Allis C.D. Translating the histone code. Science. 293:2001;1074-1080.
21. Jenuwein T., Laible G., Dorn R., Reuter G. SET domain proteins modulate chromatin domains in eu- and heterochromatin. Cell. Mol. Life Sci. 54:1998;80-93.
22. Jones T.A., Kjeldgard M. Electron-density map interpretation. Methods Enzymol. 277:1997;173-208.
23. Kouzarides T. Histone methylation in transcriptional control. Curr. Opin. Genet. Dev. 12:2002;198-209.
24. Krogan N.J., Dover J., Khorrami S., Greenblatt J.F., Schneider J., Johnston M., Shilatifard A. COMPASS, a histone H3 (lysine 4) methyltransferase required for telomeric silencing of gene expression. J. Biol. Chem. 277:2002;10753-10755.
25. Lachner M., O'Carroll D., Rea S., Mechtler K., Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature. 410:2001;116-120.
26. Lacoste N., Utley R.T., Hunter J., Poirier G.G., Cote J. Disruptor of telomeric silencing-1 is a chromatin-specific histone H3 methyltransferase. J. Biol. Chem. 277:2002;30421-30424.
27. Laskowski R.A. Procheck. a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26:1993;283-291.
28. Litt M.D., Simpson M., Gaszner M., Allis C.D., Felsenfeld G. Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus. Science. 293:2001;2453-2455.
29. Ma H., Baumann C.T., Li H., Strahl B.D., Rice R., Jelinek M.A., Aswad D.W., Allis C.D., Hager G.L., Stallcup M.R. Hormone-dependent, CARM1-directed, arginine-specific methylation of histone H3 on a steroid-regulated promoter. Curr. Biol. 11:2001;1981-1985.
30. Nakahigashi K., Kubo N., Narita S., Shimaoka T., Goto S., Oshima T., Mori H., Maeda M., Wada C., Inokuchi H. HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination. Proc. Natl. Acad. Sci. USA. 99:2002;1473-1478.
31. Nakayama J., Rice J.C., Strahl B.D., Allis C.D., Grewal S.I. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science. 292:2001;110-113.
32. Ng H.H., Feng Q., Wang H., Erdjument-Bromage H., Tempst P., Zhang Y., Struhl K. Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev. 16:2002;1518-1527.
33. Nicholls A., Sharp K.A., Honig B. Protein folding and association. insights from the interfacial and thermodynamic properties of hydrocarbons Proteins. 11:1991;281-296.
34. Nielsen S.J., Schneider R., Bauer U.M., Bannister A.J., Morrison A., O'Carroll D., Firestein R., Cleary M., Jenuwein T., Herrera R.E., Kouzarides T. Rb targets histone H3 methylation and HP1 to promoters. Nature. 412:2001;561-565.
35. Nielsen P.R., Nietlispach D., Mott H.R., Callaghan J., Bannister A., Kouzarides T., Murzin A.G., Murzina N.V., Laue E.D. Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature. 416:2002;103-107.
36. Nishioka K., Chuikov S., Sarma K., Erdjument-Bromage H., Allis C.D., Tempst P., Reinberg D. Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation. Genes Dev. 16:2002;479-489. a.
37. Nishioka K., Rice J.C., Sarma K., Erdjument-Bromage H., Werner J., Wang Y., Chuikov S., Valenzuela P., Tempst P., Steward R.et al. PR-Set7 Is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol. Cell. 9:2002;1201-1213. b.
38. O'Carroll D., Scherthan H., Peters A.H., Opravil S., Haynes A.R., Laible G., Rea S., Schmid M., Lebersorger A., Jerratsch M.et al. Isolation and characterization of Suv39h2, a second histone H3 methyltransferase gene that displays testis-specific expression. Mol. Cell. Biol. 20:2000;9423-9433.
39. Ogawa H., Ishiguro K., Gaubatz S., Livingston D.M., Nakatani Y. A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in G0 cells. Science. 296:2002;1132-1136.
40. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
41. Rea S., Eisenhaber F., O'Carroll D., Strahl B.D., Sun Z.W., Schmid M., Opravil S., Mechtler K., Ponting C.P., Allis C.D., Jenuwein T. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature. 406:2000;593-599.
42. Robbins A.H., McRee D.E., Williamson M., Collett S.A., Xuong N.H., Furey W.F., Wang B.C., Stout C.D. Refined crystal structure of Cd, Zn metallothionein at 2.0 Å resolution. J. Mol. Biol. 221:1991;1269-1293.
43. Schultz D.C., Ayyanathan K., Negorev D., Maul G.G., Rauscher F.J. 3rd. SETDB1. a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by krab zinc-finger proteins Genes Dev. 16:2002;919-932.
44. Strahl B.D., Allis C.D. The language of covalent histone modifications. Nature. 403:2000;41-45.
45. Strahl B.D., Briggs S.D., Brame C.J., Caldwell J.A., Koh S.S., Ma H., Cook R.G., Shabanowitz J., Hunt D.F., Stallcup M.R., Allis C.D. Methylation of histone H4 at arginine 3 occurs in vivo and is mediated by the nuclear receptor coactivator PRMT1. Curr. Biol. 11:2001;996-1000.
46. Tachibana M., Sugimoto K., Fukushima T., Shinkai Y. Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J. Biol. Chem. 276:2001;25309-25317.
47. Tamaru H., Selker E.U. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature. 414:2001;277-283.
48. Terwilliger T.C. Maximum-likelihood density modification. Acta Crystallogr. D. 56:2000;965-972.
49. Terwilliger T.C., Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr. D. 55:1999;849-861.
50. van Leeuwen F., Gafken P.R., Gottschling D.E. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell. 109:2002;745-756.
51. Vasak M., Hasler D.W. Metallothioneins. new functional and structural insights Curr. Opin. Chem. Biol. 4:2000;177-183.
52. Wang H., Cao R., Xia L., Erdjument-Bromage H., Borchers C., Tempst P., Zhang Y. Purification and functional characterization of a histone H3-lysine 4-specific methyltransferase. Mol. Cell. 8:2001;1207-1217. a.
53. Wang H., Huang Z.Q., Xia L., Feng Q., Erdjument-Bromage H., Strahl B.D., Briggs S.D., Allis C.D., Wong J., Tempst P., Zhang Y. Methylation of histone H4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor. Science. 293:2001;853-857. b.
54. Zhang X., Zhou L., Cheng X. Crystal structure of the conserved core of protein arginine methyltransferase PRMT3. EMBO J. 19:2000;3509-3519.