Bibliography
- Cheng X , BlumenthalRM (Eds): S-adenosylmethionine-dependent methyltransferases: structures and functions. World Scientific, Singapore (1999).
- Berman BP , WeisenbergerDJ, LairdPW: Locking in on the human methylome.Nature27(4) , 341–342 (2009).
- Jeltsch A : Molecular enzymology of mammalian DNA methyltransferases.Curr. Top. Microbiol. Immunol.301 , 203–225 (2006).
- Kim JK , SamaranayakeM, PardhanS: Epigenetics mechanisms in mammals.Cell. Mol. Life Sci.66(4) , 596–612 (2009).
- Ng SS , YueWW, OppermannU, KloseRJ: Dynamic protein methylation in chromatin biology.Cell. Mol. Life Sci.66(3) , 407–422 (2009).
- Zhao Q , RankG, TanYT et al.: PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing.Nat. Struct. Mol. Biol.16(3) , 304–311 (2009).
- Couture JF , TrievelRC: Histone-modifying enzymes: encrypting an enigmatic epigenetic code.Curr. Opin. Struct. Biol.16(6) , 753–760 (2006).
- Horwich MD , LiC, MatrangaC et al.: The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC.Current Biol.17(14) , 1265–1272 (2007).
- Wassenegger M : The role of the RNAi machinery in heterochromatin formation.Cell122(1) , 13–16 (2005).
- Yu B , YangZ, LiJ et al.: Methylation as a crucial step in plant microRNA biogenesis.Science307(5711) , 932–935 (2005).
- Li J , YangZ, YuB, LiuJ, ChenX: Methylation protects miRNAs and siRNAs from a 3´-end uridylation activity in Arabidopsis.Current Biol.15(16) , 1501–1507 (2005).
- Tkaczuk KL , Dunin-HorkawiczS, PurtaE, BujnickiJM: Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.BMC Bioinformatics8 , 73 (2007).
- Petrossian TC , ClarkeSG: Multiple motif scanning to identify methyltransferases from the yeast proteome.Mol. Cell. Proteomics8(7) , 1516–1526 (2009).
- Kozbial PZ , MushegianAR: Natural history of S-adenosylmethionine-binding proteins.BMC Struct. Biol.5 , 19 (2005).
- Schubert HL , BlumenthalRM, ChengX: Many paths to methyltransfer: a chronicle of convergence.Trends Biochem. Sci.28(6) , 329–335 (2003).
- Martin JL , McMillanFM: SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold.Curr. Opin. Struct. Biol.12(6) , 783–793 (2002).
- Okano M , BellDW, HaberDA, LiE: DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development.Cell99(3) , 247–257 (1999).
- Pavlopoulou A , KossidaS: Plant cytosine-5 DNA methyltransferases: structure, function and molecular evolution.Genomics90(4) , 530–541 (2007).
- Sawada K , YangZ, HortonJR, CollinsRE, ZhangX, ChengX: Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine 79 methyltransferase.J. Biol. Chem.279(41) , 43296–43306 (2004).
- Ingrosso D , FowlerAV, BleibaumJ, ClarkeS: Sequence of the D-aspartyl/D-isoaspartyl protein methyltransferase from human erythrocytes. Common sequence motifs for protein, DNA, RNA and small molecule S-adenosylmethionine-dependent methyltransferases.J. Biol. Chem.264(33) , 20131–20139 (1989).
- Niewmierzycka A , ClarkeS: S-sdenosylmethionine-dependent methylation in Saccharomyces cerevisiae. Identification of a novel protein arginine methyltransferase.J. Biol. Chem.274(2) , 814–824 (1999).
- Kossykh VG , SchlagmanSL, HattmanS: Conserved sequence motif DPPY in region IV of the phage T4 Dam DNA-[N6-adenine]-methyltransferase is important for S-adenosyl-l-methionine binding.Nucl. Acids Res.21(20) , 4659–4662 (1993).
- Zhang X , ZhouL, ChengX: Crystal structure of the conserved core of protein arginine methyltransferase PRMT3.EMBO J.19(14) , 3509–3519 (2000).
- Singer MS , KahanaA, WolfAJ et al.: Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae.Genetics150(2) , 613–632 (1998).
- Fingerman IM , LiHC, BriggsSD: A charge-based interaction between histone H4 and Dot1 is required for H3K79 methylation and telomere silencing: identification of a new trans-histone pathway.Genes Develop.21(16) , 2018–2029 (2007).
- Cheng XD , CollinsRE, ZhangX: Structural and sequence motifs of protein (histone) methylation enzymes.Annu. Rev. Biophys. Biomol. Struct.34 , 267–294 (2005).
- Ng HH , FengQ, WangH et al.: Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association.Genes Develop.16(12) , 1518–1527 (2002).
- Gary JD , LinWJ, YangMC, HerschmanHR, ClarkeS: The predominant protein-arginine methyltransferase from Saccharomyces cerevisiae.J. Biol. Chem.271(21) , 12585–12594 (1996).
- Kagan RM , ClarkeS: Widespread occurrence of three sequence motifs in diverse S-adenosylmethionine-dependent methyltransferases suggests a common structure for these enzymes.Arch. Biochem. Biophys.310(2) , 417–427 (1994).
- Timothy LB , CharlesE: Fitting a mixture model by expectation maximization to discover motifs in biopolymers, in proceedings of the second international conference on intelligent systems for molecular biology, AAAI Press, CA, USA, 28–36 (1994).
- Katz JE , DlakićM, ClarkeS: Automated identification of putative methyltransferases from genomic open reading frames.Mol. Cell. Proteomics2(8) , 525–540 (2003).
- Bailey TL , GribskovM: Combining evidence using p-values: application to sequence homology searches.Bioinformatics14(1) , 48–54 (1998).
- Ansari MZ , SharmaJ, GokhaleRS, MohantyD: In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites.BMC Bioinformatics9 , 454 (2008).
- Söding J , BiegertA, LupasAN: The HHpred interactive server for protein homology detection and structure prediction.Nucl. Acids Res.33 , W244–W248 (2005).
- Huerta-Cepas J , BuenoA, DopazoJ, GabaldónT: PhylomeDB: a database for genome-wide collections of gene phylogenies.Nucl. Acids Res.36 , D491–D496 (2007).
- Atkinson HJ , MorrisJH, FerrinTE, BabbittPC: Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.PLoS ONE4(2) , e4345 (2009).
- Rea S , EisenhaberF, O‘CarrollD et al.: Regulation of chromatin structure by site-specific histone H3 methyltransferases.Nature406(6796) , 593–599 (2000).
- Wang Y : Methylation and demethylation of histone arg and lys residues in chromatin structure and function. In: The Enzymes: Protein Methyltransferases. Clarke SG, Tamanoi F (Eds). Elsevier, Amsterdam, The Netherlands, 123–153 (2006).
- Southall SM , WongPS, OdhoZ, RoeSM, WilsonJR: Structural basis for the requirement of additional factors for mll1 set domain activity and recognition of epigenetic marks.Mol. Cell33(2) , 181–191 (2009).
- Dillon SC , ZhangX, TrievelRC, ChengX: The SET-domain protein superfamily: protein lysine methyltransferases.Genome Biol.6(8) , 227 (2005).
- Xiao B , GamblinSJ, WilsonJR: Structure of set domain protein lysine methyltransferases, In: The Enzymes: Protein Methyltransferases. Clarke SG, Tamanoi F (Eds.). Elsevier, Amsterdam, The Netherlands (2006).
- Aravind L , IyerLM: Provenance of SET-domain histone methyltransferases through duplication of a simple structural unit.Cell Cycle2(4) , 369–376 (2003).
- Xiao B , JingC, WilsonJR et al.: Structure and catalytic mechanism of the human histone methyltransferase SET7/9.Nature421(6923) , 652–656 (2003).
- Couture JF , DirkLM, BrunzelleJS, HoutzRL, TrievelRC: Structural origins for the product specificity of SET domain protein methyltransferases.Proc. Natl Acad. Sci. USA105(52) , 20659–20664 (2008).
- Zhang X , YangZ, KhanSI et al.: Structural basis for the product specificity of histone lysine methyltransferases.Mol. Cell12(1) , 177–185 (2003).
- Qian C , ZhouM: SET domain protein lysine methyltransferases: structure, specificity and catalysis.Cell. Mol. Life Sci.63(23) , 2755–2763 (2006).
- Marmorstein R : Structure of SET domain proteins: a new twist on histone methylation.Trends Biochem. Sci.28(2) , 59–62 (2003).
- Porras-Yakushi TR , WhiteleggeJP, ClarkeS: A novel SET domain methyltransferase in yeast: Rkm2-dependent trimethylation of ribosomal protein L12ab at lysine 10.J. Biol. Chem.281(47) , 35835–35835 (2006).
- Bottomley MJ : Structure of protein domains that create or recognize histone modifications.EMBO Reports5(5) , 464–469 (2004).
- Letunic I , DoerksT, BorkP: SMART 6: recent updates and new developments.Nucleic Acids Res.37(Database issue) , D229–D232 (2009).
- Baumbusch LO , ThorstensenT, KraussV et al.: The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes.Nucl. Acids Res.29(21) , 4319–4333 (2001).
- Springer NM , NapoliCA, SelingerDA et al.: Comparative analysis of set domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots.Plant Physiol.132(2) , 907–925 (2003).
- Ng DW , WangT, ChandrasekharanMB, AramayoR, KertbunditS, HallTC: Plant SET domain-containing proteins: structure, function and regulation.Biochim. Biophys. Acta1769(5–6) , 316–329 (2007).
- Dirk LMA , TrievelRC, HoutzRL: Nonhistone protein lysine methyltransferases: structure and catalytic roles, in the enzymes: protein methyltransferases. Clarke SG, Tamanoi F (Eds.), Elsevier, Amsterdam, The Netherlands, 178–228 (2006).
- Anantharaman V , KooninEV, AravindL: SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies and novel superfamilies of predicted prokaryotic RNA methylases.J. Mol. Microbiol. Biotechnol.4(1) , 71–75 (2002).
- Das K , ActonT, ChiangY, ShihL, ArnoldE, MontelioneGT: Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site.Proc. Natl Acad. Sci. USA101(12) , (2003).
- Michel G , SauveV, LarocqueR, LiY, MatteA, CyglerM: The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot.Structure10(10) , 1303–1315 (2002).
- Nureki O , WatanabeK, FukaiS et al.: Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme.Structure12(4) , 593–602 (2004).
- Watanabe K , NurekiO, FukaiS et al.: Roles of conserved amino acid sequence motifs in the SpoU (TrmH) RNA methyltransferase family.J. Biol. Chem.280(11) , 10368–10377 (2005).
- Taylor AB , MeyerB, LealBZ et al.: The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a preorganized SAM-binding site.Nucleic Acids Res.36(5) , 1542–1554 (2008).
- Leulliot N , BohnsackMT, GrailleM, TollerveyD, VanTH: The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of α/β knot fold methyltransferases.Nucleic Acids Res.36(2) , 626–639 (2008).
- Matthews RG , KoutmosM, DattaS: Cobalamin-dependent and cobamide-dependent methyltransferases.Curr. Opin. Struct. Biol.18(6) , 658–666 (2009).
- Dixon MM , HuangS, MatthewsRG, LudwigM: The structure of the C-terminal domain of methionine synthase: presenting S-adenosylmethionine for reductive methylation of B12.Structure4(11) , 1263–1275 (1996).
- Sali A , PottertonL, YuanF, van Vlijmen H, Karplus M: Evaluation of comparative protein modelling by MODELLER. Proteins23(3) , 318–326 (1995).
- Kelley LA , SternbergMJE: Protein structure prediction on the web: a case study using the Phyre server.Nat. Protoc.4(3) , 363–371 (2009).
- Vinci CR , ClarkeSG: Recognition of age-damaged (R,S)-adenosyl-L-methionine by two methyltransferases in the yeast Saccharomyces cerevisiae.J. Biol. Chem.282(12) , 8604–8612 (2007).
- Koutmos M , PejchalR, BomerTM, MatthewsRG, SmithJL, LudwigML: Metal active site elasticity linked to activation of homocysteine in methionine synthases.Proc. Natl Acad. Sci. USA105(9) , 3286–3291 (2008).
- Ferrer J -L, Ravanel S, Robert M, Dumas R: Crystal structures of cobalamin-independent methionine synthase complexed with zinc, homocysteine, and methyltetrahydrofolate. J. Biol. Chem.279(43) , 44235–44238 (2004).
- Sofia HJ , ChenG, HetzlerBG, Reyes-SpindolaJF, MillerNE: Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods.Nucl. Acids Res.29(5) , 1097–1106 (2001).
- Berkovitch F , NicoletY, WanJT, JarrettJT, DrennanCL: Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.Science303(5654) , 76–79 (2004).
- Wang SC , FreyPA: S-adenosylmethionine as an oxidant: the radical SAM superfamily.Cell32(3) , 101–110 (2007).
- Booker SJ : Anaerobic functionalization of unactivated C-H bonds.Curr. Opin. Chem. Biol.13(1) , 58–73 (2009).
- Pruitt KD , TatusovaT, MaglottDR: NCBI reference sequences (RefSeq): a curated nonredundant sequence database of genomes, transcripts and proteins.Nucleic Acids Res.35(Database issue) , D61–D65 (2007).
- Schubert HL , WilsonKS, RauxE, WoodcockSC, WarrenMJ: The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase.Nature Struct. Biol.5(7) , 585–592 (1998).
- Romano JD , MichaelisS: Topological and mutational analysis of Saccharomyces cerevisiae Ste14p, founding member of the isoprenylcysteine carboxyl methyltransferase family.Mol. Biol. Cell12(7) , 1957–1971 (2001).
- Finn RD , TateJ, MistryJ et al.: The Pfam protein families database.Nucleic Acids Res.36(Database Issue) , D281–D288 (2008).
- Clancy MJ , ShambaughME, TimpteCS, BokarJA: Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: a potential mechanism for the activity of the IME4 gene.Nucl. Acids Res.30(20) , 4509–4518 (2002).
- Subbaramaiah K , SimmsSA: Photolabeling of CheR methyltransferase with S-adenosyl-L-methionine (AdoMet). Studies on the AdoMet binding site.J. Biol. Chem.267(12) , 8636–8642 (1992).
- Zhou S , BaileyMJ, DunnMJ, PreedyVR, EmeryPW: A systematic investigation into the recovery of radioactively labeled proteins from sodium dodecyl sulfate-polyacrylamide gels.Electrophoresis25(1) , 1–7 (2003).
- Zhou S , MannCJ, DunnMJ, PreedyVR, EmeryPW: Measurement of specific radioactivity in proteins separated by two-dimensional gel electrophoresis.Electrophoresis27(5–6) , 1147–1153 (2006).
- Zhu H , BilginM, BanghamR et al.: Global analysis of protein activities using proteome chips.Science293(5537) , 2101–2105 (2001).
- Rathert P , DhayalanA, MaH, JeltschA: Specificity of protein lysine methyltransferases and methods for detection of lysine methylation of nonhistone proteins.Mol. Biosyst.4(12) , 1186–1190 (2008).
- Laskowski RA : PDBsum new things.Nucl. Acids Res.37 , D355–D359 (2009).
- Tatusov RL , FedorovaND, JacksonJD et al.: The COG database: an updated version includes eukaryotes.BMC Bioinformatics4 , 41 (2003).
▪Websites
- Download of the Multiple Motif Scanning program, which is freely available www.chem.ucla.edu/files/MotifSetup.Zip
- Saccharomyces Genome Database (SGD), the scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiaewww.yeastgenome.org/
- UniProt website: comprehensive database of protein information www.uniprot.org