Natural history of S-adenosylmethionine-binding proteins

BMC Structural Biology

Volumn 5, Issue , 2005, Pages

  Kozbial, Piotr Z ^a   Mushegian, Arcady R ^a,b  

^a STOWERS INSTITUTE FOR MEDICAL RESEARCH   (United States)

^b UNIVERSITY OF KANSAS SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

1 AMINCYCLOPROPANE 1 CARBOXYLATE SYNTHASE; 5' FLUORO 5 DEOXY ADENOSINE SYNTHASE; ACYL HOMOSERINE LACTONE SYNTHASE; ADENOSYLMETHIONINE DECARBOXYLASE; BINDING PROTEIN; CYCLOPROPANE FATTY ACID SYNTHETASE; ENZYME; METHIONINE ADENOSYLTRANSFERASE; METHYLTRANSFERASE; METJ METHIONINE REPRESSOR; NICOTIANAMINE SYNTHASE; NUCLEIC ACID; POLYAMINE; PORPHYRIN C METHYLTRANSFERASE; ROSSMANN FOLD METHYLTRANSFERASE; S ADENOSYLMETHIONINE; S ADENOSYLMETHIONINE DEPENDENT RADICAL ENZYME; SET DOMAIN METHYLTRANSFERASE; SPERMIDINE SYNTHASE; SPOUT METHYLTRANSFERASE; TRANSFER RNA RIBOSYL TRANSFERASE ISOMERASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BIOSYNTHESIS; CHEMICAL PROCEDURES; GENETIC VARIABILITY; METHYLATION; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; BIOCHEMISTRY; CARBOXY-LYASES; CARRIER PROTEINS; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PHYLOGENY; PORPHYRINS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOMICS; S-ADENOSYLMETHIONINE; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 27844530636     PISSN: 14726807     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-5-19     Document Type: Article

References (148)

1. Waddell TG, Eilders LL, Patel BP, Sims M: Prebiotic methylation and the evolution of methyl transfer reactions in living cells. Orig Life Evol Biosph 2000, 30:539-548.
2. Thomas DJ, Waters SB, Styblo M: Elucidating the pathway for arsenic methylation. Toxicol Appl Pharmacol 2004, 198:319-326.
3. Wuosmaa AM, Hager LP: Methyl chloride transferase: a carbocation route for biosynthesis of halometabolites. Science 1990, 249:160-162.
4. Saxena D, Aouad S, Attieh J, Saini HS: Biochemical characterization of chloromethane emission from the wood-rotting fungus Phellinus pomaceus. Appl Environ Microbiol 1998, 64:2831-2835.
5. Anantharaman V, Koonin EV, Aravind L: Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res 2002, 30:1427-1464.
6. Hopper AK, Phizicky EM: tRNA transfers to the limelight. Genes Dev 2003, 17:162-180.
7. Kouzarides T: Histone methylation in transcriptional control. Curr Opin Genet Dev 2002, 12:198-209.
8. Aravind L, Koonin EV: Novel predicted RNA-binding domains associated with the translation machinery. J Mol Evol 1999, 48:291-302.
9. Romano JD, Michaelis S: Topological and mutational analysis of Saccharomyces cerevisiae Ste14p, founding member of the isoprenylcysteine carboxyl methyltransferase family. Mol Biol Cell 2001, 12:1957-1971.
10. Anderson JL, Frase H, Michaelis S, Hrycyna CA: Purification, functional reconstitution, and characterization of the Saccharomyces cerevisiae isoprenylcysteine carboxylmethyltransferase Ste14p. J Biol Chem 2005, 280:7336-7345.
11. Peterson YK, Winter-Vann AM, Casey PJ: Icmt. AfCS-Nature Molecule Pages 2005, : [http://www.signaling-gateway.org/molecule/query?afcsid=A001154]. doi:10.1038/mp.a001154.01
12. Schubert HL, Blumenthal RM, Cheng X: Many paths to methyltransfer: a chronicle of convergence. Trends Biochem Sci 2003, 28:329-335.
13. Fontecave M, Atta M, Mulliez E: S-adenosylmethionine: nothing goes to waste. Trends Biochem Sci 2004, 29:243-249.
14. Lesk AM: NAD-binding domains of dehydrogenases. Curr Opin Struct Biol 1995, 5:775-783.
15. Wolf YI, Brenner SE, Bash PA, Koonin EV: Distribution of protein folds in the three superkingdoms of life. Genome Res 1999, 9:17-26.
16. Martin JL, McMillan FM: SAM (dependent) I AM: the S-adenosylmethionine- dependent methyltransferase fold. Curr Opin Struct Biol 2002, 12:783-793.
17. Bujnicki JM: Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation. In Silico Biol 1999, 1:175-182.
18. Posfai J, Bhagwat AS, Posfai G, Roberts RJ: Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res 1989, 17:2421-2435.
19. Fauman EB, Blumenthal RM, Cheng X: Structure and evolution of AdoMet-dependent MTases. In In S-Adenosylmethionine-dependent methyltransferases: structures and functions Edited by: Cheng X and Blumenthal RM. Singapore, World Scientific Inc.; 1999:1-38.
20. Bujnicki JM: Sequence permutations in the molecular evolution of DNA methyltransferases. BMC Evol Biol 2002, 2:3.
21. Sankpal UT, Rao DN: Mutational analysis of conserved residues in HhaI DNA methyltransferase. Nucleic Acids Res 2002, 30:2628-2638.
22. Cheng X: Structure and function of DNA methyltransferases. Annu Rev Biophys Biomol Struct 1995, 24:293-318.
23. Kumar S, Cheng X, Klimasauskas S, Mi S, Posfai J, Roberts RJ, Wilson GG: The DNA (cytosine-5) methyltransferases. Nucleic Acids Res 1994, 22:1-10.
24. Bugl H, Fauman EB, Staker BL, Zheng F, Kushner SR, Saper MA, Bardwell JC, Jakob U: RNA methylation under heat shock control. Mol Cell 2000, 6:349-360.
25. Feder M, Pas J, Wyrwicz LS, Bujnicki JM: Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2′-O-methyltransferases. Gene 2003, 302:129-138.
26. Liu J, Mushegian A: Three monophyletic superfamilies account for the majority of the known glycosyltransferases. Protein Sci 2003, 12:1418-1431.
27. Cheek S, Zhang H, Grishin NV: Sequence and structure classification of kinases. J Mol Biol 2002, 320:855-881.
28. Unligil UM, Zhou S, Yuwaraj S, Sarkar M, Schachter H, Rini JM: X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily. EMBO J 2000, 19:5269-5280.
29. Qasba PK, Ramakrishnan B, Boeggeman E: Substrate-induced conformational changes in glycosyltransferases. Trends Biochem Sci 2005, 30:53-62.
30. Nes WD, Marshall JA, Jia Z, Jaradat TT, Song Z, Jayasimha P: Active site mapping and substrate channeling in the sterol methyltransferase pathway. J Biol Chem 2002, 277:42549-42556.
31. Zubieta C, He XZ, Dixon RA, Noel JP: Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases. Nat Struct Biol 2001, 8:271-279.
32. Huang CC, Smith CV, Glickman MS, Jacobs JWR, Sacchettini JC: Crystal structures of mycolic acid cyclopropane synthases from Mycobacterium tuberculosis. J Biol Chem 2002, 277:11559-11569.
33. Takahashi M, Terada Y, Nakai I, Nakanishi H, Yoshimura E, Mori S, Nishizawa NK: Role of nicotianamine in the intracellular delivery of metals and plant reproductive development. Plant Cell 2003, 15:1263-1280.
34. Dela Vega AL, Delcour AH: Polyamines decrease Escherichia coli outer membrane permeability. J Bacteriol 1996, 178:3715-3721.
35. Nikaido H: Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev 2003, 67:593-656.
36. Korolev S, Ikeguchi Y, Skarina T, Beasley S, Arrowsmith C, Edwards A, Joachimiak A, Pegg AE, Savchenko A: The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor. Nat Struct Biol 2002, 9:27-31.
37. Jansson A, Koskiniemi H, Erola A, Wang J, Mantsala P, Schneider G, Niemi J: Aclacinomycin 10-hydroxylase is a novel substrate-assisted hydroxylase requiring S-adenosyl-L-methionine as cofactor. J Biol Chem 2005, 280:3636-3644.
38. McCulloch V, Shadel GS: Human mitochondrial transcription factor B1 interacts with the C-terminal activation region of h-mtTFA and stimulates transcription independently of its RNA methyltransferase activity. Mol Cell Biol 2003, 23:5816-5824.
39. Bujnicki JM: In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea. FEBS Lett 2001, 507:123-127.
40. Anderson J, Phan L, Hinnebusch AG: The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2000, 97:5173-5178.
41. Bujnicki JM, Feder M, Radlinska M, Blumenthal RM: Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m(6)A methyltransferase. J Mol Evol 2002, 55:431-444.
42. Bujnicki JM, Rychlewski L: RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited-bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure. BMC Bioinformatics 2002, 3:10.
43. Chen ZX, Mann JR, Hsieh CL, Riggs AD, Chedin F: Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family. J Cell Biochem 2005, 95:902-917.
44. Gowher H, Liebert K, Hermann A, Xu G, Jeltsch A: Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L. J Biol Chem 2005, 280:13341-13348.
45. Bourc'his D, Bestor TH: Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 2004, 431:96-99.
46. Dong C, Huang F, Deng H, Schaffrath C, Spencer JB, O'Hagan D, Naismith JH: Crystal structure and mechanism of a bacterial fluorinating enzyme. Nature 2004, 427:561-565.
47. Anantharaman V, Koonin EV, Aravind L: 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 2002, 4:71-75.
48. Jackman JE, Montange RK, Malik HS, Phizicky EM: Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9. RNA 2003, 9:574-585.
49. Ginalski K, von Grotthuss M, Grishin NV, Rychlewski L: Detecting distant homology with Meta-BASIC. Nucleic Acids Res 2004, 32:W576-81.
50. Ahn HJ, Kim HW, Yoon HJ, Lee BI, Suh SW, Yang JK: Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition. EMBO J 2003, 22:2593-2603.
51. Gerstein M: A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure. J Mol Biol 1997, 274:562-576.
52. Nagano N, Orengo CA, Thornton JM: One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol 2002, 321:741-765.
53. Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE: 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. Nucleic Acids Res 2001, 29:1097-1106.
54. Ollagnier-de Choudens S, Sanakis Y, Hewitson KS, Roach P, Munck E, Fontecave M: Reductive cleavage of S-adenosylmethionine by biotin synthase from Escherichia coli. J Biol Chem 2002, 277:13449-13454.
55. Nicolet Y, Drennan CL: AdoMet radical proteins-from structure to evolution-alignment of divergent protein sequences reveals strong secondary structure element conservation. Nucleic Acids Res 2004, 32:4015-4025.
56. Ginalski K, Elofsson A, Fischer D, Rychlewski L: 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003, 19:1015-1018.
57. Marton LJ, Pegg AE: Polyamines as targets for therapeutic intervention. Annu Rev Pharmacol Toxicol 1995, 35:55-91.
58. Gerner EW, Meyskens FLJ: Polyamines and cancer: old molecules, new understanding. Nat Rev Cancer 2004, 4:781-792.
59. Kim AD, Graham DE, Seeholzer SH, Markham GD: S-Adenosylmethionine decarboxylase from the archaeon Methanococcus jannaschii: identification of a novel family of pyruvoyl enzymes. J Bacteriol 2000, 182:6667-6672.
60. Sekowska A, Coppee JY, Le Caer JP, Martin-Verstraete I, Danchin A: S-adenosylmethionine decarboxylase of Bacillus subtilis is closely related to archaebacterial counterparts. Mol Microbiol 2000, 36:1135-1147.
61. Ekstrom JL, Mathews II, Stanley BA, Pegg AE, Ealick SE: The crystal structure of human S-adenosylmethionine decarboxylase at 2.25 A resolution reveals a novel fold. Structure Fold Des 1999, 7:583-595.
62. Toms AV, Kinsland C, McCloskey DE, Pegg AE, Ealick SE: Evolutionary links as revealed by the structure of Thermotoga maritima S-adenosylmethionine decarboxylase. J Biol Chem 2004, 279:33837-33846.
63. Lu ZJ, Markham GD: Catalytic properties of the archaeal S-adenosylmethionine decarboxylase from Methanococcus jannaschii. J Biol Chem 2004, 279:265-273.
64. Bennett EM, Ekstrom JL, Pegg AE, Ealick SE: Monomeric S-adenosylmethionine decarboxylase from plants provides an alternative to putrescine stimulation. Biochemistry 2002, 41:14509-14517.
65. Trievel RC, Beach BM, Dirk LM, Houtz RL, Hurley JH: Structure and catalytic mechanism of a SET domain protein methyltransferase. Cell 2002, 111:91-103.
66. Yokoyama A, Wang Z, Wysocka J, Sanyal M, Aufiero DJ, Kitabayashi I, Herr W, Cleary ML: Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression. Mol Cell Biol 2004, 24:5639-5649.
67. Kouskouti A, Scheer E, Staub A, Tora L, Talianidis I: Gene-specific modulation of TAF10 function by SET9-mediated methylation. Mol Cell 2004, 14:175-182.
68. Chuikov S, Kurash JK, Wilson JR, Xiao B, Justin N, Ivanov GS, McKinney K, Tempst P, Prives C, Gamblin SJ, Barlev NA, Reinberg D: Regulation of p53 activity through lysine methylation. Nature 2004, 432:353-360.
69. Xiao B, Jing C, Wilson JR, Walker PA, Vasisht N, Kelly G, Howell S, Taylor IA, Blackburn GM, Gamblin SJ: Structure and catalytic mechanism of the human histone methyltransferase SET7/9. Nature 2003, 421:652-656.
70. Manzur KL, Farooq A, Zeng L, Plotnikova O, Koch AW, Sachchidanand, Zhou MM: A dimeric viral SET domain methyltransferase specific to Lys27 of histone H3. Nat Struct Biol 2003, 10:187-196.
71. Aravind L, Iyer LM: Provenance of SET-domain histone methyltransferases through duplication of a simple structural unit. Cell Cycle 2003, 2:369-376.
72. Iyer LM, Aravind L: The emergence of catalytic and structural diversity within the beta-clip fold. Proteins 2004, 55:977-991.
73. Sanchez-Perez GF, Bautista JM, Pajares MA: Methionine adenosyltransferase as a useful molecular systematics tool revealed by phylogenetic and structural analyses. J Mol Biol 2004, 335:693-706.
74. Komoto J, Yamada T, Takata Y, Markham GD, Takusagawa F: Crystal structure of the S-adenosylmethionine synthetase ternary complex: a novel catalytic mechanism of S-adenosylmethionine synthesis from ATP and Met. Biochemistry 2004, 43:1821-1831.
75. Graham DE, Bock CL, Schalk-Hihi C, Lu ZJ, Markham GD: Identification of a highly diverged class of S-adenosylmethionine synthetases in the archaea. J Biol Chem 2000, 275:4055-4059.
76. Huai Q, Xia Y, Chen Y, Callahan B, Li N, Ke H: Crystal structures of 1-aminocyclopropane-1-carboxylate (ACC) synthase in complex with aminoethoxyvinylglycine and pyridoxal-5′-phosphate provide new insight into catalytic mechanisms. J Biol Chem 2001, 276:38210-38216.
77. Jakubowicz M: Structure, catalytic activity and evolutionary relationships of 1-aminocyclopropane-1-carboxylate synthase, the key enzyme of ethylene synthesis in higher plants. Acta Biochim Pol 2002, 49:757-774.
78. Capitani G, Eliot AC, Gut H, Khomutov RM, Kirsch JF, Grutter MG: Structure of 1-aminocyclopropane-1-carboxylate synthase in complex with an amino-oxy analogue of the substrate: implications for substrate binding. Biochim Biophys Acta 2003, 1647:55-60.
79. Tsuchisaka A, Theologis A: Heterodimeric interactions among the 1-amino-cyclopropane-1-carboxylate synthase polypeptides encoded by the Arabidopsis gene family. Proc Natl Acad Sci U S A 2004, 101:2275-2280.
80. Eliot AC, Kirsch JF: Avoiding the road less traveled: how the topology of enzyme-substrate complexes can dictate product selection. Acc Chem Res 2003, 36:757-765.
81. Feng L, Geck MK, Eliot AC, Kirsch JF: Aminotransferase activity and bioinformatic analysis of 1-aminocyclopropane-1-carboxylate synthase. Biochemistry 2000, 39:15242-15249.
82. Fuqua C, Parsek MR, Greenberg EP: Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. Annu Rev Genet 2001, 35:439-468.
83. Redfield RJ: Is quorum sensing a side effect of diffusion sensing? Trends Microbiol 2002, 10:365-370.
84. Lerat E, Moran NA: The evolutionary history of quorum-sensing systems in bacteria. Mol Biol Evol 2004, 21:903-913.
85. Val DL, Cronan JEJ: In vivo evidence that S-adenosylmethionine and fatty acid synthesis intermediates are the substrates for the LuxI family of autoinducer synthases. J Bacteriol 1998, 180:2644-2651.
86. Watson WT, Minogue TD, Val DL, von Bodman SB, Churchill ME: Structural basis and specificity of acyl-homoserine lactone signal production in bacterial quorum sensing. Mol Cell 2002, 9:685-694.
87. Gould TA, Schweizer HP, Churchill ME: Structure of the Pseudomonas aeruginosa acyl-homoserinelactone synthase LasI. Mol Microbiol 2004, 53:1135-1146.
88. He YY, Stockley PG, Gold L: In vitro evolution of the DNA binding sites of Escherichia coli methionine repressor, MetJ. J Mol Biol 1996, 255:55-66.
89. Saint-Girons I, Belfaiza J, Guillou Y, Perrin D, Guiso N, Barzu O, Cohen GN: Interactions of the Escherichia coli methionine repressor with the metF operator and with its corepressor, S-adenosylmethionine. J Biol Chem 1986, 261:10936-10940.
90. Cooper A, McAlpine A, Stockley PG: Calorimetric studies of the energetics of protein-DNA interactions in the E. coli methionine repressor (MetJ) system. FEBS Lett 1994, 348:41-45.
91. Rafferty JB, Somers WS, Saint-Girons I, Phillips SE: Three-dimensional crystal structures of Escherichia coli met repressor with and without corepressor. Nature 1989, 341:705-710.
92. Somers WS, Phillips SE: Crystal structure of the met repressoroperator complex at 2.8 A resolution reveals DNA recognition by beta-strands. Nature 1992, 359:387-393.
93. Phillips K, Phillips SE: Electrostatic activation of Escherichia coli methionine repressor. Structure 1994, 2:309-316.
94. Parsons ID, Persson B, Mekhalfia A, Blackburn GM, Stockley PG: Probing the molecular mechanism of action of co-repressor in the E. coli methionine repressor-operator complex using surface plasmon resonance (SPR). Nucleic Acids Res 1995, 23:211-216.
95. Aravind L, Koonin EV: DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res 1999, 27:4658-4670.
96. Scott JW, Hawley SA, Green KA, Anis M, Stewart G, Scullion GA, Norman DG, Hardie DG: CBS domains form energy-sensing modules whose binding of adenosine ligands is disrupted by disease mutations. J Clin Invest 2004, 113:274-284.
97. Kemp BE: Bateman domains and adenosine derivatives form a binding contract. J Clin Invest 2004, 113:182-184.
98. Banerjee R, Zou CG: Redox regulation and reaction mechanism of human cystathionine-beta-synthase: a PLP-dependent hemesensor protein. Arch Biochem Biophys 2005, 433:144-156.
99. McLean JE, Hamaguchi N, Belenky P, Mortimer SE, Stanton M, Hedstrom L: Inosine 5′-monophosphate dehydrogenase binds nucleic acids in vitro and in vivo. Biochem J 2004, 379:243-251.
100. Koonin EV, Wolf YI, Karev GP: The structure of the protein universe and genome evolution. Nature 2002, 420:218-223.
101. Stroupe ME, Leech HK, Daniels DS, Warren MJ, Getzoff ED: CysG structure reveals tetrapyrrole-binding features and novel regulation of siroheme biosynthesis. Nat Struct Biol 2003, 10:1064-1073.
102. Vevodova J, Graham RM, Raux E, Schubert HL, Roper DI, Brindley AA, Ian Scott A, Roessner CA, Stamford NP, Stroupe ME, Getzoff ED, Warren MJ, Wilson KS: Structure/function studies on a S-adenosyl-L-methionine-dependent uroporphyrinogen III C methyltransferase (SUMT), a key regulatory enzyme of tetrapyrrole biosynthesis. J Mol Biol 2004, 344:419-433.
103. Dixon MM, Huang S, Matthews RG, Ludwig M: The structure of the C-terminal domain of methionine synthase: presenting S-adenosylmethionine for reductive methylation of B12. Structure 1996, 4:1263-1275.
104. Bandarian V, Pattridge KA, Lennon BW, Huddler DP, Matthews RG, Ludwig ML: Domain alternation switches B(12)-dependent methionine synthase to the activation conformation. Nat Struct Biol 2002, 9:53-56.
105. Jarrett JT, Huang S, Matthews RG: Methionine synthase exists in two distinct conformations that differ in reactivity toward methyltetrahydrofolate, adenosylmethionine, and flavodoxin. Biochemistry 1998, 37:5372-5382.
106. England JL, Shakhnovich BE, Shakhnovich EI: Natural selection of more designable folds: a mechanism for thermophilic adaptation. Proc Natl Acad Sci U S A 2003, 100:8727-8731.
107. Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
108. Teichmann SA, Park J, Chothia C: Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc Natl Acad Sci U S A 1998, 95:14658-14663.
109. Gough J, Karplus K, Hughey R, Chothia C: Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 2001, 313:903-919.
110. Madera M, Vogel C, Kummerfeld SK, Chothia C, Gough J: The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res 2004, 32:D235-9.
111. Muller A, MacCallum RM, Sternberg MJ: Structural characterization of the human proteome. Genome Res 2002, 12:1625-1641.
112. Keller JP, Smith PM, Benach J, Christendat D, deTitta GT, Hunt JF: The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase. Structure (Camb) 2002, 10:1475-1487.
113. Min J, Feng Q, Li Z, Zhang Y, Xu RM: Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase. Cell 2003, 112:711-723.
114. Christian T, Evilia C, Williams S, Hou YM: Distinct origins of tRNA(m1G37) methyltransferase. J Mol Biol 2004, 339:707-719.
115. Perez-Rueda E, Collado-Vides J, Segovia L: Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem 2004, 28:341-350.
116. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA: The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4:41.
117. Anantharaman V, Aravind L, Koonin EV: Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins. Curr Opin Chem Biol 2003, 7:12-20.
118. Mushegian A: Protein content of minimal and ancestral ribosome. RNA 2005, 11:1400-1406.
119. Copley RR, Bork P: Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways. J Mol Biol 2000, 303:627-641.
120. Walker DR, Koonin EV: SEALS: a system for easy analysis of lots of sequences. Proc Int Conf Intell Syst Mol Biol 1997, 5:333-339.
121. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
122. Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
123. Sadreyev R, Grishin N: COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol 2003, 326:317-336.
124. Guda C, Lu S, Scheeff ED, Bourne PE, Shindyalov IN: CE-MC: a multiple protein structure alignment server. Nucleic Acids Res 2004, 32:W100-3.
125. Holm L, Sander C: Searching protein structure databases has come of age. Proteins 1994, 19:165-173.
126. Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797.
127. DeLano WL: The PyMOL Molecular Graphics System. 2002, http://www.pymol.org:.
128. McGuffin LJ, Bryson K, Jones DT: The PSIPRED protein structure prediction server. Bioinformatics 2000, 16:404-405.
129. Rost B, Yachdav G, Liu J: The PredictProtein server. Nucleic Acids Res 2004, 32:W321-6.
130. Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R: Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 2003, 53 Suppl 6:491-496.
131. Rychlewski L, Jaroszewski L, Li W, Godzik A: Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000, 9:232-241.
132. Kelley LA, MacCallum RM, Sternberg MJ: Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000, 299:499-520.
133. Fischer D: Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac Symp Biocomput 2000:119-130.
134. Ginalski K, Pas J, Wyrwicz LS, von Grotthuss M, Bujnicki JM, Rychlewski L: ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res 2003, 31:3804-3807.
135. Shi J, Blundell TL, Mizuguchi K: FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001, 310:243-257.
136. Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A: Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001, 10:2354-2362.
137. Michalopoulos I, Torrance GM, Gilbert DR, Westhead DR: TOPS: an enhanced database of protein structural topology. Nucleic Acids Res 2004, 32:D251-4.
138. Mirkin BG, Fenner TI, Galperin MY, Koonin EV: Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol 2003, 3:2.
139. SCOP Superfamily: S-adenosyl-L-methionine-dependent methyltransferases. [http://scop.mrc-lmb.cam.ac.uk/scop/searchcgi?sunid=53335] .
140. UniProt Knowledgebase: list of organism identification codes. [http://www.expasy.org/cgi-bin/speclist] .
141. Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH: CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res 2003, 31:383-387.
142. Imai A, Matsuyama T, Hanzawa Y, Akiyama T, Tamaoki M, Saji H, Shirano Y, Kato T, Hayashi H, Shibata D, Tabata S, Komeda Y, Takahashi T: Spermidine synthase genes are essential for survival of Arabidopsis. Plant Physiol 2004, 135:1565-1573.
143. Imai A, Akiyama T, Kato T, Sato S, Tabata S, Yamamoto KT, Takahashi T: Spermine is not essential for survival of Arabidopsis. FEBS Lett 2004, 556:148-152.
144. Chattopadhyay MK, Tabor CW, Tabor H: Spermidine but not spermine is essential for hypusine biosynthesis and growth in Saccharomyces cerevisiae: spermine is converted to spermidine in vivo by the FMS1-amine oxidase. Proc Natl Acad Sci U S A 2003, 100:13869-13874.
145. Sapperstein S, Berkower C, Michaelis S: Nucleotide sequence of the yeast STE14 gene, which encodes farnesylcysteine carboxyl methyltransferase, and demonstration of its essential role in a-factor export. Mol Cell Biol 1994, 14:1438-1449.
146. Gomez-Gomez L, Carrasco P: Differential expression of the Sadenosyl-L-methionine synthase genes during pea development. Plant Physiol 1998, 117:397-405.
147. Sanchez-Aguayo I, Rodriguez-Galan JM, Garcia R, Torreblanca J, Pardo JM: Salt stress enhances xylem development and expression of S-adenosyl-L-methionine synthase in lignifying tissues of tomato plants. Planta 2004, 220:278-285.
148. Jarrett JT: The generation of 5′-deoxyadenosyl radicals by adenosylmethionine-dependent radical enzymes. Curr Opin Chem Biol 2003, 7:174-182.