S-Adenosylmethionine-dependent alkylation reactions: When are radical reactions used?

Bioorganic Chemistry

Volumn 39, Issue 5-6, 2011, Pages 161-170

  Lin, Hening ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

3 Amino 3 carboxypropylation; Cyclopropane fatty acid synthase; Diphthamide; Methylation; Radical SAM enzymes; RNA methylation; Wybutosine

Indexed keywords

ADENINE; ADENOSINE DERIVATIVE; BICARBONATE; CARBON; CARBONYL DERIVATIVE; CYCLOPROPANE; CYTOSINE DERIVATIVE; DNA CYTOSINE; DNA METHYLTRANSFERASE; ELECTROPHILE; FATTY ACID SYNTHASE; MYCOLIC ACID; MYCOLIC ACID CYCLOPROPANE SYNTHASE; NUCLEOSIDE DERIVATIVE; RIBOSOME RNA; RNA ADENOSINE; S ADENOSYLMETHIONINE; SODIUM DITHIONITE; SULFONIUM DERIVATIVE; SYNTHETASE; THYMIDYLATE SYNTHASE; UNCLASSIFIED DRUG; WYBUTOSINE;

3 AMINO 3 CARBOXYPROPYLATION REACTION; ALKYLATION; BIOSYNTHESIS; CHEMICAL MODIFICATION; CRYSTAL STRUCTURE; CYCLOPROPANATION; DNA METHYLATION; ENZYME MECHANISM; ENZYME SYNTHESIS; EPIGENETICS; ESCHERICHIA COLI; FATTY ACID SYNTHESIS; METHYLATION; MICHAEL ADDITION; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOPHILICITY; OXIDATION; PRIORITY JOURNAL; PROTEIN METHYLATION; PYROCOCCUS HORIKOSHII; RADICAL REACTION; REVIEW;

ADENOSINE; ALKYLATION; CYCLOPROPANES; CYTOSINE; DNA; HISTIDINE; METHYLATION; METHYLTRANSFERASES; NUCLEOSIDES; RNA; RNA, RIBOSOMAL, 23S; S-ADENOSYLMETHIONINE;

EID: 80053560047     PISSN: 00452068     EISSN: 10902120     Source Type: Journal    
DOI: 10.1016/j.bioorg.2011.06.001     Document Type: Review

References (60)

1. M. Fontecave, M. Atta, and E. Mulliez S-adenosylmethionine: nothing goes to waste Trends Biochem. Sci. 29 2004 243 249 (Pubitemid 38591318)
2. F. Yan, J.M. LaMarre, R. Rôhrich, J. Wiesner, H. Jomaa, A.S. Mankin, and D.G. Fujimori RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA J. Am. Chem. Soc. 132 2010 3953 3964
3. F. Yan, and D.G. Fujimori RNA methylation by radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift Proc. Natl. Acad. Sci. USA 108 2011 3930 3934
4. T.L. Grove, J.S. Benner, M.I. Radle, J.H. Ahlum, B.J. Landgraf, C. Krebs, and S.J. Booker A radically different mechanism for S-adenosylmethionine- dependent methyltransferases Science 2011
5. Y. Zhang, X. Zhu, A.T. Torelli, M. Lee, B. Dzikovski, R.M. Koralewski, E. Wang, J. Freed, C. Krebs, S.E. Ealick, and H. Lin Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme Nature 465 2010 891 896
6. X. Zhu, B. Dzikovski, X. Su, A.T. Torelli, Y. Zhang, S.E. Ealick, J.H. Freed, and H. Lin Mechanistic understanding of Pyrococcus horikoshii Dph2, a [4Fe-4S] enzyme required for diphthamide biosynthesis Mol. BioSyst. 7 2011 74 81
7. H.L. Schubert, R.M. Blumenthal, and X. Cheng Many paths to methyltransfer: a chronicle of convergence Trends Biochem. Sci. 28 2003 329 335 (Pubitemid 36776296)
8. B. Xiao, C. Jing, J.R. Wilson, P.A. Walker, N. Vasisht, G. Kelly, S. Howell, I.A. Taylor, G.M. Blackburn, and S.J. Gamblin Structure and catalytic mechanism of the human histone methyltransferase SET7/9 Nature 421 2003 652 656 (Pubitemid 36227675)
9. S. Chuikov, J.K. Kurash, J.R. Wilson, B. Xiao, N. Justin, G.S. Ivanov, K. McKinney, P. Tempst, C. Prives, S.J. Gamblin, N.A. Barlev, and D. Reinberg Regulation of p53 activity through lysine methylation Nature 432 2004 353 360 (Pubitemid 39551664)
10. R.C. Trievel, B.M. Beach, L.M.A. Dirk, R.L. Houtz, and J.H. Hurley Structure and catalytic mechanism of a SET domain protein methyltransferase Cell 111 2002 91 103
11. W.R. Riekhof, C. Andre, and C. Benning Two enzymes, BtaA and BtaB, are sufficient for betaine lipid biosynthesis in bacteria Arch. Biochem. Biophys. 441 2005 96 105 (Pubitemid 41188356)
12. A.M. Reeve, S.D. Breazeale, and C.A. Townsend Purification, characterization, and cloning of an S-adenosylmethionine-dependent 3-amino-3-carboxypropyltransferase in nocardicin biosynthesis J. Biol. Chem. 273 1998 30695 30703 (Pubitemid 28545551)
13. Z. Ohashi, M. Maeda, J.A. McCloskey, and S. Nishimura 3-(3-Amino-3-carboxypropyl)uridine. Novel modified nucleoside isolated from Escherichia coli phenylalanine transfer ribonucleic acid Biochemistry 13 1974 2620 2625
14. J.A. Kowalak, E. Bruenger, P.F. Crain, and J.A. McCloskey Identities and phylogenetic comparisons of posttranscriptional modifications in 16 S ribosomal RNA from Haloferax volcanii J. Biol. Chem. 275 2000 24484 24489 (Pubitemid 30626541)
15. S. Friedman, H.J. Li, K. Nakanishi, and G. Van Lear 3-(3-Amino-3- carboxypropyl)uridine. Structure of the nucleoside in Escherichia coli transfer ribonucleic acid that reacts with phenoxyacetoxysuccinimide Biochemistry 13 1974 2932 2937
16. S. Nishimura, Y. Taya, Y. Kuchino, and Z. Ohashi Enzymatic synthesis of 3-(3-amino-3-carboxypropyl) uridine in phenylalanine transfer RNA: transfer of the 3-amino-3-carboxypropyl group from S-adenosylmethionine Biochem. Biophys. Res. Commun. 57 1974 702 708
17. A.G. Saponara, and M.D. Enger The isolation from ribonucleic acid of substituted uridines containing alpha-aminobutyrate moieties derived from methionine Biochim. Biophys. Acta 349 1974 61 77
18. B.E.H. Maden, J. Forbes, P. de Jonge, and J. Klootwijk Presence of a hypermodified nucleotide in hela cell 18 S and Saccharomyces carlsbergensis 17 S ribosomal RNAs FEBS Lett. 59 1975 60 63
19. F. Ikegami, R. Sakai, T. Ishikawa, Y.H. Kuo, F. Lambein, and I. Murakoshi Biosynthesis in vitro of 2-(3-amino-3-carboxypropyl)-isoxazolin-5-one, the neurotoxic amino acid in Lathyrus odoratus Biol. Pharm. Bull. 16 1993 732 734 (Pubitemid 23275928)
20. Y. Ikeguchi, M.C. Bewley, and A.E. Pegg Aminopropyltransferases: function, structure and genetics J. Biochem. 139 2006 1 9 (Pubitemid 43258840)
21. P.A. Frey, A.D. Hegeman, and F.J. Ruzicka The radical SAM superfamily Crit. Rev. Biochem. Mol. Biol. 43 2008 63 88 (Pubitemid 351315858)
22. K.S. Duschene, S.E. Veneziano, S.C. Silver, and J.B. Broderick Control of radical chemistry in the AdoMet radical enzymes Curr. Opin. Chem. Biol. 13 2009 74 83
23. J.L. Vey, and C.L. Drennan Structural insights into radical generation by the radical SAM superfamily Chem. Rev. 111 2011 2487 2506
24. C.-c. Huang, C.V. Smith, M.S. Glickman, W.R. Jacobs, and J.C. Sacchettini Crystal structures of mycolic acid cyclopropane synthases from Mycobacterium tuberculosis J. Biol. Chem. 277 2002 11559 11569 (Pubitemid 34952927)
25. D.F. Iwig, A.T. Grippe, T.A. McIntyre, and S.J. Booker Isotope and elemental effects indicate a rate-limiting methyl transfer as the initial step in the reaction catalyzed by Escherichia coli cyclopropane fatty acid synthase Biochemistry 43 2004 13510 13524 (Pubitemid 39391152)
26. D.F. Iwig, A. Uchida, J.A. Stromberg, and S.J. Booker The activity of Escherichia coli cyclopropane fatty acid synthase depends on the presence of bicarbonate J. Am. Chem. Soc. 127 2005 11612 11613 (Pubitemid 41208741)
27. F. Courtois, and O. Ploux Escherichia coli cyclopropane fatty acid synthase: is a bound bicarbonate ion the active-site base? Biochemistry 44 2005 13583 13590 (Pubitemid 41443686)
28. Y. Yuan, and C.E. Barry A common mechanism for the biosynthesis of methoxy and cyclopropyl mycolic acids in Mycobacterium tuberculosis Proc. Natl. Acad. Sci. USA 93 1996 12828 12833 (Pubitemid 26382728)
29. S. Pohl, J.H. Law, and R. Ryhage The path of hydrogen in the formation of cyclopropane fatty acids Biochim. Biophys. Acta 70 1963 583 585
30. T. Cohen, G. Herman, T.M. Chapman, and D. Kuhn Laboratory model for the biosynthesis of cyclopropane rings. Copper-catalyzed cyclopropanation of olefins by sulfur ylides J. Am. Chem. Soc. 96 1974 5627 5628
31. A. Rios, A.C. O'Donoghue, T.L. Amyes, and J.P. Richard Formation and stability of organic zwitterions - the carbon acid pK as of the trimethylsulfonium and tetramethylphosphonium cations in water Can. J. Chem. 83 2005 1536 1542
32. E.J. Molitor, B.M. Paschal, and H.-w. Liu Cyclopropane fatty acid synthase from Escherichia coli: enzyme purification and inhibition by vinylfluorine and epoxide-containing substrate analogues ChemBioChem 4 2003 1352 1356 (Pubitemid 38036419)
33. M.M. Suzuki, and A. Bird DNA methylation landscapes: provocative insights from epigenomics Nat. Rev. Genet. 9 2008 465 476 (Pubitemid 351693975)
34. R. Bonaccorsi, A. Pullman, E. Scrocco, and J. Tomasi The molecular electrostatic potentials for the nucleic acid bases: adenine, thymine, and cytosine Theor. Chem. Acc.: Theory, Comput., Model. (Theor. Chim. Acta) 24 1972 51 60
35. J.C. Wu, and D.V. Santi Kinetic and catalytic mechanism of HhaI methyltransferase J. Biol. Chem. 262 1987 4778 4786 (Pubitemid 17102852)
36. S. Klimasauskas, S. Kumar, R.J. Roberts, and X. Cheng Hhal methyltransferase flips its target base out of the DNA helix Cell 76 1994 357 369 (Pubitemid 24046697)
37. L. Chen, A.M. MacMillan, and G.L. Verdine Mutational separation of DNA binding from catalysis in a DNA cytosine methyltransferase J. Am. Chem. Soc. 115 1993 5318 5319
38. L. Chen, A.M. MacMillan, W. Chang, K. Ezaz-Nikpay, W.S. Lane, and G.L. Verdine Direct identification of the active-site nucleophile in a DNA (cytosine-5)-methyltransferase Biochemistry 30 1991 11018 11025
39. 5U54)methyltransferase Biochimie 76 1994 1133 1142
40. 5U methyltransferases Proc. Natl. Acad. Sci. USA 105 2008 6876 6881 (Pubitemid 351754498)
41. 5C DNA methyl transferases use different cysteine residues as catalysts Proc. Natl. Acad. Sci. USA 97 2000 8263 8265 (Pubitemid 30639660)
42. 5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate Structure 11 2003 1609 1620 (Pubitemid 37510359)
43. C.W. Carreras, and D.V. Santi The catalytic mechanism and structure of thymidylate synthase Annu. Rev. Biochem. 64 1995 721 762
44. A.M.B. Giessing, S.r.S. Jensen, A. Rasmussen, L.H. Hansen, A. Gondela, K. Long, B. Vester, and F. Kirpekar Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria RNA 15 2009 327 336
45. S.-M. Toh, L. Xiong, T. Bae, and A.S. Mankin The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA RNA 14 2008 98 106
46. C. Kehrenberg, S. Schwarz, L. Jacobsen, L.H. Hansen, and B. Vester A new mechanism for chloramphenicol, florfenicol and clindamycin resistance: methylation of 23S ribosomal RNA at A2503 Mol. Microbiol. 57 2005 1064 1073 (Pubitemid 41139866)
47. H.J. Sofia, G. Chen, B.G. Hetzler, J.F. Reyes-Spindola, and N.E. Miller 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 2001 1097 1106 (Pubitemid 32186195)
48. A. Noma, Y. Kirino, Y. Ikeuchi, and T. Suzuki Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA EMBO J. 25 2006 2142 2154
49. M. Umitsu, H. Nishimasu, A. Noma, T. Suzuki, R. Ishitani, and O. Nureki Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2 Proc. Natl. Acad. Sci. USA 106 2009 15616 15621
50. P.C. Dunlop, and J.W. Bodley Biosynthetic labeling of diphthamide in Saccharomyces cerevisiae J. Biol. Chem. 258 1983 4754 4758 (Pubitemid 13096364)
51. J.Y. Chen, J.W. Bodley, and D.M. Livingston Diphtheria toxin-resistant mutants of Saccharomyces cerevisiae Mol. Cell. Biol. 5 1985 3357 3360 (Pubitemid 16233041)
52. L. Mattheakis, W. Shen, and R. Collier DPH5, a methyltransferase gene required for diphthamide biosynthesis in Saccharomyces cerevisiae Mol. Cell. Biol. 12 1992 4026 4037
53. L.C. Mattheakis, F. Sor, and R.J. Collier Diphthamide synthesis in Saccharomyces cerevisiae: structure of the DPH2 gene Gene 132 1993 149
54. T.J. Moehring, D.E. Danley, and J.M. Moehring In vitro biosynthesis of diphthamide, studied with mutant Chinese hamster ovary cells resistant to diphtheria toxin Mol. Cell. Biol. 4 1984 642 650 (Pubitemid 14130360)
55. S. Liu, G.T. Milne, J.G. Kuremsky, G.R. Fink, and S.H. Leppla Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2 Mol. Cell. Biol. 24 2004 9487 9497 (Pubitemid 39391685)
56. J.E. Carette, C.P. Guimaraes, M. Varadarajan, A.S. Park, I. Wuethrich, A. Godarova, M. Kotecki, B.H. Cochran, E. Spooner, H.L. Ploegh, and T.R. Brummelkamp Haploid genetic screens in human cells identify host factors used by pathogens Science 326 2009 1231 1235
57. J.B. Broderick Biochemistry: a radically different enzyme Nature 465 2010 877 878
58. J.A.M. Simcies, A. Greenberg, and J.F. Liehmun Energetics of Organic Free Radicals vol. 4 1996 Chapman and Hall London
59. S.H. Blobstein, D. Grunberger, I.B. Weinstein, and K. Nakanishi Isolation and structure determination of the fluorescent base from bovine liver phenylalanine transfer ribonucleic acid Biochemistry 12 1973 188 193
60. Y. Suzuki, A. Noma, T. Suzuki, M. Senda, T. Senda, R. Ishitani, and O. Nureki Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA J. Mol. Biol. 372 2007 1204 1214 (Pubitemid 47376935)