RNA-modifying metalloenzymes

DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution

Volumn , Issue , 2009, Pages 347-362

  Atta, Mohamed ^a   Fontecave, Marc ^a   Mulliez, Etienne ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 78649656820     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (83)

1. Björk GR. In: tRNA: Strucwre, Biosynthesis and Function. Washington, D. C.: ASM Press 1995
2. Rozenski J, Crain PF, McCloskey JA. The RNA Modification Database: 1999 update. Nucleic Acids Res 1999; 27(1):196-7.
3. Dunin-Horkawicz S, Czerwoniec A, Gajda MJ et al. MODOMICS: a database of RNA modification pathways. Nucleic Acids Res 2006; 34(Database issue):D145-9.
4. Hopper AK, Phizicky EM. tRNA transfers to the limelight. Genes Dev 2003; 17(2):162-80.
5. Darrell DR. Biophysical and Conformational properties of Modified Nucleosides in RNA. Washington, DC: ASM press. 1998.
6. Morris RC, Brown KG, Elliott MS. The effect of qucuosine on tRNA structure and function. J Biomol Struct Dyn 1999; 16(4):757-74.
7. Iwata-Reuyl D. An embarrassment of riches: the cnzymology of RNA modification. Curr Opin Chem Biol 2008; 12(2): 126-33.
8. de Crccy-Lagard V. Identification of genes encoding tRNA modification enzymes by comparative genomics. Methods Enzymol 2007; 425:153-83.
9. Lippard SJ, Berg, J. M. Principles of Bioinorganic Chemistry. Mill Valley:University Science Books, 1994.
10. Ragsdale SW. Metals and their scaffolds to promote difficult enzymatic reactions. Chem Rev 2006; 106(8):3317-37.
11. Holm RH, Kennepohl P, Solomon EI. Structural and Functional Aspects of Metal Sites in Biology. Chem Rev 1996; 96(7):2239-314.
12. Sofia HJ, Chen G, Hetzler BG et al 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(5):1097-106.
13. PietTel F, Bjork GR, Fontecave M et al Enzymatic modification of tRNAs: MiaB is an iron-sulfur protein. J Biol Chem 2002; 277(16):13367-70.
14. Pierrel F, Douki T, Fontecave M et al. MiaB protein is a bifunctional radical-S-adenosylmcthionine enzyme involved in thiolation and méthylation of tRNA. J Biol Chem 2004; 279(46):47555-63.
15. Pierrel F, Hernandez HL, Johnson MK et al MiaB protein from Thetmotoga maritima. Characterization of an extremely thermophilic tRNA-methylthiotransferase. J Biol Chem 2003; 278(32):29515-24.
16. Hernandez HL, Pierrel F, Elicingand E et al. MiaB, a bifunctional radical-S-adenosylmcthionine enzyme involved in the thiolation and méthylation of tRNA, contains two essential [4Fe-4S] clusters. Biochemistry 2007; 46(17):5140-7.
17. Suzuki Y, Noma A, Suzuki T et al Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA. J Mol Biol 2007; 372(5):1204-14.
18. Goto-Ito S, Ishii R, Ito T et al. Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis. Acta Crystallogr D Biol Crystallogr 2007; 63(10):1059-68.
19. Reader JS, Mctzgar D, Schimmel P, de Crecy-Lagard V. Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine. J Biol Chem 2004; 279(8):6280-5.
20. Toh SM, Xiong L, Bae T, Mankin AS. The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA. RNA. 2008; 14(1):98-106.
21. Frey PA, Hegeman AD, Ruzicka FJ. The Radical SAM Superfamily. Crit Rev Biochem Mol Biol 2008; 43(l):63-88.
22. Fontecave M, Mulliez E, Ollagnier-de-Choudcns S. Adenosylmethioninc as a source of 5’-deoxyadenosyl radicals. Curr Opin Chem Biol 2001; 5(5):506-11.
23. Grosjean H, Nicoghosian K, Haumont E et al. Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs. Nucleic Acids Res1985; 13(15):5697-706.
24. Caillet J, Droogmans L. Molecular cloning of the Escherichia coli miaA gene involved in the formation of delta 2-isopentenyl adenosine in tRNA. J Bactcriol 1988; 170(9):4147-52.
25. Moore JA, Poulter CD. Escherichia coli dimethylallyl diphosphate:tRNA dimcthylallyltransferasc: a binding mechanism for recombinant enzyme. Biochemistry 1997; 36(3):604-14.
26. Sodcrberg T, Poulter CD. Escherichia coli dimethylallyl diphosphate:tRNA dimcthylallyltransferase: essential elements for recognition of tRNA substrates within the anticodon stem-loop. Biochemistry2000; 39(21):6546-53.
27. Void BS, Lazar JM, Gray AM. Characterization of a deficiency of N6-(delta 2-isopentenyl)-2-meth-ylthioadenosinc in the Escherichia coli mutant trpX by use of antibodies to N6-(delta 2-isopentenyl) adenosine. J Biol Chem. 1979; 254(15):7362-7.
28. Fontecave M, Mulliez E, Atta M. New light on methylthiolation reactions. Chemistry & biology 2008; 15(3):209-10.
29. Fontecave M, Ollagnier-de-Choudens S, Mulliez E. Biological radical sulfur insertion reactions. Chem Rev 2003; 103(6):2149-66.
30. Anton BP, Saleh L, Benner JS et al. RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli. Proc Natl Acad Sci USA 2008; 105(6): 1826-31.
31. Lauhon CT. Requirement for IscS in biosynthesis of all thionuclcosides in Escherichia coli. J Bactcriol 2002; 184(24):6820-9.
32. Nilsson K, Lundgren HK, Hagervall TG et al. The cysteine desulfurase IscS is required for synthesis of all five thiolated nucleosides present in tRNA from Salmonella enterica serovar typhimurium. J Bacteriol 2002; 184(24):6830-5.
33. Zheng L, White RH, Cash VL et al. Mechanism for the desulfurization of L-cystcine catalyzed by the nifS gene product. Biochemistry 1994; 33(15):4714-20.
34. Wright CM, Christman GD, Snellinger AM et al. Direct evidence for enzyme persulfide and disulfide intermediates during 4-thiouridinc biosynthesis. Chem Commun (Camb) 2006; 7(29):3104-6.
35. Mueller EG. Trafficking in persulfides: delivering sulfur in biosynthetic pathways. Nat Chem Biol 2006; 2(4):185-94.
36. Ugulava NB, Sacanell CJ, Jarrett JT. Spectroscopic changes during a single turnover of biotin synthase: destruction of a [2Fe-2S] cluster accompanies sulfur insertion. Biochemistry 2001; 40(28):8352-8.
37. Berkovitch F, Nicolet Y, Wan JT et al. Crystal structure of biotin synthase, an S-adenosylmcthionine-de-pendent radical enzyme. Science 2004; 303(5654):76-9.
38. Cicchillo RM, Lee KH, Baleanu-Gogonea C et al. Escherichia coli lipoyl synthase binds two distinct [4Fe-4S] clusters per polypeptide. Biochemistry 2004; 43(37):11770-81.
39. Jameson GN, Cosper MM, Hernandez HL et al. Role of the [2Fe-2S] cluster in recombinant Escherichia coli biotin synthase. Biochemistry 2004; 43(7):2022-31.
40. Li HJ, Nakanishi K, Grunberger D et al. Biosynthetic studies of the Y base in yeast phenylalanine tRNA. Incorporation of guanine. Biochem Biophys Res Commun 1973; 55(3):818-23.
41. Thicbc R, Poralla K. Origin of the nucleoside Y in yeast tRNAPhe. FEBS Lett 1973; 38(l):27-8.
42. Hanzclmann P, Schindelin H. Binding of 5’-GTP to the C-terminal FeS cluster of the radical S-ade-nosylmcthionine enzyme MoaA provides insights into its mechanism. Proc Natl Acad Sci USA 2006; 103(18);6829-34.
43. Harada F, Nishimura S. Possible anticodon sequences of tRNA His, tRNA Asm, and tRNA Asp from Escherichia coli B. Universal presence of nucleoside Q in the first postion of the anticondons of these transfer ribonucleic acids. Biochemistry 1972; 11(2):301-8.
44. Iwata-Reuyl D. Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA. Bioorg Chem. 2003; 31(1):24-43.
45. Van Lanen SG, Reader JS, Swairjo MA et al From cyclohydrolase to oxidoreductasc: discovery of nitrile reductase activity in a common fold. Proc Natl Acad Sei USA. 2005; 102(12):4264-9.
46. Banerjec RV, Matthews RG. Cobalamin-dependent methionine synthase. FASEB J. 1990; 4(5); 1450-9.
47. Persson BC, Bjork GR. Isolation of the gene (miaE) encoding the hydroxylase involved in the synthesis of 2-methylthio-cis-ribozeatin in tRNA of Salmonella typhimurium and characterization of mutants. J Bacteriol 1993; 175(24):7776-85.
48. Persson BC, Olafsson O, Lundgren HK et al The ms2io6A37 modification of tRNA in Salmonella typhimurium regulates growth on citric acid cycle intermediates. J Bacteriol 1998; 180(12):3144-51.
49. Mathevon C, Picrrel F, Oddou JL et al. tRNA-modifying MiaE protein from Salmonella typhimurium is a nonheme diiron monooxygenase. Proc Natl Acad Sei USA. 2007; 104(33):13295-300.
50. Baik MH, Newcomb M, Friesner RA et al Mechanistic studies on the hydroxylation of methane by methane monooxygenase. Chem Rev. 2003; 103(6):2385-419.
51. Merkx M, Kopp DA, Sazinsky MF et al Dioxygen activation and methane hydroxylation by soluble methane monooxygenase: A tale of two irons and three proteins. Angew Chem Int Ed. 2001; 40(15):2782-807.
52. Wallar BJ, Lipscomb JD. Dioxygen activation by enzymes containing binuclear non-heme iron clusters. Chem Rev. 1996; 96(7):2625-57.
53. Schneider J, Shilatifard A. Histone déméthylation by hydroxylation: chemistry in action. ACS Chem BioL 2006; 1(2):75-81.
54. Mishina Y, Chen LX, He C. Preparation and characterization of the native iron(II)-containing DNA repair AlkB protein directly from Escherichia coli. J Am Chem Soc. 2004; 126(51):16930-6.
55. Trewick SC, Hcnshaw TF, Hausinger RP et al Oxidative déméthylation by Escherichia coli AlkB directly reverts DNA base damage. Nature. 2002; 419(6903):174-8.
56. Yu B, Edstrom WC, Benach J et al. Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB. Nature. 2006; 439(7078):879-84.
57. Lee TT, Agarwalla S, Stroud RM. Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase. Structure. 2004; 12(3):397-407.
58. Agarwalla S, Stroud RM, Gaflhey BJ. Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies. J Biol Chem. 2004; 279(33):34123-9.
59. Lee TT, Agarwalla S, Stroud RM. A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell. 2005; 120(5):599-611.
60. Alian A, Lee TT, Griner SL, Stroud RM et al. Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases. Proc Natl Acad Sci U S A. 2008; 105(19):6876-81.
61. Leipuviene R, Qian Q, Bjork GR. Formation of thiolated nucleosides present in tRNA from Salmonella enterica serovar Typhimurium occurs in two principally distinct pathways. J BacterioL 2004; 186(3):758-66.
62. Jager G, Leipuviene R, Pollard MG et al The conserved Cys-Xl-X2-Cys motif present in the TtcA protein is required for the thiolation of cytidine in position 32 of tRNA from Salmonella enterica serovar Typhimurium. J BactcrioL 2004; 186(3):750-7.
63. Liu Y, Cowan JA. Iron sulfur cluster biosynthesis. Human NFU mediates sulfide delivery to ISU in the final step of [2Fe-2S] cluster assembly. Chem Commun (Camb). 2007; 14(30):3192-4.
64. Tong WH, Jameson GN, Huynh BH et al Subcellular compartmentalization of human Nfii, an iron-sulfur cluster scaffold protein, and its ability to assemble a [4Fe-4S] cluster. Proc Natl Acad Sci U S A. 2003; 100(17):9762-7.
65. Angelini S, Gérez C, Ollagnier-de Choudens S et al. NfuA, a new factor required for maturing Fe/S proteins in Escherichia coli under oxidative stress and iron starvation conditions. J Biol Chem. 2008; 283(20):14084-91.
66. Romier C, Reuter K, Suck D et al Crystal structure of tRNA-guanine transglycosylasc: RNA modification by base exchange. EMBO J. 1996; 15(11):2850-7.
67. Vallee BL, Auld DS. Zinc coordination, function, and structure of zinc enzymes and other proteins. Biochemistry. 1990; 29(24):5647-59.
68. Vallee BL, Auld DS. Active-site zinc ligands and activated H20 of zinc enzymes. Proc Natl Acad Sei USA. 1990; 87(1):220-4.
69. McCall KA, Huang C, Ficrke CA. Function and mechanism of zinc mctalloenzymes. J Nutr. 2000; 130(5S Suppl):1437S-146S.
70. Koonin EV. Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases. Nucleic Acids Res. 1996; 24(12):2411-5.
71. Kaya Y, Ofengand J. A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaca, and cukarya. RNA. 2003; 9(6):711-21.
72. Hamma T, Ferre-DAmarc AR. Pseudouridine synthases. Chem Biol. 2006; 13(11):1125-35.
73. Raychaudhuri S, Niu L, Conrad J et al. Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA. J Biol Chem. 1999; 274(27): 18880-6.
74. Del Campo M, Kaya Y, Ofengand J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA. 2001; 7(11):1603-15.
75. Ramamurthy V, Swann SL, Paulson JL et al Critical aspartic acid residues in pseudouridine synthases. J Biol Chem. 1999; 274(32):22225-30.
76. Fluang L, Pookanjanatavip M, Gu X et al. A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophilic catalyst. Biochemistry. 1998; 37(1):344-51.
77. Arluison V, Hountondji C, Robert B et al. Transfer RNA-pseudouridinc synthetase Pusl of Saccharomyces cerevisiae contains one atom of zinc essential for its native conformation and tRNA recognition. Biochemistry. 1998; 37(20):7268-76.
78. McCleverty CJ, Hornsby M, Spraggon G et al Crystal structure of human PuslO, a novel pseudouridine synthase. J Mol Biol. 2007; 373(5): 1243-54.
79. Marck C, Grosjean H. tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA. 2002; 8(10):1189-232.
80. Kim J, Malashkevich V, Roday S et al. Structural and kinetic characterization of Escherichia coli Tad A, the wobble-specific tRNA deaminase. Biochemistry. 2006; 45(20):6407-16.
81. Kuratani M, Ishii R, Bessho Yx et al Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus. J Biol Chem. 2005; 280(16):16002-8.
82. Gaur R, Varshney U. Genetic analysis identifies a function for the queC (ybaX) gene product at an initial step in the queuosine biosynthetic pathway in Escherichia coli. J BactcrioL 2005; 187(20):6893-901.
83. Higgins DG, Thompson JD, Gibson TJ. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 1996; 266:383-402.