4-Demethylwyosine synthase from Pyrococcus abyssi is a radical-S-adenosyl- L-methionine enzyme with an additional [4FE-4S]+2 cluster that interacts with the pyruvate Co-substrate

Journal of Biological Chemistry

Volumn 287, Issue 49, 2012, Pages 41174-41185

  Perche Letuvée, Phanélie ^a   Kathirvelu, Velavan ^a,b,c   Berggren, Gustav ^a   Clemancey, Martin ^c   Latour, Jean Marc ^c   Maurel, Vincent ^b   Douki, Thierry ^d   Armengaud, Jean ^e   Mulliez, Etienne ^a   Fontecave, Marc ^a,f   Garcia Serres, Ricardo ^c   Gambarelli, Serge ^b   Atta, Mohamed ^a  

^a DIF   (France)

^b UMR E3   (France)

^c CEA GRENOBLE   (France)

^d UNIV GRENOBLE ALPES   (France)

^e Institut de Biologie Environnementale et Biotechnologie IBEB SBTN/LBSP   (France)

^f l'alimentation et l'Environnement   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; CO-SUBSTRATE; COORDINATION SITES; HYSCORE; IRON-SULFUR CLUSTERS; L-METHIONINE; METALLOENZYMES; MOSSBAUER; N-TERMINALS; PYRUVATES; S ADENOSYL L METHIONINES; SEQUENCE ANALYSIS; SPECTROSCOPIC METHOD; SYNTHASES; UV-VISIBLE ABSORPTION;

AMINO ACIDS; BIOCHEMISTRY; COBALT COMPOUNDS; COORDINATION REACTIONS; ELECTRON SPIN RESONANCE SPECTROSCOPY; ENZYMES; PROTEINS; SPECTROSCOPIC ANALYSIS; SULFUR;

COBALT;

4 DEMETHYLWYOSINE SYNTHASE; BACTERIAL ENZYME; PYRUVIC ACID; S ADENOSYLMETHIONINE; UNCLASSIFIED DRUG;

4 DEMETHYLWYOSINE SYNTHASE GENE; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; CHEMICAL COMPOSITION; CONTROLLED STUDY; ENZYME ACTIVATION; ENZYME ACTIVITY; ENZYME BINDING; ENZYME MECHANISM; GENE CLUSTER; GENE OVEREXPRESSION; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PYROCOCCUS ABYSSI; SEQUENCE ALIGNMENT; SUICIDE SUBSTRATE;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; CARBOXY-LYASES; CATALYSIS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CLONING, MOLECULAR; CLUSTER ANALYSIS; CYSTEINE; ELECTRON SPIN RESONANCE SPECTROSCOPY; GUANOSINE; IRON-SULFUR PROTEINS; MASS SPECTROMETRY; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; OXIDOREDUCTASES; PYROCOCCUS ABYSSI; PYRUVIC ACID; RNA, TRANSFER; S-ADENOSYLMETHIONINE; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY; ULTRAVIOLET RAYS;

EUKARYOTA; PYROCOCCUS ABYSSI;

EID: 84870350421     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M112.405019     Document Type: Article

References (31)

1. Grosjean, H. (ed) (2009) DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution., Landes Bioscience, Texas
2. 2+ in RNA structure and function. Prog. Nucleic Acid Res. Mol. Biol. 53, 79-129
3. Kirino, Y., and Suzuki, T. (2005) Human mitochondrial diseases associated with tRNA wobble modification deficiency. RNA Biology 2, 41-44 (Pubitemid 41359797)
4. Kirino, Y., Goto, Y., Campos, Y., Arenas, J., and Suzuki, T. (2005) Specific correlation between the wobble modification deficiency in mutant tRNAs and the clinical features of a human mitochondrial disease. Proc. Natl. Acad. Sci. U.S.A. 102, 7127-7132 (Pubitemid 40696345)
5. Atta, M., Fontecave, M., and Mulliez, E. (2009) in DNA and RNA Modification Enzymes: Structure Mechanism, Function and Evolution (Grosjean, H., ed) pp. 347-357, Landes Bioscience, Austin, TX
6. Limbach, P. A., Crain, P. F., and McCloskey, J. A. (1994) Summary. The modified nucleosides of RNA. Nucleic Acids Res. 22, 2183-2196
7. Waas, W. F., de Crécy-Lagard, V., and Schimmel, P. (2005) Discovery of a gene family critical to wyosine base formation in a subset of phenylalanine-specific transfer RNAs. J. Biol. Chem. 280, 37616-37622 (Pubitemid 41642370)
8. Urbonavicius, J., Droogmans, L., Armengaud, J., and Grosjean, H. (2009) in DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution (Grosjean, H., ed) pp. 423-435, Lands Bioscience, Austin, TX
9. de Crécy-Lagard, V., Brochier-Armanet, C., Urbonavicius, J., Fernandez, B., Phillips, G., Lyons, B., Noma, A., Alvarez, S., Droogmans, L., Armengaud, J., and Grosjean, H. (2010) Biosynthesis of wyosine derivatives in tRNA. An ancient and highly diverse pathway in archaea. Mol. Biol. Evol. 27, 2062-2077
10. Sofia, H. J., Chen, G., Hetzler, B. G., Reyes-Spindola, J. F., and Miller, N. E. (2001) 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. 29, 1097-1106 (Pubitemid 32186195)
11. Fontecave, M., Atta, M., and Mulliez, E. (2004) S-Adenosylmethionine. Nothing goes to waste. Trends Biochem. Sci. 29, 243-249
12. Young, A. P., and Bandarian, V. (2011) Pyruvate is the source of the two carbons that are required for formation of the imidazoline ring of 4-demethylwyosine. Biochemistry 50, 10573-10575
13. Suzuki, Y., Noma, A., Suzuki, T., Senda, M., Senda, T., Ishitani, R., and Nureki, O. (2007) Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA. J. Mol. Biol. 372, 1204-1214 (Pubitemid 47376935)
14. Goto-Ito, S., Ishii, R., Ito, T., Shibata, R., Fusatomi, E., Sekine, S. I., Bessho, Y., and Yokoyama, S. (2007) Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis. Acta Crystallogr. D Biol. Crystallogr. 63, 1059-1068 (Pubitemid 47480518)
15. Lees, N. S., Hänzelmann, P., Hernandez, H. L., Subramanian, S., Schindelin, H., Johnson, M. K., and Hoffman, B. M. (2009) ENDOR spectroscopy shows that guanine N1 binds to [4Fe-4S] cluster II of the S-adenosylmethionine- dependent enzyme MoaA. Mechanistic implications. J. Am. Chem. Soc. 131, 9184-9185
16. Grove, T. L., Ahlum, J. H., Sharma, P., Krebs, C., and Booker, S. J. (2010) A consensus mechanism for radical SAM-dependent dehydrogenation? BtrN contains two [4Fe-4S] clusters. Biochemistry 49, 3783-3785
17. Flühe, L., Knappe, T. A., Gattner, M. J., Schäfer, A., Burghaus, O., Linne, U., and Marahiel, M. A. (2012) The radical SAM enzyme AlbA catalyzes thioether bond formation in subtilosin A. Nat. Chem. Biol. 8, 350-357
18. Fish, W. W. (1988) Rapid colorimetric micromethod for the quantitation of complexed iron in biological samples. Methods Enzymol. 158, 357-364
19. Beinert, H. (1983) Semi-micro methods for analysis of labile sulfide and of labile sulfide plus sulfane sulfur in unusually stable iron-sulfur proteins. Anal. Biochem. 131, 373-378
20. Gehrke, C. W., and Kuo, K. C. (1989) Ribonucleoside analysis by reversed phase high performance liquid chromatography. J. Chromatogr. 471, 3-36 (Pubitemid 19144813)
21. Tyryshkin, A. M., Dikanov, S. A., Reijerse, E. J., Burgard, C., and Huttermann, J. (1999) Characterization of bimodal coordination structure in nitrosyl heme complexes through hyperfine couplings with pyrrole and protein nitrogens. J. Am. Chem. Soc. 121, 3396-3406 (Pubitemid 29190905)
22. Emptage, M. H., Kent, T. A., Kennedy, M. C., Beinert, H., and Münck, E. (1983)Mössbauer and EPR studies of activated aconitase. Development of a localized valence state at a subsite of the [4Fe-4S] cluster on binding of citrate. Proc. Natl. Acad. Sci. U.S.A. 80, 4674-4678
23. Gambarelli, S., Luttringer, F., Padovani, D., Mulliez, E., and Fontecave, M. (2005) Activation of the anaerobic ribonucleotide reductase by S-adenosylmethionine. Chembiochem. 6, 1960-1962 (Pubitemid 41598165)
24. Chandor, A., Douki, T., Gasparutto, D., Gambarelli, S., Sanakis, Y., Nicolet, Y., Ollagnier-De-Choudens, S., Atta, M., and Fontecave, M. (2007) Characterization of the DNA repair spore photoproduct lyase enzyme from Clostridium acetobutylicum. A radical-SAM enzyme. Comptes Rendus Chimie 10, 756-765
25. Chen, D., Walsby, C., Hoffman, B. M., and Frey, P. A. (2003) Coordination and mechanism of reversible cleavage of S-adenosylmethionine by the [4Fe-4S] center in lysine 2,3-aminomutase. J. Am. Chem. Soc. 125, 11788-11789 (Pubitemid 37175392)
26. Kasai, H., Goto, M., Ikeda, K., Zama, M., Mizuno, Y., Takemura, S., Matsuura, S., Sugimoto, T., and Goto, T. (1976) Structure of wye (Yt base) and wyosine (Yt) from Torulopsis utilis phenylalanine transfer ribonucleic acid. Biochemistry 15, 898-904
27. 2+ cluster in reconstituted biotin synthase binds S-adenosyl-L-methionine. J. Am. Chem. Soc. 124, 14006-14007
28. 2+ center with unusual coordination sphere in the LytB protein. J. Am. Chem. Soc. 131, 13184-13185
29. Chan, A., Clemancey, M., Mouesca, J. M., Amara, P., Hamelin, O., Latour, J. M., and Ollagnier de Choudens, S. (2012) Studies of inhibitor binding to the [4Fe-4S] cluster of quinolinate synthase. Angew. Chem. Int. Ed. Engl. 51, 7711-7714
30. Loenarz, C., and Schofield, C. J. (2008) Expanding chemical biology of 2-oxoglutarate oxygenases. Nat. Chem. Biol. 4, 152-156 (Pubitemid 351264133)
31. Ahrens-Botzong, A., Janthawornpong, K., Wolny, J. A., Tambou, E. N., Rohmer, M., Krasutsky, S., Poulter, C. D., Schünemann, V., and Seemann, M. (2011) Biosynthesis of isoprene units. Mössbauer spectroscopy of substrate and inhibitor binding to the [4Fe-4S] cluster of the LytB/IspH enzyme. Angew. Chem. Int. Ed. Engl. 50, 11976-11979