2zzk › Citations

Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.

Suzuki Y, Noma A, Suzuki T, Ishitani R, Nureki O
Nucleic Acids Res 37 2910-25 (2009)
Related entries: 2zw9, 2zwa

Cited: 25 times
EuropePMC logo PMID: 19287006

Abstract

Wybutosine (yW), one of the most complicated modified nucleosides, is found in the anticodon loop of eukaryotic phenylalanine tRNA. This hypermodified nucleoside ensures correct codon recognition by stabilizing codon-anticodon pairings during the decoding process in the ribosome. TYW4 is an S-adenosylmethionine (SAM)-dependent enzyme that catalyzes the final step of yW biosynthesis, methylation and methoxycarbonylation. However, the structural basis for the catalytic mechanism by TYW4, and especially that for the methoxycarbonylation, have remained elusive. Here we report the apo and cofactor-bound crystal structures of yeast TYW4. The structures revealed that the C-terminal domain folds into a beta-propeller structure, forming part of the binding pocket for the target nucleoside. A comparison of the apo, SAM-bound, and S-adenosylhomocysteine-bound structures of TYW4 revealed a drastic structural change upon cofactor binding, which may sequester solvent from the catalytic site during the reaction and facilitate product release after the reaction. In conjunction with the functional analysis, our results suggest that TYW4 catalyzes both methylation and methoxycarbonylation at a single catalytic site, and in the latter reaction, the methoxycarbonyl group is formed through the fixation of carbon dioxide.

Articles - 2zzk mentioned but not cited (1)

  1. Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4. Suzuki Y, Noma A, Suzuki T, Ishitani R, Nureki O. Nucleic Acids Res 37 2910-2925 (2009)


Reviews citing this publication (13)

  1. tRNA biology charges to the front. Phizicky EM, Hopper AK. Genes Dev 24 1832-1860 (2010)
  2. Transfer RNA modifications: nature's combinatorial chemistry playground. Jackman JE, Alfonzo JD. Wiley Interdiscip Rev RNA 4 35-48 (2013)
  3. Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland. Helm M, Alfonzo JD. Chem Biol 21 174-185 (2014)
  4. Structure and function of noncanonical nucleobases. Carell T, Brandmayr C, Hienzsch A, Müller M, Pearson D, Reiter V, Thoma I, Thumbs P, Wagner M. Angew Chem Int Ed Engl 51 7110-7131 (2012)
  5. Naturally occurring modified ribonucleosides. McCown PJ, Ruszkowska A, Kunkler CN, Breger K, Hulewicz JP, Wang MC, Springer NA, Brown JA. Wiley Interdiscip Rev RNA 11 e1595 (2020)
  6. Biosynthesis and function of tRNA modifications in Archaea. Phillips G, de Crécy-Lagard V. Curr Opin Microbiol 14 335-341 (2011)
  7. Wybutosine biosynthesis: structural and mechanistic overview. Perche-Letuvée P, Molle T, Forouhar F, Mulliez E, Atta M. RNA Biol 11 1508-1518 (2014)
  8. Keeping an eye on myocilin: a complex molecule associated with primary open-angle glaucoma susceptibility. Menaa F, Braghini CA, Vasconcellos JP, Menaa B, Costa VP, Figueiredo ES, Melo MB. Molecules 16 5402-5421 (2011)
  9. Radical mediated ring formation in the biosynthesis of the hypermodified tRNA base wybutosine. Young AP, Bandarian V. Curr Opin Chem Biol 17 613-618 (2013)
  10. From Prebiotics to Probiotics: The Evolution and Functions of tRNA Modifications. McKenney KM, Alfonzo JD. Life (Basel) 6 E13 (2016)
  11. Biosynthesis of wyosine derivatives in tRNA(Phe) of Archaea: role of a remarkable bifunctional tRNA(Phe):m1G/imG2 methyltransferase. Urbonavičius J, Meškys R, Grosjean H. RNA 20 747-753 (2014)
  12. Radical SAM enzymes involved in the biosynthesis of purine-based natural products. Bandarian V. Biochim Biophys Acta 1824 1245-1253 (2012)
  13. Investigations of Single-Subunit tRNA Methyltransferases from Yeast. Wang Z, Xu X, Li X, Fang J, Huang Z, Zhang M, Liu J, Qiu X. J Fungi (Basel) 9 1030 (2023)

Articles citing this publication (11)

  1. Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. de Crécy-Lagard V, Brochier-Armanet C, Urbonavicius J, Fernandez B, Phillips G, Lyons B, Noma A, Alvarez S, Droogmans L, Armengaud J, Grosjean H. Mol Biol Evol 27 2062-2077 (2010)
  2. Expanding role of the jumonji C domain as an RNA hydroxylase. Noma A, Ishitani R, Kato M, Nagao A, Nureki O, Suzuki T. J Biol Chem 285 34503-34507 (2010)
  3. Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Kato M, Araiso Y, Noma A, Nagao A, Suzuki T, Ishitani R, Nureki O. Nucleic Acids Res 39 1576-1585 (2011)
  4. Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase. Iyer LM, Abhiman S, de Souza RF, Aravind L. Nucleic Acids Res 38 5261-5279 (2010)
  5. Identification and characterization of a novel member of the radical AdoMet enzyme superfamily and implications for the biosynthesis of the Hmd hydrogenase active site cofactor. McGlynn SE, Boyd ES, Shepard EM, Lange RK, Gerlach R, Broderick JB, Peters JW. J Bacteriol 192 595-598 (2010)
  6. Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure. Létoquart J, van Tran N, Caroline V, Aleksandrov A, Lazar N, van Tilbeurgh H, Liger D, Graille M. Nucleic Acids Res 43 10989-11002 (2015)
  7. Probabilistic approach to predicting substrate specificity of methyltransferases. Szczepińska T, Kutner J, Kopczyński M, Pawłowski K, Dziembowski A, Kudlicki A, Ginalski K, Rowicka M. PLoS Comput Biol 10 e1003514 (2014)
  8. Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin. Kuratani M, Hirano M, Goto-Ito S, Itoh Y, Hikida Y, Nishimoto M, Sekine S, Bessho Y, Ito T, Grosjean H, Yokoyama S. J Mol Biol 401 323-333 (2010)
  9. Structural and functional characterization of the TYW3/Taw3 class of SAM-dependent methyltransferases. Currie MA, Brown G, Wong A, Ohira T, Sugiyama K, Suzuki T, Yakunin AF, Jia Z. RNA 23 346-354 (2017)
  10. Clinical profiles and outcomes of acute aortic dissection in a predominantly Hispanic population. Alkhateeb H, Said S, Cooper CJ, Rodriguez-Castro C, Dwivedi A, Onate E, Quansah R, Mukherjee D. Med Sci Monit 20 747-751 (2014)
  11. Genetic Susceptibility for Low Testosterone in Men and Its Implications in Biology and Screening: Data from the UK Biobank. Fantus RJ, Na R, Wei J, Shi Z, Resurreccion WK, Halpern JA, Franco O, Hayward SW, Isaacs WB, Zheng SL, Xu J, Helfand BT. Eur Urol Open Sci 29 36-46 (2021)


Quick links