wybutosine - CAS 55196-46-8

Catalog number: BRB-015

A modified nucleoside of phenylalanine tRNA.

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Synonyms
3H-Imidazo[1,2-a]purine-7-butanoic acid, 4,9-dihydro-a-[(methoxycarbonyl)amino]-4,6-dimethyl-9-oxo-3-b-D-ribofuranosyl-, methyl ester, (S)-
CAS
55196-46-8
IUPAC Name
methyl (2S)-4-[3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4,6-dimethyl-9-oxoimidazo[1,2-a]purin-7-yl]-2-(methoxycarbonylamino)butanoate
Molecular Weight
508.49
Molecular Formula
C21H28N6O9
Canonical SMILES
CC1=C(N2C(=O)C3=C(N(C2=N1)C)N(C=N3)C4C(C(C(O4)CO)O)O)CCC(C(=O)OC)NC(=O)OC
InChI
InChI=1S/C21H28N6O9/c1-9-11(6-5-10(19(32)34-3)24-21(33)35-4)27-17(31)13-16(25(2)20(27)23-9)26(8-22-13)18-15(30)14(29)12(7-28)36-18/h8,10,12,14-15,18,28-30H,5-7H2,1-4H3,(H,24,33)/t10-,12+,14+,15+,18+/m0/s1
InChIKey
QAOHCFGKCWTBGC-QHOAOGIMSA-N
Purity
≥98%
Symbol
yW

Chemical Structure:

Reference Reading

1. Radical mediated ring formation in the biosynthesis of the hypermodified tRNA base wybutosine
Anthony P Young, Vahe Bandarian. Curr Opin Chem Biol. 2013 Aug;17(4):613-8. doi: 10.1016/j.cbpa.2013.05.035.
Wyosine and its derivatives are highly modified, acid labile tricyclic bases found at position 37 of tRNA(Phe) in archaea and eukarya. The formation of the common 4-demethylwyosine structural feature entails condensation of pyruvate and N-methylguanosine catalyzed by TYW1. This review will focus on the mechanism of this complex radical mediated transformation.
2. Role of Wybutosine and Mg2+ Ions in Modulating the Structure and Function of tRNAPhe: A Molecular Dynamics Study
Prayagraj M Fandilolu, Asmita S Kamble, Ambika S Dound, Kailas D Sonawane. ACS Omega. 2019 Dec 2;4(25):21327-21339. doi: 10.1021/acsomega.9b02238.
Transfer RNA remains to be a mysterious molecule of the cell repertoire. With its modified bases and selectivity of codon recognition, it remains to be flexible inside the ribosomal machinery for smooth and hassle-free protein biosynthesis. Structural changes occurring in tRNA due to the presence or absence of wybutosine, with and without Mg2+ ions, have remained a point of interest for structural biologists. Very few studies have come to a conclusion correlating the changes either with the structure and flexibility or with the codon recognition. Considering the above facts, we have implemented molecular modeling methods to address these problems using multiple molecular dynamics (MD) simulations of tRNAPhe along with codons. Our results highlight some of the earlier findings and also shed light on some novel structural and functional aspects. Changes in the stability of tRNAPhe in native or codon-bound states result from the conformations of constituent nucleotides with respect to each other. A smaller change in their conformations leads to structural distortions in the base-pairing geometry and eventually in the ribose-phosphate backbone. MD simulation studies highlight the preference of UUC codons over UUU by tRNAPhe in the presence of wybutosine and Mg2+ ions. This study also suggests that magnesium ions are required by tRNAPhe for proper recognition of UUC/UUU codons during ribosomal interactions with tRNA.
3. Accuracy mechanism of eukaryotic ribosome translocation
Muminjon Djumagulov, Natalia Demeshkina, Lasse Jenner, Alexey Rozov, Marat Yusupov, Gulnara Yusupova. Nature. 2021 Dec;600(7889):543-546. doi: 10.1038/s41586-021-04131-9.
Translation of the genetic code into proteins is realized through repetitions of synchronous translocation of messenger RNA (mRNA) and transfer RNAs (tRNA) through the ribosome. In eukaryotes translocation is ensured by elongation factor 2 (eEF2), which catalyses the process and actively contributes to its accuracy1. Although numerous studies point to critical roles for both the conserved eukaryotic posttranslational modification diphthamide in eEF2 and tRNA modifications in supporting the accuracy of translocation, detailed molecular mechanisms describing their specific functions are poorly understood. Here we report a high-resolution X-ray structure of the eukaryotic 80S ribosome in a translocation-intermediate state containing mRNA, naturally modified eEF2 and tRNAs. The crystal structure reveals a network of stabilization of codon-anticodon interactions involving diphthamide1 and the hypermodified nucleoside wybutosine at position 37 of phenylalanine tRNA, which is also known to enhance translation accuracy2. The model demonstrates how the decoding centre releases a codon-anticodon duplex, allowing its movement on the ribosome, and emphasizes the function of eEF2 as a 'pawl' defining the directionality of translocation3. This model suggests how eukaryote-specific elements of the 80S ribosome, eEF2 and tRNAs undergo large-scale molecular reorganizations to ensure maintenance of the mRNA reading frame during the complex process of translocation.
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