Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA.

@article{Suzuki2007CrystalSO,
  title={Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA.},
  author={Yoko Suzuki and A. Noma and Tsutomu Suzuki and M. Senda and T. Senda and R. Ishitani and O. Nureki},
  journal={Journal of molecular biology},
  year={2007},
  volume={372 5},
  pages={
          1204-14
        }
}
Wyosine and its derivatives, such as wybutosine, found in eukaryotic and archaeal tRNAs, are tricyclic hypermodified nucleosides. In eukaryotes, wybutosine exists exclusively in position 37, 3'-adjacent to the anticodon, of tRNA(Phe), where it ensures correct translation by stabilizing the codon-anticodon base-pairing during the ribosomal decoding process. Recent studies revealed that the wyosine biosynthetic pathway consists of multistep enzymatic reactions starting from a guanosine residue… Expand
Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4†
TLDR
The structures revealed that the C-terminal domain folds into a β-propeller structure, forming part of the binding pocket for the target nucleoside, and suggest that TYW4 catalyzes both methylation and methoxy carbonylation at a single catalytic site, and in the latter reaction, the methoxycarbonyl group is formed through the fixation of carbon dioxide. Expand
Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2
TLDR
These findings, which were confirmed by extensive mutagenesis studies, explain why TYW2 transfers the “acp” group, and not the methyl group, from AdoMet to the nucleobase. Expand
Structural studies of S-adenosyl-L-methionine radical enzymes involved in tRNA and natural product biosynthesis
Members of the S-adenosyl-L-methionine (AdoMet) radical enzyme superfamily catalyze a myriad of diverse and challenging biotransformations using a [4Fe-4S] cluster and a molecule of AdoMet toExpand
Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification
Wybutosine (yW) is a hypermodified nucleoside found in position 37 of tRNAPhe, and is essential for correct phenylalanine codon translation. yW derivatives widely exist in eukaryotes and archaea, andExpand
Spectroscopic evidence for cofactor-substrate interaction in the radical-SAM enzyme TYW1.
TLDR
The results highlight an interaction between pyruvate and SAM, indicating that they bind in close vicinity inside the catalytic pocket and indicate a chelating binding mode of pyruVate to the accessible Fe site of the corresponding FeS cluster. Expand
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*
TLDR
This study helps to understand how radical-SAM enzymes with two Fe-S centers can synergistically achieve challenging radical insertion reactions by combining analytical and spectroscopic methods. Expand
Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea.
TLDR
Four of the five wybutosine biosynthetic enzymes are ancient and may have been present in the last common ancestor of Archaea and Eucarya and the variations in the distribution pattern of biosynthesis enzymes reflect the diversity of the wyosine derivatives found in different Archaea. Expand
Biochemical Pathways Leading to the Formation of Wyosine Derivatives in tRNA of Archaea
TLDR
In this review, current knowledge regarding the archaeal enzymes involved in this process and their reaction mechanisms are summarized and the experiments aimed to elucidate missing steps in biosynthesis pathways leading to the formation of wyosine derivatives are suggested. Expand
Structural diversity in the AdoMet radical enzyme superfamily.
TLDR
Reexamine the 'traditional' structural motifs responsible for binding the [4Fe-4S] cluster and AdoMet, and compare and contrast these motifs with the ThiC case, and review how structural data combine with biochemical, spectroscopic, and computational data to help understand key features of this enzyme superfamily. Expand
Radical SAM enzymes involved in the biosynthesis of purine-based natural products.
  • V. Bandarian
  • Chemistry, Medicine
  • Biochimica et biophysica acta
  • 2012
TLDR
This review will highlight three radical SAM enzymes that catalyze reactions involving modified guanosines in the biosynthesis pathways of the hypermodified tRNA base wybutosine; secondary metabolites of 7-deazapurine structure; and the redox cofactor F(420). Expand
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References

SHOWING 1-10 OF 37 REFERENCES
Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate
Prokaryotic tRNA guanine transglycosylase (TGT) catalyzes replacement of guanine (G) by 7-aminomethyl-7-deazaguanine (PreQ1) at the wobble position of four specific tRNAs. Addition of 9-deazaguanineExpand
Biosynthesis of wybutosine, a hyper‐modified nucleoside in eukaryotic phenylalanine tRNA
TLDR
To identify genes responsible for yW synthesis from uncharacterized genes of Saccharomyces cerevisiae, a systematic reverse genetic approach combined with mass spectrometry (‘ribonucleome analysis’) revealed its sequential biosynthetic pathway. Expand
Snapshots of tRNA sulphuration via an adenylated intermediate
TLDR
The crystal structures of the MnmA thiouridylase–tRNA complex are presented in three discrete forms, which provide snapshots of the sequential chemical reactions during RNA sulphuration and provide the structural basis for a general mechanism whereby an enzyme incorporates a reactive atom at a precise position in a biological molecule. Expand
Structures of two new "minimalist" modified nucleosides from archaeal tRNA.
TLDR
The structures of two minimally elaborated wye derivatives from archaea suggest a minimal role for wye methyl groups and side chains in maintenance of anticodon stem-loop structures, and support the concept that archaeal tRNA nucleoside modification motifs are generally simpler than those of their counterparts in eukarya and bacteria. Expand
Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans.
TLDR
A defined in vitro system is described, which generates precursor Z and led to the identification of 5'-GTP as the substrate and help to define the defects caused by mutations in the human ortholog of MoaA that lead to molybdenum cofactor deficiency, a usually fatal disease accompanied by severe neurological symptoms. Expand
Structure and function of radical SAM enzymes.
TLDR
The availability of two protein structures supported by biochemical and biophysical data underscores common features, anticipating the structural elements of other family members, and remaining differences emphasize the plasticity of the protein scaffold in functionally accommodating 600 family members. Expand
Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes
TLDR
The structure of HemN reveals the cofactor geometry required for Radical SAM catalysis and sets the stage for the development of inhibitors with antibacterial function due to the uniquely bacterial occurrence of the enzyme. Expand
How an enzyme tames reactive intermediates: positioning of the active-site components of lysine 2,3-aminomutase during enzymatic turnover as determined by ENDOR spectroscopy.
TLDR
It is concluded that the active site facilitates hydrogen atom transfer by enforcing van der Waals contact between radicals and their reacting partners, which enables the enzyme to minimize and even eliminate side reactions of highly reactive species such as the 5'-deoxyadensosyl radical. Expand
Discovery of a Gene Family Critical to Wyosine Base Formation in a Subset of Phenylalanine-specific Transfer RNAs*
A large number of post-transcriptional base modifications in transfer RNAs have been described (Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A., and Steinberg, S. (1998) Nucleic Acids Res. 26,Expand
Naturally-occurring modification restricts the anticodon domain conformational space of tRNA(Phe).
TLDR
A comparison of the resulting structures indicates that modification of position 37 affects the accuracy of decoding and the maintenance of the mRNA reading frame by restricting anticodon loop conformational space. Expand
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