ArticleProceedings of the National Academy of Sciences of the United States of America2015
Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Molecular basis of tRNA substrate recognition and modification by the atypical SPOUT methyltransferase Trm10.Nucleic acids research · 2026Article
- Tied to Work: Topologically Knotted SPOUT Methyltransferases and UCH Deubiquitinases in Cellular Biochemistry.Journal of cellular biochemistry · 2026Review
- Nicotinamide-Based Covalent Inhibitors of tRNA (mACS medicinal chemistry letters · 2026Article
- Nanoscale Direct-to-Biology Optimization and Structural Insights into SelectiveJournal of medicinal chemistry · 2025Article
- A transfer RNA methyltransferase with an unusual domain composition catalyzes 2'-O-methylation at position 6 in tRNA.Nucleic acids research · 2025Article
- Structural insight into the novel Thermus thermophilus SPOUT methyltransferase RlmR catalysing Um2552 formation in the 23S rRNA A-loop: a case of convergent evolution.Nucleic acids research · 2025Article
- tRNA and tsRNA: From Heterogeneity to Multifaceted Regulators.Biomolecules · 2024Review
- tRNA mbioRxiv : the preprint server for biology · 2023Article
- Are there double knots in proteins? Prediction andFrontiers in molecular biosciences · 2023Article
- Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study.Computational and structural biotechnology journal · 2023Article
- Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases.The Journal of biological chemistry · 2022Review
- Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation.Nucleic acids research · 2021Article
- Loss ofeLife · 2021Article
- Article
- tRNA methylation: An unexpected link to bacterial resistance and persistence to antibiotics and beyond.Wiley interdisciplinary reviews. RNA · 2020Review
- Mechanically tightening, untying and retying a protein trefoil knot by single-molecule force spectroscopy.Chemical science · 2020Article
- Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction.Nucleic acids research · 2020Article
- Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification.Nucleic acids research · 2020Article
- MgACS catalysis · 2020Article
- Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites.PLoS computational biology · 2020Article
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8 authors.
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Abstract
The deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life. In bacteria, TrmD catalyzes the N(1)-methylguanosine (m(1)G) modification at position 37 in transfer RNAs (tRNAs) with the (36)GG(37) sequence, using S-adenosyl-l-methionine (AdoMet) as the methyl donor. The m(1)G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome. Here we report the crystal structure of the TrmD homodimer in complex with a substrate tRNA and an AdoMet analog. Our structural analysis revealed the mechanism by which TrmD binds the substrate tRNA in an AdoMet-dependent manner. The trefoil-knot center, which is structurally conserved among SPOUT MTases, accommodates the adenosine moiety of AdoMet by loosening/retightening of the knot. The TrmD-specific regions surrounding the trefoil knot recognize the methionine moiety of AdoMet, and thereby establish the entire TrmD structure for global interactions with tRNA and sequential and specific accommodations of G37 and G36, resulting in the synthesis of m(1)G37-tRNA.
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