ArticleNucleic acids research2014
An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 22 citations in OpenAlex.
- The pseudouridine synthase PUSL1 modifies U39 of mitochondrial tRNAs and is linked to human neurological phenotypes.Nucleic acids research · 2026Article
- Mechanistic insight into the pseudouridylation of RNA.RNA biology · 2025Review
- Combining Nanopore direct RNA sequencing with genetics and mass spectrometry for analysis of T-loop base modifications across 42 yeast tRNA isoacceptors.Nucleic acids research · 2024Article
- H/ACA Small Ribonucleoproteins: Structural and Functional Comparison Between Archaea and Eukaryotes.Frontiers in microbiology · 2021Review
- The tRNA pseudouridine synthase TruB1 regulates the maturation of let-7 miRNA.The EMBO journal · 2020Article
- tRNA elbow modifications affect the tRNA pseudouridine synthase TruB and the methyltransferase TrmA.RNA (New York, N.Y.) · 2020Article
- Multiquantum Chemical Exchange Saturation Transfer NMR to Quantify Symmetrical Exchange: Application to Rotational Dynamics of the Guanidinium Group in Arginine Side Chains.The journal of physical chemistry letters · 2020Article
- Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides.Beilstein journal of organic chemistry · 2018Review
- AJournal of biomolecular NMR · 2017Article
- RNA modification enzyme TruB is a tRNA chaperone.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Pseudouridine in the Anticodon of Escherichia coli tRNATyr(QΨA) Is Catalyzed by the Dual Specificity Enzyme RluF.The Journal of biological chemistry · 2016Article
- Dye label interference with RNA modification reveals 5-fluorouridine as non-covalent inhibitor.Nucleic acids research · 2014Article
- Pseudouridine: still mysterious, but never a fake (uridine)!RNA biology · 2014Review
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pseudouridine synthases introduce the most common RNA modification and likely use the same catalytic mechanism. Besides a catalytic aspartate residue, the contributions of other residues for catalysis of pseudouridine formation are poorly understood. Here, we have tested the role of a conserved basic residue in the active site for catalysis using the bacterial pseudouridine synthase TruB targeting U55 in tRNAs. Substitution of arginine 181 with lysine results in a 2500-fold reduction of TruB's catalytic rate without affecting tRNA binding. Furthermore, we analyzed the function of a second-shell aspartate residue (D90) that is conserved in all TruB enzymes and interacts with C56 of tRNA. Site-directed mutagenesis, biochemical and kinetic studies reveal that this residue is not critical for substrate binding but influences catalysis significantly as replacement of D90 with glutamate or asparagine reduces the catalytic rate 30- and 50-fold, respectively. In agreement with molecular dynamics simulations of TruB wild type and TruB D90N, we propose an electrostatic network composed of the catalytic aspartate (D48), R181 and D90 that is important for catalysis by fine-tuning the D48-R181 interaction. Conserved, negatively charged residues similar to D90 are found in a number of pseudouridine synthases, suggesting that this might be a general mechanism.
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