ArticleNucleic acids research2014
The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs.
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 19 papers.
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Who cites it
19 citing papers in PubMed.
- Compendium of RNA modifications for bacterial stress adaptation.Microbiology and molecular biology reviews : MMBR · 2026Review
- Major bioactive metabolites derived fromFrontiers in pharmacology · 2026Review
- Mechanistic insight into the pseudouridylation of RNA.RNA biology · 2025Review
- Protonated Glutamate and Aspartate Side Chains Can Recognize Phosphodiester Groups via Strong and Short Hydrogen Bonds in Biomacromolecular Complexes.Angewandte Chemie (International ed. in English) · 2025Article
- tRNA pseudouridine synthase D (TruD) fromRNA (New York, N.Y.) · 2025Article
- The molecular basis of tRNA selectivity by human pseudouridine synthase 3.Molecular cell · 2024Article
- The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1.PloS one · 2023Article
- Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey.Molecules (Basel, Switzerland) · 2022Article
- Recent technical advances in the study of nucleic acid modifications.Molecular cell · 2021Review
- A unified dinucleotide alphabet describing both RNA and DNA structures.Nucleic acids research · 2020Article
- Identification of drug target candidates of the swine pathogen Actinobacillus pleuropneumoniae by construction of protein-protein interaction network.Genes & genomics · 2018Article
- Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops.RNA (New York, N.Y.) · 2017Article
- Pseudouridine in the Anticodon of Escherichia coli tRNATyr(QΨA) Is Catalyzed by the Dual Specificity Enzyme RluF.The Journal of biological chemistry · 2016Article
- The Pseudouridine Synthases Proceed through a Glycal Intermediate.Journal of the American Chemical Society · 2016Article
- Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae.3 Biotech · 2015Article
- Accurate placement of substrate RNA by Gar1 in H/ACA RNA-guided pseudouridylation.Nucleic acids research · 2015Article
- 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
- Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
RluB catalyses the modification of U2605 to pseudouridine (Ψ) in a stem-loop at the peptidyl transferase center of Escherichia coli 23S rRNA. The homolog RluF is specific to the adjacent nucleotide in the stem, U2604. The 1.3 Å resolution crystal structure of the complex between the catalytic domain of RluB and the isolated substrate stem-loop, in which the target uridine is substituted by 5-fluorouridine (5-FU), reveals a covalent bond between the isomerized target base and tyrosine 140. The structure is compared with the catalytic domain alone determined at 2.5 Å resolution. The RluB-bound stem-loop has essentially the same secondary structure as in the ribosome, with a bulge at A2602, but with 5-FU2605 flipped into the active site. We showed earlier that RluF induced a frame-shift of the RNA, moving A2602 into the stem and translating its target, U2604, into the active site. A hydrogen-bonding network stabilizes the bulge in the RluB-RNA but is not conserved in RluF and so RluF cannot stabilize the bulge. On the basis of the covalent bond between enzyme and isomerized 5-FU we propose a Michael addition mechanism for pseudouridine formation that is consistent with all experimental data.
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