ArticleNature chemical biology2022
Structural basis for substrate binding and catalysis by a self-alkylating ribozyme.
Article in Nature chemical biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 22 citations in OpenAlex.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- A magic methyl effect in the active site of a methyltransferase ribozyme.Nature communications · 2026Article
- Structure and catalytic activity of the SAM-utilizing ribozyme SAMURI.Nature chemical biology · 2026Article
- A universal Fab targeting a conserved U1A-RNA epitope for RNA structure determination by cryo-EM.Nucleic acids research · 2026Article
- Structural basis of double-stranded RNA recognition by the J2 monoclonal antibody.Nature communications · 2025Article
- Engineering covalent small molecule-RNA complexes in living cells.Nature chemical biology · 2025Article
- Site-Selective Modification and Labeling of Native RNA.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Review
- Synthesis of HBC fluorophores with an electrophilic handle for covalent attachment to Pepper RNA.Beilstein journal of organic chemistry · 2025Article
- Synthesis of electrophile-tethered preQBeilstein journal of organic chemistry · 2025Article
- The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme.ACS catalysis · 2024Article
- Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields.The journal of physical chemistry. B · 2024Article
- Structure of saguaro cactus virus 3' translational enhancer mimics 5' cap for eIF4E binding.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells.Nature chemistry · 2023Article
- RNA structure determination: From 2D to 3D.Fundamental research · 2023Review
- Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.Nucleic acids research · 2023Article
- Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element.Nature communications · 2023Article
- Article
- How does RNA fold dynamically?Journal of molecular biology · 2022Review
- Structural Basis for Fluorescence Activation by Pepper RNA.ACS chemical biology · 2022Article
- A new RNA performs old chemistry.Nature chemical biology · 2022Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
Ribozymes that react with small-molecule probes have important applications in transcriptomics and chemical biology, such as RNA labeling and imaging. Understanding the structural basis for these RNA-modifying reactions will enable the development of better tools for studying RNA. Nevertheless, high-resolution structures and underlying catalytic mechanisms for members of this ribozyme class remain elusive. Here, we focus on a self-alkylating ribozyme that catalyzes nitrogen-carbon bond formation between a specific guanine and a 2,3-disubstituted epoxide substrate and report the crystal structures of a self-alkylating ribozyme, including both alkylated and apo forms, at 1.71-Å and 2.49-Å resolution, respectively. The ribozyme assumes an elongated hairpin-like architecture preorganized to accommodate the epoxide substrate in a hook-shaped conformation. Observed reactivity of substrate analogs together with an inverse, log-linear pH dependence of the reaction rate suggests a requirement for epoxide protonation, possibly assisted by the ether oxygens within the substrate.
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