ArticleStructure (London, England : 1993)2018
Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes.
Article in Structure (London, England : 1993), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Atomistic Simulations Decode the Mechanisms of DNA and RNA Processing Enzymes: Function through Motion.Accounts of chemical research · 2026Article
- Controlled dynamic remodeling of the spliceosome active site enables the first step of splicing.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Coordinated Residue Motions at the Enzyme-Substrate Interface Promote DNA Translocation in Polymerases.Journal of the American Chemical Society · 2025Article
- Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design.Journal of chemical information and modeling · 2025Article
- Targeting the conserved active site of splicing machines with specific and selective small molecule modulators.Nature communications · 2024Article
- Monovalent metal ion binding promotes the first transesterification reaction in the spliceosome.Nature communications · 2023Article
- Article
- Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides.Nucleic acids research · 2023Article
- A metal ion-dependent conformational switch modulates activity of the Plasmodium M17 aminopeptidase.The Journal of biological chemistry · 2022Article
- The life and death of RNA across temperatures.Computational and structural biotechnology journal · 2022Review
- Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis.ACS catalysis · 2021Article
- Finding the Ion in the RNA-Stack: Can Computational Models Accurately Predict Key Functional Elements in Large Macromolecular Complexes?Journal of chemical information and modeling · 2021Article
- A Gold Nanoparticle Nanonuclease Relying on a Zn(II) Mononuclear Complex.Angewandte Chemie (International ed. in English) · 2021Article
- Visualizing group II intron dynamics between the first and second steps of splicing.Nature communications · 2020Article
- Recruiting Mechanism and Functional Role of a Third Metal Ion in the Enzymatic Activity of 5' Structure-Specific Nucleases.Journal of the American Chemical Society · 2020Article
- A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids.Nature chemistry · 2019Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Synthesis and scission of phosphodiester bonds in DNA and RNA regulate vital processes within the cell. Enzymes that catalyze these reactions operate mostly via the recognized two-metal-ion mechanism. Our analysis reveals that basic amino acids and monovalent cations occupy structurally conserved positions nearby the active site of many two-metal-ion enzymes for which high-resolution (<3 Å) structures are known, including DNA and RNA polymerases, nucleases such as Cas9, and splicing ribozymes. Integrating multiple-sequence and structural alignments with molecular dynamics simulations, electrostatic potential maps, and mutational data, we found that these elements always interact with the substrates, suggesting that they may play an active role for catalysis, in addition to their electrostatic contribution. We discuss possible mechanistic implications of this expanded two-metal-ion architecture, including inferences on medium-resolution cryoelectron microscopy structures. Ultimately, our analysis may inspire future experiments and strategies for enzyme engineering or drug design to modulate nucleic acid processing.
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