ArticleNucleic acids research2015
Two distinct modes of metal ion binding in the nuclease active site of a viral DNA-packaging terminase: insight into the two-metal-ion catalytic mechanism.
Article in Nucleic acids research, 2015. 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, 32 citations in OpenAlex.
- Dissecting the dsDNA viral packaging machinery: structural evolution and potential for therapeutics.Journal of virology · 2026Review
- How Do DICER1 Syndrome Mutations Disrupt Catalysis? Unveiling Dicer Metal Binding Architecture and Mechanism of Action Using MD Simulations and QM/MM Calculations.Journal of computational chemistry · 2026Article
- Discovery of a Baloxavir-Inspired Endonuclease Inhibitor That Prevents Herpes Simplex Virus 1 Replication in Cell Culture and In Vivo.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2.Nucleic acids research · 2025Article
- Viral Genomic DNA Packaging Machinery.Sub-cellular biochemistry · 2024Review
- Insights into a viral motor: the structure of the HK97 packaging termination assembly.Nucleic acids research · 2023Article
- RNA as a Major-Groove Ligand: RNA-RNA and RNA-DNA Triplexes Formed by GAA and UUC or TTC Sequences.ACS omega · 2022Article
- Terminase Subunits from the Pseudomonas-Phage E217.Journal of molecular biology · 2022Article
- Prototype Foamy Virus Integrase Displays Unique Biochemical Activities among Retroviral Integrases.Biomolecules · 2021Article
- Review
- Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis.Nature communications · 2018Article
- Sensitivity of the C-Terminal Nuclease Domain of Kaposi's Sarcoma-Associated Herpesvirus ORF29 to Two Classes of Active-Site Ligands.Antimicrobial agents and chemotherapy · 2018Article
- Structure-Driven Discovery of α,γ-Diketoacid Inhibitors Against UL89 Herpesvirus Terminase.ACS omega · 2018Article
- Functional details of the Mycobacterium tuberculosis VapBC26 toxin-antitoxin system based on a structural study: insights into unique binding and antibiotic peptides.Nucleic acids research · 2017Article
- Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism.Nucleic acids research · 2017Article
- The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain.Nucleic acids research · 2017Article
- Inhibition of Human Cytomegalovirus pUL89 Terminase Subunit Blocks Virus Replication and Genome Cleavage.Journal of virology · 2017Article
- Hiding in Plain Sight: The Bimetallic Magnesium Covalent Bond in Enzyme Active Sites.Inorganic chemistry · 2017Article
- Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase.ACS omega · 2016Article
- Discovery and Development of a Three-Component Oxidopyrylium [5 + 2] Cycloaddition.The Journal of organic chemistry · 2016Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg(2+). A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 Å. Such proximity of the two metal ions may play an essential role in catalysis by generating a highly positive electrostatic niche to enable formation of the negatively charged pentacovalent phosphate transition state, and provides the structural basis for distinguishing Mg(2+) from Ca(2+). Using a metal ion chelator β-thujaplicinol as a molecular probe, we observed a second mode of metal ion binding at the active site, mimicking the DNA binding state. Arrangement of the active site residues differs drastically from those in RNase H-like nucleases, suggesting a drifting of the active site configuration during evolution. The two distinct metal ion binding modes unveiled mechanistic details of the two-metal-ion catalysis at atomic resolution.
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