Three-metal-ion catalysis by ribonuclease P holoenzyme: a new mechanistic insight into transfer RNA maturation

Three-metal-ion catalysis by ribonuclease P holoenzyme: a new mechanistic insight into transfer RNA maturation | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Three-metal-ion catalysis by ribonuclease P holoenzyme: a new mechanistic insight into transfer RNA maturation Yun-Xing Wang, Yun-Tzai Lee, Maximilia Degenhardt, ilias Skeparnias, and 7 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9187222/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Ribonuclease P (RNase P) is an essential metalloenzyme responsible for tRNA 5′ maturation across all three domains of life. The catalytic mechanism, particularly the number of divalent metal ions and the role of its protein component, remains unresolved. We determined cryo-EM structures of Geobacillus Stearothermophilus RNase P holoenzyme at 2.7-3.0 Å resolution in three catalytic states. These structures reveal a three-metal-ion catalytic mechanism, challenging the long-standing two-metal-ion model. Two metal ions are substrate-dependent, one of which is also protein-dependent. The protein component, rnpA, dramatically enhances ribozyme activity by reducing conformational sampling, stabilizing the enzyme-substrate complex through direct contact with the pre-tRNA 5′-leader, and cooperatively stabilizing the third catalytic metal ion with the substrate. Biological sciences/Structural biology/Electron microscopy/Cryoelectron microscopy Biological sciences/Biochemistry/RNA Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryVideo1.mp4 Supplementary video 03062026ExtFigs.pdf Extended figures Combinedvalidationreport.pdf structural validation report 03052026SupplTables.pdf Supplementary tables 03052026SuppIFigs.pdf supplementary figures HoloES9OWT.txt pbd4 HoloESnc9OWW.txt pdb8 TLmholoE9OY5.txt pdb9 HoloE9OWR.txt pdb1 HoloES9OWU.txt pdb5 HoloE9OWS.txt pdb2 TLmholoE9OY6.txt pdb10 HoloEP9OWV.txt pdb3 HoloESLBtilt19OWX.txt pbd6 TLmholoES9OY7.txt pdb11 nrreportingsummary.pdf nr-reporting-summary Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-9187222","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":639175281,"identity":"dd2f23a4-aec0-47d1-a4ff-b3b023a093b0","order_by":0,"name":"Yun-Xing 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