Structures and activation mechanism of Gabija anti-phage system

Structures and activation mechanism of Gabija anti-phage system | 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 Biological Sciences - Article Structures and activation mechanism of Gabija anti-phage system Longfei Wang, Jing Li, Rui Cheng, Zhiming Wang, Wuliu Yuan, Jun Xiao, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3066188/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 12 Mar, 2024 Read the published version in Nature → Version 1 posted You are reading this latest preprint version Abstract Bacteria have evolved intricate innate immune systems against phage infection 1-7 . Gabija is a highly abundant prokaryotic defense system in bacteria and archaea consisting of two components, GajA and GajB 8 . We previously demonstrated that GajA functions as a DNA endonuclease and is inhibited by ATP 9 . However, the mechanism of the anti-viral defense by Gabija is elusive. Here, we utilize cryo-EM to capture the Gabija system in five states, GajA in apo or complex with DNA, GajA inhibited by ATP, and GajAB in apo or with ATP/Mg 2+ . Our structures show that GajA is a rhombus-shaped tetramer that binds DNA in a bipartite manner. GajA recognizes and bends the substrate DNA to align the DNA cleavage site with the catalytic residues in the Toprim domain. DNA binding requires the opening of the hinged clamps, which are locked in a closed conformation upon ATP-binding, therefore inhibited by ATP. GajB does not bind DNA alone but docks on the GajA tetramer and is activated by the nicked DNA generated by GajA. Thus, GajA is activated by local depletion of cellular ATP, generating nicked DNA that activates GajB and ultimately leads to cell death. Our study unveiled a ~500 kDa supramolecular assembly of GajAB and provided mechanistic insights into the Gabija system. Biological sciences/Microbiology/Bacteria/Bacterial structural biology Biological sciences/Immunology/Innate immunity/Pattern recognition receptors Full Text Additional Declarations There is NO Competing Interest. Supplementary Files nrtablescryoemGabijafinal3.pdf Extended Data Table 1 SupplementaryFigure1.pdf Supplementary Figure 1 Cite Share Download PDF Status: Published Journal Publication published 12 Mar, 2024 Read the published version in Nature → 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. 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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-3066188","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Biological Sciences - Article","associatedPublications":[],"authors":[{"id":259303614,"identity":"3f05f2c3-960b-4c92-aa8a-cbe17dd4b65d","order_by":0,"name":"Longfei 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Gabija is a highly abundant prokaryotic defense system in bacteria and archaea consisting of two components, GajA and GajB\u003csup\u003e8\u003c/sup\u003e. We previously demonstrated that GajA functions as a DNA endonuclease and is inhibited by ATP\u003csup\u003e9\u003c/sup\u003e. However, the mechanism of the anti-viral defense by Gabija is elusive. Here, we utilize cryo-EM to capture the Gabija system in five states, GajA in apo or complex with DNA, GajA inhibited by ATP, and GajAB in apo or with ATP/Mg\u003csup\u003e2+\u003c/sup\u003e. Our structures show that GajA is a rhombus-shaped tetramer that binds DNA in a bipartite manner. GajA recognizes and bends the substrate DNA to align the DNA cleavage site with the catalytic residues in the Toprim domain. DNA binding requires the opening of the hinged clamps, which are locked in a closed conformation upon ATP-binding, therefore inhibited by ATP. 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