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Using an S-adenosyl-l-methionine analog, we trapped a post-catalytic state of the Trm10\u2013tRNAGly complex for structure determination by cryogenic electron microscopy. Three distinct complexes were captured: two monomeric Trm10\u2013tRNA complexes with distinct tRNA acceptor stem orientations (\u201cclosed\u201d and \u201copen\u201d), and a minor dimeric complex with two Trm10s bound to the same tRNA. The monomeric structures identify conserved residues involved in tRNA interactions across a positively charged surface that guide G9 into the catalytic site and stabilize the flipped nucleotide. In the tRNAopen conformation, acceptor stem rotation weakens tRNA-protein contacts, consistent with a product-release state. The dimeric complex, supported by tRNA-dependent protein crosslinking and molecular dynamics (MD) simulations, positions one Trm10 on G9 similarly to the monomeric complexes, while the other contacts distal tRNA regions, suggesting a functional role in promoting functionally critical conformational transition(s). MD simulations also show how Trm10 achieves selective stabilization of G9 over A9 in the binding pocket. Overall, our findings reveal the mechanism of G9-specific tRNA methylation by Trm10 and suggest a unique mechanism of action among RNA-modifying SPOUT methyltransferases.<\/jats:p>","DOI":"10.1093\/nar\/gkag882","type":"journal-article","created":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T11:16:40Z","timestamp":1788520600000},"source":"Crossref","is-referenced-by-count":0,"title":["Molecular basis of tRNA substrate recognition and modification by the atypical SPOUT methyltransferase Trm10"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3534-8002","authenticated-orcid":false,"given":"Suparno","family":"Nandi","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Emory University School of Medicine , Atlanta, GA 30322 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7555-9608","authenticated-orcid":false,"given":"Sarah 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