{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T14:07:34Z","timestamp":1789567654996,"version":"build-2803163510"},"reference-count":53,"publisher":"American Chemical Society (ACS)","issue":"36","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22137009 and 31930002"],"award-info":[{"award-number":["22137009 and 31930002"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Science and Technology Major Project"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Nonheme iron\/\u03b1-ketoglutarate-dependent dioxygenases (Fe\/\u03b1KGDs) catalyze diverse oxidative transformations, including hydroxylation, desaturation, and ring expansion. Although these reactions are well established, Fe\/\u03b1KGD-catalyzed epimerization remains rare and has not been characterized in ribosomally synthesized and post-translationally modified peptides (RiPPs). Here, we report the RiPP-modifying enzyme YmI, a bifunctional Fe\/\u03b1KGD that catalyzes C\u03b2-hydroxylation of Phe19 and C\u03b1-epimerization of Ile20 on the precursor peptide YmA toward the formation of YM-216391. The hydroxylation generates (2S,3R)-\u03b2-hydroxyphenylalanine, whose l-threonine-like stereochemistry facilitates subsequent formation of an unusual 5-phenyloxazole moiety. Substrate profiling analyses reveal leader peptide dependence for catalytic activity. Structural and docking studies provide insights into the substrate binding and active site architecture. Deuterium labeling demonstrates that YmI catalyzes Ile epimerization by directly abstracting the C\u03b1-hydrogen, generating a C\u03b1 radical that is subsequently reprotonated by a nonexchangeable hydrogen source within the enzyme. These results unveil an unprecedented mechanism and novel bifunctionality, markedly expanding the reaction landscape for \u03b1KG-dependent enzymes in RiPP biosynthesis.<\/jats:p>","DOI":"10.1021\/jacs.6c11815","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T13:53:13Z","timestamp":1788443593000},"page":"39012-39021","source":"Crossref","is-referenced-by-count":0,"title":["Biosynthesis of YM-216391\nUnveils a Bifunctional \u03b1-Ketoglutarate-Dependent\nEnzyme Catalyzes Hydroxylation and Epimerization in RiPPs"],"prefix":"10.1021","volume":"148","author":[{"given":"Kai","family":"Zhang","sequence":"first","affiliation":[{"name":"East China University of Science and Technology , , ,","place":["Shanghai, China, 200237"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lian","family":"Wu","sequence":"additional","affiliation":[{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences , , ,","place":["Shanghai, China, 200032"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min-Jie","family":"Yang","sequence":"additional","affiliation":[{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences , , ,","place":["Shanghai, China, 200032"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun-Bin","family":"He","sequence":"additional","affiliation":[{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences , , ,","place":["Shanghai, China, 200032"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3239-6209","authenticated-orcid":true,"given":"Yifeng","family":"Chen","sequence":"additional","affiliation":[{"name":"East China University of Science and Technology , , ,","place":["Shanghai, China, 200237"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zeng-Fei","family":"Pei","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, China, 200240"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3149-4683","authenticated-orcid":true,"given":"Gong-Li","family":"Tang","sequence":"additional","affiliation":[{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences , , ,","place":["Shanghai, China, 200032"]},{"name":"University of Chinese Academy of Sciences , , ,","place":["Hangzhou, China, 310024"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,1]]},"reference":[{"issue":"1","key":"2026091609114449100_cit1","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1039\/D0NP00027B","article-title":"New Developments\nin RiPP Discovery, Enzymology and Engineering","volume":"38","author":"Montalba\u0301n-Lo\u0301pez","year":"2021","journal-title":"Nat. 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Biol."},{"issue":"7","key":"2026091609114449100_cit30","doi-asserted-by":"publisher","first-page":"2567","DOI":"10.1039\/D0SC06308H","article-title":"Identification of the Peptide Epimerase\nMslH Responsible for d-Amino Acid Introduction at the C-Terminus\nof Ribosomal Peptides","volume":"12","author":"Feng","year":"2021","journal-title":"Chem. Sci."},{"issue":"1","key":"2026091609114449100_cit31","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-40232-x","article-title":"Structure of Lasso Peptide Epimerase\nMslH Reveals Metal-Dependent Acid\/Base Catalytic Mechanism","volume":"14","author":"Nakashima","year":"2023","journal-title":"Nat. Commun."},{"issue":"2","key":"2026091609114449100_cit32","doi-asserted-by":"publisher","first-page":"1757","DOI":"10.1021\/acscatal.5c08590","article-title":"Functional\nand Mechanistic Investigation of a Distinct DUF6895 Family Epimerase\nInvolved in Lasso Peptide Modification","volume":"16","author":"Shi","year":"2026","journal-title":"ACS\nCatal."},{"issue":"41","key":"2026091609114449100_cit33","doi-asserted-by":"publisher","first-page":"18029","DOI":"10.1002\/anie.202008035","article-title":"Functional\nGenome Mining Reveals a Class V Lanthipeptide Containing a d-Amino Acid Introduced by an F420H2-Dependent\nReductase","volume":"59","author":"Xu","year":"2020","journal-title":"Angew. Chem., Int. Ed."},{"issue":"1","key":"2026091609114449100_cit34","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1038\/ja.2005.2","article-title":"YM-216391,\na Novel Cytotoxic Cyclic Peptide from Streptomyces nobilis. I. Fermentation, Isolation and Biological\nActivities","volume":"58","author":"Sohda","year":"2005","journal-title":"J. Antibiot."},{"issue":"1","key":"2026091609114449100_cit35","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1038\/ja.2005.3","article-title":"YM-216391, a Novel\nCytotoxic Cyclic\nPeptide from Streptomyces nobilis.\nII. Physico-chemical properties and structure elucidation","volume":"58","author":"Sohda","year":"2005","journal-title":"J. Antibiot."},{"issue":"4","key":"2026091609114449100_cit36","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1021\/cb200479f","article-title":"Analysis of YM-216391\nBiosynthetic Gene Cluster and Improvement of the Cyclopeptide Production\nin a Heterologous Host","volume":"7","author":"Jian","year":"2012","journal-title":"ACS Chem. Biol."},{"issue":"1","key":"2026091609114449100_cit37","doi-asserted-by":"publisher","DOI":"10.1186\/s12934-023-02136-9","article-title":"Identification\nand Characterization of a Strong Constitutive Promoter stnYp for Activating Biosynthetic Genes and Producing Natural Products\nin Streptomyces","volume":"22","author":"Guo","year":"2023","journal-title":"Microb. Cell.\nFact."},{"issue":"47","key":"2026091609114449100_cit38","doi-asserted-by":"publisher","first-page":"19858","DOI":"10.1039\/D4SC02262A","article-title":"Analysis of the\nCryptic Biosynthetic Gene Cluster Encoding the RiPP Curacozole Reveals\na Phenylalanine-Specific Peptide Hydroxylase","volume":"15","author":"Hollands","year":"2024","journal-title":"Chem. 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Biol."},{"issue":"6175","key":"2026091609114449100_cit44","doi-asserted-by":"publisher","first-page":"1140","DOI":"10.1126\/science.1248000","article-title":"Mechanism\nof the C5 Stereoinversion Reaction in the Biosynthesis of Carbapenem\nAntibiotics","volume":"343","author":"Chang","year":"2014","journal-title":"Science"},{"issue":"9","key":"2026091609114449100_cit45","doi-asserted-by":"publisher","first-page":"5556","DOI":"10.1021\/acscatal.5b01275","article-title":"Uncoupled Epimerization\nand Desaturation by Carbapenem Synthase: Mechanistic Insights from\nQM\/MM Studies","volume":"5","author":"Ma","year":"2015","journal-title":"ACS Catal."},{"issue":"20","key":"2026091609114449100_cit46","doi-asserted-by":"publisher","first-page":"7496","DOI":"10.1021\/ja311078s","article-title":"Mechanistic Insights\ninto the Bifunctional Non-Heme\nIron Oxygenase Carbapenem Synthase by Active Site Saturation Mutagenesis","volume":"135","author":"Phelan","year":"2013","journal-title":"J. Am. Chem. Soc."},{"issue":"30","key":"2026091609114449100_cit47","doi-asserted-by":"publisher","first-page":"20188","DOI":"10.1039\/C7CP02687K","article-title":"Mechanistic\nInsights into Dioxygen Activation, Oxygen\nAtom Exchange and Substrate Epoxidation by AsqJ Dioxygenase from Quantum\nMechanical\/Molecular Mechanical Calculations","volume":"19","author":"Song","year":"2017","journal-title":"Phys. Chem. Chem. Phys."},{"issue":"1","key":"2026091609114449100_cit48","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-03442-2","article-title":"Catalytic Mechanism\nand Molecular Engineering of Quinolone Biosynthesis in Dioxygenase\nAsqJ","volume":"9","author":"Mader","year":"2018","journal-title":"Nat. Commun."},{"issue":"5","key":"2026091609114449100_cit49","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1093\/abbs\/gmab036","article-title":"A Modified\npCas\/pTargetF System for CRISPR-Cas9-Assisted Genome Editing in Escherichia coli","volume":"53","author":"Li","year":"2021","journal-title":"Acta. Biochim.\nBiophys. Sin."},{"issue":"2","key":"2026091609114449100_cit50","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1007\/s00775-016-1414-3","article-title":"Beyond Ferryl-Mediated Hydroxylation: 40 Years of the\nRebound Mechanism and C-H Activation.","volume":"22","author":"Huang","year":"2017","journal-title":"J. Biol.\nInorg. Chem."},{"issue":"14","key":"2026091609114449100_cit51","doi-asserted-by":"publisher","DOI":"10.1002\/anie.202216989","article-title":"Hydroxylation with Unusual Stereoinversion\nCatalyzed by an FeII\/2-OG Dependent Oxidase and 3,6-Diene-2,5-diketopiperazine\nFormation in the Biosynthesis of Brevianamide K","volume":"62","author":"Xu","year":"2023","journal-title":"Angew. Chem., Int. 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