{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T15:16:13Z","timestamp":1793114173360,"version":"4.5.0"},"reference-count":117,"publisher":"American Chemical Society (ACS)","issue":"7","license":[{"start":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T00:00:00Z","timestamp":1780704000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["2R15GM139118"],"award-info":[{"award-number":["2R15GM139118"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The nonheme Fe(II)\/2-oxoglutarate (2OG)-dependent histone demethylase KDM6B (JMJD3) has demonstrated a capacity for diversity in the oxidative transformations of N\u03b5-alkylated lysine residues in histone H3 peptides; however, the mechanisms of such dealkylations, compared with standard KDM-catalyzed demethylations, remain unexplored. We implemented molecular dynamics and quantum mechanics\/molecular mechanics to investigate the catalytic strategies for the sequential oxidation reactions of KDM6B with different N-alkylated forms of lysine K27 in the H3 peptide chain, that is N\u03b5, N\u03b5-methyl ethyl lysine (Lys(Me\/Eth)) and N\u03b5-isopropyl lysine (Lys(iPr)). The results for sequential oxidations, which yield alcohol, aldehyde, and then carboxylic acid products, reveal that variations in the conformational positioning of different N-alkylated groups are enabled by second coordination sphere (SCS) interactions and long-range correlated motions. Specifically, access of the different N-alkylated groups to the reactive Fe(IV)=O intermediate, leading to hydroxylation, is controlled by a network of SCS interactions, in particular involving N344 and Y239, which was also demonstrated by MD and QM\/MM calculations on N344A and Y239A mutants. Subsequent oxidations of the alcohols to aldehyde and acid derivatives are also guided by the conformational positioning of the hydroxylated\/aldehyde substituent. QM\/MM calculations predicted regio- and chemo-selective oxidation can be initiated through hydrogen atom transfer involving \u03c3- or \u03c0-mechanisms. The insights would guide experimental efforts to design Fe(II)\/2OG enzymes with non-native catalytic activities and altered substrate selectivity. Furthermore, the results reveal mechanistic features that can be leveraged to design biocatalytic platforms for the selective functionalization of peptide-based drugs.<\/jats:p>","DOI":"10.1021\/jacsau.6c00575","type":"journal-article","created":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T13:01:16Z","timestamp":1780750876000},"page":"4048-4072","source":"Crossref","is-referenced-by-count":4,"title":["Beyond Histone Demethylation: Mechanisms of\n                    <i>N<\/i>\n                    -Alkyl Consecutive Oxidations by the Non-Heme Fe(II)\/2-Oxoglutarate\nOxygenase KDM6B"],"prefix":"10.1021","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8557-078X","authenticated-orcid":true,"given":"Simahudeen Bathir","family":"Jaber Sathik Rifayee","sequence":"first","affiliation":[{"name":"Michigan Technological University , , , ,","place":["Houghton, Michigan, United States, 49931"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sudheesh","family":"Devadas","sequence":"additional","affiliation":[{"name":"Michigan Technological University , , , ,","place":["Houghton, Michigan, United States, 49931"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6298-7061","authenticated-orcid":true,"given":"Midhun George","family":"Thomas","sequence":"additional","affiliation":[{"name":"Michigan Technological University , , , ,","place":["Houghton, Michigan, United States, 49931"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bhargav","family":"Varada","sequence":"additional","affiliation":[{"name":"Michigan Technological University , , , ,","place":["Houghton, Michigan, United States, 49931"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ethan","family":"Sommer","sequence":"additional","affiliation":[{"name":"Michigan Technological University , , , ,","place":["Houghton, Michigan, United States, 49931"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cassandra","family":"Talaba","sequence":"additional","affiliation":[{"name":"Michigan Technological University , , , ,","place":["Houghton, Michigan, United States, 49931"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0290-6565","authenticated-orcid":true,"given":"Christopher","family":"Schofield","sequence":"additional","affiliation":[{"name":"University of Oxford , , ,","place":["Oxford, U.K., OX1 3TA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4481-0246","authenticated-orcid":true,"given":"Christo Z.","family":"Christov","sequence":"additional","affiliation":[{"name":"Michigan Technological University , , , ,","place":["Houghton, Michigan, United States, 49931"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,6,6]]},"reference":[{"issue":"4","key":"2026073100193492800_cit1","doi-asserted-by":"publisher","first-page":"2003","DOI":"10.1039\/C0CS00067A","article-title":"Enzymatic Functionalization of Carbon-Hydrogen\nBonds","volume":"40","author":"Lewis","year":"2011","journal-title":"Chem. 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Biol."},{"issue":"10","key":"2026073100193492800_cit5","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1038\/s41589-019-0355-x","article-title":"A Family of Radical\nHalogenases for the Engineering\nof Amino-Acid-Based Products","volume":"15","author":"Neugebauer","year":"2019","journal-title":"Nat. Chem. Biol."},{"issue":"1","key":"2026073100193492800_cit6","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1038\/s43586-021-00041-2","article-title":"C-H Activation","volume":"1","author":"Rogge","year":"2021","journal-title":"Nat. Rev. Methods Primers"},{"issue":"4","key":"2026073100193492800_cit7","doi-asserted-by":"publisher","first-page":"2192","DOI":"10.1021\/acs.chemrev.8b00507","article-title":"3d Transition\nMetals for C-H Activation","volume":"119","author":"Gandeepan","year":"2019","journal-title":"Chem. 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Natl. Acad.\nSci. U. S. A."},{"issue":"5\u20136","key":"2026073100193492800_cit32","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1016\/j.cbpa.2012.09.015","article-title":"Mechanisms of Human Histone and Nucleic\nAcid Demethylases","volume":"16","author":"Walport","year":"2012","journal-title":"Curr. Opin. Chem. Biol."},{"issue":"1","key":"2026073100193492800_cit33","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1038\/nsmb.1753","article-title":"Enzymatic and Structural\nInsights for Substrate Specificity of a\nFamily of Jumonji Histone Lysine Demethylases","volume":"17","author":"Horton","year":"2010","journal-title":"Nat. Struct. Mol. Biol."},{"issue":"1","key":"2026073100193492800_cit34","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1002\/chem.201604219","article-title":"Two-State\nReactivity of Histone Demethylases Containing Jumonji-C Active Sites:\nDifferent Mechanisms for Different Methylation Degrees","volume":"23","author":"Alberro","year":"2017","journal-title":"Chem. - Eur. 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J."},{"issue":"7","key":"2026073100193492800_cit37","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1002\/1873-3468.14586","article-title":"The Catalytic Domains of All Human\nKDM5 JmjC Demethylases Catalyse N -methyl Arginine Demethylation","volume":"597","author":"Bonnici","year":"2023","journal-title":"FEBS Lett."},{"issue":"5","key":"2026073100193492800_cit38","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1021\/acs.biochem.7b01152","article-title":"Structural Basis of Histone Demethylase\nKDM6B Histone 3 Lysine 27 Specificity","volume":"57","author":"Jones","year":"2018","journal-title":"Biochemistry"},{"issue":"21","key":"2026073100193492800_cit39","doi-asserted-by":"publisher","first-page":"2266","DOI":"10.1101\/gad.172296.111","article-title":"Structural Basis for\nHistone H3 Lys 27 Demethylation\nby UTX\/KDM6A","volume":"25","author":"Sengoku","year":"2011","journal-title":"Genes Dev."},{"issue":"1","key":"2026073100193492800_cit40","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/j.ymgme.2019.04.012","article-title":"Lysine Demethylases\nKDM6A and UTY:\nThe X and Y of Histone Demethylation","volume":"127","author":"Gaz\u030cova\u0301","year":"2019","journal-title":"Mol. Genet.\nMetab."},{"issue":"26","key":"2026073100193492800_cit41","doi-asserted-by":"publisher","first-page":"18302","DOI":"10.1074\/jbc.M114.555052","article-title":"Human UTY(KDM6C)\nIs a Male-Specific N\u03f5-Methyl Lysyl Demethylase","volume":"289","author":"Walport","year":"2014","journal-title":"J. Biol. Chem."},{"issue":"51","key":"2026073100193492800_cit42","doi-asserted-by":"publisher","DOI":"10.1002\/chem.202301305","article-title":"Catalysis by KDM6 Histone Demethylases - A Synergy\nbetween the Non-Heme Iron(II) Center, Second Coordination Sphere,\nand Long-Range Interactions","volume":"29","author":"Rifayee","year":"2023","journal-title":"Chem.\u2013Eur.\nJ."},{"issue":"57","key":"2026073100193492800_cit43","doi-asserted-by":"publisher","first-page":"7975","DOI":"10.1039\/C8CC04057E","article-title":"Human Histone Demethylase KDM6B Can Catalyse Sequential\nOxidations","volume":"54","author":"Hopkinson","year":"2018","journal-title":"Chem. 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Res. 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(Tokyo)"},{"issue":"7","key":"2026073100193492800_cit55","doi-asserted-by":"publisher","first-page":"3877","DOI":"10.1021\/acscatal.0c05034","article-title":"Catalytic\nMechanism of Human Ten-Eleven Translocation-2 (TET2) Enzyme: Effects\nof Conformational Changes, Electric Field, and Mutations","volume":"11","author":"Waheed","year":"2021","journal-title":"ACS Catal."},{"issue":"6","key":"2026073100193492800_cit56","doi-asserted-by":"publisher","first-page":"4728","DOI":"10.1039\/C5CP07266B","article-title":"A Computational\nInvestigation on the Substrate Preference of Ten-Eleven-Translocation\n2 (TET2)","volume":"18","author":"Lu","year":"2016","journal-title":"Phys. Chem. Chem. 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