{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,2]],"date-time":"2025-08-02T16:21:06Z","timestamp":1754151666202,"version":"3.41.2"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2025,7,19]],"date-time":"2025-07-19T00:00:00Z","timestamp":1752883200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIHGMS","award":["5T32GM007491","R01-GM134021","R35-GM126945"],"award-info":[{"award-number":["5T32GM007491","R01-GM134021","R35-GM126945"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["S10 OD020068"],"award-info":[{"award-number":["S10 OD020068"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","award":["P30CA013330"],"award-info":[{"award-number":["P30CA013330"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The essential enzyme messenger RNA (mRNA) (guanine-N7)\u00a0methyltransferase catalyzes S-adenosylmethionine (SAM)-dependent conversion of GpppRNA ends to the m7GpppRNA cap structure characteristic of eukaryal mRNAs. The antibiotic sinefungin (SFG) is a SAM analog in which the S-CH3 sulfonium moiety of SAM is replaced by a C-NH2 amine. Available evidence indicates that the antifungal activity of SFG is exerted via inhibition of fungal cap methyltransferase Abd1. Here we report that recombinant Kluyveromyces lactis and Saccharomyces cerevisiae Abd1 are 240-fold and 485-fold more sensitive to inhibition by SFG than by the reaction product S-adenosylhomocysteine (SAH). Crystal structures of K. lactis and S. cerevisiae Abd1 as binary complexes with SAH or SFG and ternary complexes with GTP\u2022SFG highlight how SFG makes two hydrogen bonds from its C-NH2 amine to the guanine-O6 and -N7 atoms of GTP that account for its higher affinity vis-\u00e0-vis SAH and SAM. Through a genetic screen to isolate SFG-resistant S. cerevisiae strains, a conserved tyrosine (Tyr416) that interacts with the cap guanine in Abd1 was identified as a key determinant of SFG potency. Tyr416 Abd1 variants confer SFG resistance in vitro by weakening cap-assisted SFG interactions with Abd1. Our study illuminates the basis for the exquisite SFG sensitivity of fungal cap methyltransferases.<\/jats:p>","DOI":"10.1093\/nar\/gkaf538","type":"journal-article","created":{"date-parts":[[2025,7,19]],"date-time":"2025-07-19T18:48:15Z","timestamp":1752950895000},"source":"Crossref","is-referenced-by-count":0,"title":["Structural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic sinefungin"],"prefix":"10.1093","volume":"53","author":[{"given":"Daniel\u00a0J","family":"Nilson","sequence":"first","affiliation":[{"name":"Albert Einstein College of Medicine Department of Biochemistry, , 1300 Morris Park Avenue , Bronx , New York,\u00a0NY\u00a010461,\u00a0","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beate","family":"Schwer","sequence":"additional","affiliation":[{"name":"Weill Cornell Medical College Department of Microbiology and Immunology, ,\u00a0New York,\u00a0NY\u00a010021,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven\u00a0C","family":"Almo","sequence":"additional","affiliation":[{"name":"Albert Einstein College of Medicine Department of Biochemistry, , 1300 Morris Park Avenue , Bronx , New York,\u00a0NY\u00a010461,\u00a0","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stewart","family":"Shuman","sequence":"additional","affiliation":[{"name":"Molecular Biology Program, Memorial Sloan Kettering Cancer Center ,\u00a0New York,\u00a0NY\u00a010021,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7753-0240","authenticated-orcid":false,"given":"Agnidipta","family":"Ghosh","sequence":"additional","affiliation":[{"name":"Albert Einstein College of Medicine Department of Biochemistry, , 1300 Morris Park Avenue , Bronx , New York,\u00a0NY\u00a010461,\u00a0","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,7,19]]},"reference":[{"key":"2025071914481388100_B1","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1002\/wrna.19","article-title":"Enzymology of RNA cap synthesis","volume":"1","author":"Ghosh","year":"2010","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"2025071914481388100_B2","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1101\/sqb.2001.66.301","article-title":"The mRNA capping apparatus as drug target and guide to eukaryotic phylogeny","volume":"66","author":"Shuman","year":"2001","journal-title":"Cold Spring Harbor Symp Quant Biol"},{"key":"2025071914481388100_B3","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1021\/jm00348a004","article-title":"Carbocyclic analogue of 3-deazaadenosine: a novel antiviral agent using S-adenosylhomocysteine hydrolase as a pharmacological target","volume":"25","author":"Montgomery","year":"1982","journal-title":"J Med Chem"},{"key":"2025071914481388100_B4","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1177\/1087057104273333","article-title":"Cell-based assays to detect inhibitors of fungal mRNA capping enzymes and characterization of sinefungin as a cap methyltransferase inhibitor","volume":"10","author":"Chrebet","year":"2005","journal-title":"J Biomol Screen"},{"key":"2025071914481388100_B5","doi-asserted-by":"publisher","first-page":"16553","DOI":"10.1074\/jbc.274.23.16553","article-title":"Characterization of human, Schizosaccharomyces pombe, and Candida albicans mRNA cap methyltransferases and complete replacement of the yeast capping apparatus by mammalian enzymes","volume":"274","author":"Saha","year":"1999","journal-title":"J Biol Chem"},{"key":"2025071914481388100_B6","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1074\/jbc.M109649200","article-title":"Characterization of the mRNA capping apparatus of the microsporidian parasite Encephalitozoon cuniculi","volume":"277","author":"Hausmann","year":"2002","journal-title":"J Biol Chem"},{"key":"2025071914481388100_B7","doi-asserted-by":"publisher","first-page":"35904","DOI":"10.1074\/jbc.M607292200","article-title":"Mutational analysis of Encephalitozoon cuniculi mRNA cap (guanine-N7) methyltransferase, structure of the enzyme bound to sinefungin, and evidence that cap methyltransferase is the target of sinefungin\u2019s antifungal activity","volume":"281","author":"Zheng","year":"2006","journal-title":"J Biol Chem"},{"key":"2025071914481388100_B8","doi-asserted-by":"publisher","first-page":"1549","DOI":"10.1016\/S1097-2765(03)00187-4","article-title":"Structure of an mRNA capping enzyme bound to the phosphorylated carboxy-terminal domain of RNA polymerase II","volume":"11","author":"Fabrega","year":"2003","journal-title":"Mol Cell"},{"key":"2025071914481388100_B9","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/S1097-2765(03)00522-7","article-title":"Structure and mechanism of mRNA cap (guanine-N7) methyltransferase","volume":"13","author":"Fabrega","year":"2004","journal-title":"Mol Cell"},{"key":"2025071914481388100_B10","doi-asserted-by":"publisher","first-page":"8394","DOI":"10.1021\/bi034245a","article-title":"Catalytic mechanism of glycine N-methyltransferase","volume":"42","author":"Takata","year":"2003","journal-title":"Biochemistry"},{"key":"2025071914481388100_B11","doi-asserted-by":"publisher","first-page":"20404","DOI":"10.1074\/jbc.M501073200","article-title":"Encephalitozoon cuniculi mRNA cap (guanine N-7) methyltransferase: methyl acceptor specificity, inhibition by S-adenosylmethionine analogs, and structure-guided mutational analysis","volume":"280","author":"Hausmann","year":"2005","journal-title":"J Biol Chem"},{"key":"2025071914481388100_B12","doi-asserted-by":"publisher","first-page":"4167","DOI":"10.1128\/MCB.15.8.4167","article-title":"Yeast mRNA cap methyltransferase is a 50-kilodalton protein encoded by an essential gene","volume":"15","author":"Mao","year":"1995","journal-title":"Mol Cell Biol"},{"key":"2025071914481388100_B13","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1128\/MCB.16.2.475","article-title":"Mutational analysis of the Saccharomyces cerevisiae ABD1 gene: cap methyltransferase activity is essential for cell growth","volume":"16","author":"Mao","year":"1996","journal-title":"Mol Cell Biol"},{"key":"2025071914481388100_B14","doi-asserted-by":"publisher","first-page":"1561","DOI":"10.1093\/genetics\/155.4.1561","article-title":"Structure\u2013function analysis of yeast mRNA cap methyltransferase and high-copy suppression of conditional mutants by AdoMet synthase and the ubiquitin conjugating enzyme Cdc34p","volume":"155","author":"Schwer","year":"2000","journal-title":"Genetics"},{"key":"2025071914481388100_B15","doi-asserted-by":"publisher","first-page":"14683","DOI":"10.1074\/jbc.272.23.14683","article-title":"Structure\u2013function analysis of the mRNA cap methyltransferase of Saccharomyces cerevisiae","volume":"272","author":"Wang","year":"1997","journal-title":"J Biol Chem"},{"key":"2025071914481388100_B16","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1016\/S1097-2765(00)80326-3","article-title":"Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast","volume":"5","author":"Mossessova","year":"2000","journal-title":"Mol Cell"},{"volume-title":"R: A Language and Environment for Statistical Computing","year":"2024","author":"R Core Team","key":"2025071914481388100_B17"},{"key":"2025071914481388100_B18","doi-asserted-by":"publisher","first-page":"e0146021","DOI":"10.1371\/journal.pone.0146021","article-title":"Dose-response analysis using R","volume":"10","author":"Ritz","year":"2016","journal-title":"PLoS One"},{"key":"2025071914481388100_B19","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016","edition":"2nd edn"},{"key":"2025071914481388100_B20","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1107\/S2059798323003595","article-title":"The CCP4 suite: integrative software for macromolecular crystallography","volume":"79","author":"Agirre","year":"2023","journal-title":"Acta Crystallogr D Struct Biol"},{"key":"2025071914481388100_B21","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1107\/S0907444910007493","article-title":"Features and development of Coot","volume":"66","author":"Emsley","year":"2010","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"2025071914481388100_B22","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1107\/S0907444911001314","article-title":"REFMAC5 for the refinement of macromolecular crystal structures","volume":"67","author":"Murshudov","year":"2011","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"2025071914481388100_B23","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1107\/S2059798319011471","article-title":"Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix","volume":"75","author":"Liebschner","year":"2019","journal-title":"Acta Crystallogr D Struct Biol"},{"key":"2025071914481388100_B24","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1002\/pro.3330","article-title":"MolProbity: more and better reference data for improved all-atom structure validation","volume":"27","author":"Williams","year":"2018","journal-title":"Protein Sci"},{"key":"2025071914481388100_B25","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/S0022-2836(63)80023-6","article-title":"Stereochemistry of polypeptide chain configurations","volume":"7","author":"Ramachandran","year":"1963","journal-title":"J Mol Biol"},{"key":"2025071914481388100_B26","doi-asserted-by":"publisher","first-page":"6895","DOI":"10.1093\/nar\/gkm817","article-title":"Sinefungin resistance of Saccharomyces cerevisiae arising from Sam3 mutations that inactivate the AdoMet transporter or from increased expression of AdoMet synthase plus mRNA cap guanine-N7 methyltransferase","volume":"35","author":"Zheng","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2025071914481388100_B27","doi-asserted-by":"publisher","first-page":"4913","DOI":"10.1038\/sj.emboj.7601912","article-title":"Structural insights into the mechanism and evolution of the vaccinia virus mRNA cap N7 methyl-transferase","volume":"26","author":"De","year":"2007","journal-title":"EMBO J"},{"key":"2025071914481388100_B28","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1016\/j.str.2013.12.014","article-title":"Crystal structure of vaccinia virus mRNA capping enzyme provides insights into the mechanism and evolution of the capping apparatus","volume":"22","author":"Kyrieleis","year":"2014","journal-title":"Structure"},{"key":"2025071914481388100_B29","doi-asserted-by":"publisher","first-page":"10423","DOI":"10.1093\/nar\/gkw637","article-title":"Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM","volume":"44","author":"Varshney","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2025071914481388100_B30","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1261\/rna.928208","article-title":"Structure-function analysis of vaccinia virus mRNA cap (guanine-N7) methyltransferase","volume":"14","author":"Zheng","year":"2008","journal-title":"RNA"},{"key":"2025071914481388100_B31","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1038\/s44259-024-00040-9","article-title":"Sinefungin, a natural nucleoside analog of S-adenosyl methionine, impairs the pathogenicity of Candida albicans","volume":"2","author":"Nayak","year":"2024","journal-title":"NPJ Antimicrob Resist"},{"key":"2025071914481388100_B32","doi-asserted-by":"publisher","first-page":"463","DOI":"10.7164\/antibiotics.26.463","article-title":"A9145, a new adenine-containing antifungal antibiotic. I. Discovery and isolation","volume":"26","author":"Hamil","year":"1973","journal-title":"J Antibiot"},{"key":"2025071914481388100_B33","doi-asserted-by":"publisher","first-page":"4075","DOI":"10.1016\/S0021-9258(17)34682-3","article-title":"Sinefungin, a potent inhibitor of virion mRNA (guanine-7-)-methyltransferase, mRNA (nucleoside-2\u2032-)-methyltransferase, and viral multiplication","volume":"253","author":"Pugh","year":"1978","journal-title":"J Biol Chem"},{"key":"2025071914481388100_B34","doi-asserted-by":"publisher","first-page":"466","DOI":"10.7164\/antibiotics.26.466","article-title":"A9145, a new adenine-containing antifungal antibiotic. II. Biological activity","volume":"26","author":"Gordee","year":"1973","journal-title":"J Antibiot"},{"key":"2025071914481388100_B35","doi-asserted-by":"publisher","first-page":"1857","DOI":"10.1074\/jbc.M006072200","article-title":"Characterization of the mRNA capping apparatus of Candida albicans","volume":"276","author":"Schwer","year":"2001","journal-title":"J Biol Chem"},{"key":"2025071914481388100_B36","doi-asserted-by":"publisher","first-page":"7733","DOI":"10.1074\/jbc.M611105200","article-title":"Polyamine uptake by DUR3 and SAM3 in Saccharomyces cerevisiae","volume":"282","author":"Uemura","year":"2007","journal-title":"J Biol Chem"},{"key":"2025071914481388100_B37","doi-asserted-by":"publisher","first-page":"28096","DOI":"10.1074\/jbc.274.40.28096","article-title":"Transport of sulfonium compounds. Characterization of the S-adenosylmethionine and S-methylmethionine permeases from the yeast Saccharomyces cerevisiae","volume":"274","author":"Rouillon","year":"1999","journal-title":"J Biol Chem"},{"key":"2025071914481388100_B38","doi-asserted-by":"publisher","first-page":"4509","DOI":"10.1038\/s41598-024-55184-5","article-title":"Kinetic characterization of human mRNA guanine-N7 methyltransferase","volume":"14","author":"Perveen","year":"2024","journal-title":"Sci Rep"},{"key":"2025071914481388100_B39","first-page":"BCJ20240608","article-title":"Characterisation of RNA guanine-7 methyltransferase (RNMT) using a small molecule approach","volume":"482","author":"Pearson","year":"2025","journal-title":"Biochem J"},{"volume-title":"WHO Fungal Priority Pathogens List to Guide Research, Development and Public Health Action","year":"2022","author":"WHO","key":"2025071914481388100_B40"},{"key":"2025071914481388100_B41","doi-asserted-by":"publisher","first-page":"1981","DOI":"10.1016\/0006-2952(78)90018-7","article-title":"Inhibition of methyltransferases by some new analogs of S-adenosylhomocysteine","volume":"27","author":"Fuller","year":"1978","journal-title":"Biochem Pharmacol"},{"key":"2025071914481388100_B42","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/53\/14\/gkaf538\/63802638\/gkaf538.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/53\/14\/gkaf538\/63802638\/gkaf538.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,19]],"date-time":"2025-07-19T18:48:18Z","timestamp":1752950898000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/doi\/10.1093\/nar\/gkaf538\/8208108"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,19]]},"references-count":42,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2025,7,19]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaf538","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"type":"print","value":"0305-1048"},{"type":"electronic","value":"1362-4962"}],"subject":[],"published-other":{"date-parts":[[2025,8,12]]},"published":{"date-parts":[[2025,7,19]]},"article-number":"gkaf538"}}