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Kenichi Yokoyama - Publications

Affiliations: 
Department of Biochemistry Duke University School of Medicine, Durham, NC, United States 
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35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Böhringer N, Kramer JC, de la Mora E, Padva L, Wuisan ZG, Liu Y, Kurz M, Marner M, Nguyen H, Amara P, Yokoyama K, Nicolet Y, Mettal U, Schäberle TF. Genome- and metabolome-guided discovery of marine BamA inhibitors revealed a dedicated darobactin halogenase. Cell Chemical Biology. PMID 37451267 DOI: 10.1016/j.chembiol.2023.06.011  0.408
2023 Du Y, Thanapipatsiri A, Yokoyama KK. Biosynthesis and Genome Mining Potentials of Nucleoside Natural Products. Chembiochem : a European Journal of Chemical Biology. e202300342. PMID 37357819 DOI: 10.1002/cbic.202300342  0.314
2022 Nguyen H, Made Kresna ID, Böhringer N, Ruel J, Mora E, Kramer JC, Lewis K, Nicolet Y, Schäberle TF, Yokoyama K. Characterization of a Radical SAM Oxygenase for the Ether Crosslinking in Darobactin Biosynthesis. Journal of the American Chemical Society. PMID 36194754 DOI: 10.1021/jacs.2c05565  0.524
2021 Yokoyama K, Li D, Pang H. Resolving the Multidecade-Long Mystery in MoaA Radical SAM Enzyme Reveals New Opportunities to Tackle Human Health Problems. Acs Bio & Med Chem Au. 2: 94-108. PMID 35480226 DOI: 10.1021/acsbiomedchemau.1c00046  0.312
2021 Cáceres JC, Bailey CA, Yokoyama K, Greene BL. Selenocysteine substitutions in thiyl radical enzymes. Methods in Enzymology. 662: 119-141. PMID 35101207 DOI: 10.1016/bs.mie.2021.10.014  0.348
2021 Pang H, Walker LM, Silakov A, Zhang P, Yang W, Elliott SJ, Yokoyama K. Mechanism of Reduction of an Aminyl Radical Intermediate in the Radical SAM GTP 3',8-Cyclase MoaA. Journal of the American Chemical Society. PMID 34423974 DOI: 10.1021/jacs.1c06268  0.321
2020 Pang H, Lilla EA, Zhang P, Zhang D, Shields TP, Scott LG, Yang W, Yokoyama K. Mechanism of rate acceleration of radical C-C bond formation reaction by a radical SAM GTP 3',8-cyclase. Journal of the American Chemical Society. PMID 32348669 DOI: 10.1021/Jacs.0C01200  0.463
2020 Chhetri A, Loksztejn A, Nguyen H, Pianalto KM, Kim MJ, Hong J, Alspaugh JA, Yokoyama K. Length specificity and polymerization mechanism of (1,3)-β-D-glucan synthase in fungal cell wall biosynthesis. Biochemistry. PMID 31899625 DOI: 10.1021/Acs.Biochem.9B00896  0.483
2019 Yang H, McDaniel E, Impano S, Byer AS, Jodts RJ, Yokoyama K, Broderick WE, Broderick JB, Hoffman BM. The Elusive 5'-Deoxyadenosyl Radical: Captured and Characterized by EPR and ENDOR Spectroscopies. Journal of the American Chemical Society. PMID 31274303 DOI: 10.1021/Jacs.9B05926  0.409
2019 Nguyen HP, Yokoyama K. Characterization of Acyl Carrier Protein-Dependent Glycosyltransferase in Mitomycin C Biosynthesis. Biochemistry. PMID 31188570 DOI: 10.1021/Acs.Biochem.9B00379  0.504
2018 Pang H, Yokoyama K. Lessons From the Studies of a CC Bond Forming Radical SAM Enzyme in Molybdenum Cofactor Biosynthesis. Methods in Enzymology. 606: 485-522. PMID 30097104 DOI: 10.1016/Bs.Mie.2018.04.014  0.458
2018 Kuhnert E, Li Y, Lan N, Yue Q, Chen L, Cox RJ, An Z, Yokoyama K, Bills GF. Enfumafungin synthase represents a novel lineage of fungal triterpene cyclases. Environmental Microbiology. PMID 30051576 DOI: 10.1111/1462-2920.14333  0.339
2018 Byer AS, Yang H, McDaniel EC, Kathiresan V, Impano S, Pagnier A, Watts H, Denler C, Vagstad A, Piel J, Duschene KS, Shepard EM, Shields TP, Scott LG, Lilla EA, ... Yokoyama K, et al. A paradigm shift for radical SAM reactions: The organometallic intermediate Ω is central to catalysis. Journal of the American Chemical Society. PMID 29954180 DOI: 10.1021/Jacs.8B04061  0.442
2018 Yokoyama K, Lilla EA. C-C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products. Natural Product Reports. PMID 29633774 DOI: 10.1039/C8Np00006A  0.438
2017 Yokoyama K. Radical Breakthroughs in Natural Product and Cofactor Biosynthesis. Biochemistry. PMID 29072833 DOI: 10.1021/Acs.Biochem.7B00878  0.463
2017 Ravichandran KR, Minnihan EC, Lin Q, Yokoyama K, Taguchi AT, Shao J, Nocera DG, Stubbe J. Glutamate 350 plays an essential role in conformational gating of long range radical transport in E. coli class Ia ribonucleotide reductase. Biochemistry. PMID 28103007 DOI: 10.1021/Acs.Biochem.6B01145  0.352
2016 Lilla EA, Yokoyama K. Carbon extension in peptidylnucleoside biosynthesis by radical SAM enzymes. Nature Chemical Biology. 12: 905-907. PMID 27642865 DOI: 10.1038/Nchembio.2187  0.451
2016 Chen L, Li Y, Yue Q, Loksztejn A, Yokoyama K, Felix EA, Liu X, Zhang N, An Z, Bills GF. Engineering of new pneumocandin side-chain analogues from Glarea lozoyensis by mutasynthesis and evaluation of their antifungal activity. Acs Chemical Biology. PMID 27494047 DOI: 10.1021/Acschembio.6B00604  0.372
2015 Hover BM, Lilla EA, Yokoyama K. Mechanistic Investigation of cPMP Synthase in Molybdenum Cofactor Biosynthesis Using an Uncleavable Substrate Analogue. Biochemistry. 54: 7229-36. PMID 26575208 DOI: 10.1021/Acs.Biochem.5B00857  0.39
2015 Hover BM, Tonthat NK, Schumacher MA, Yokoyama K. Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 112: 6347-52. PMID 25941396 DOI: 10.1073/Pnas.1500697112  0.467
2015 Hover BM, Yokoyama K. C-Terminal glycine-gated radical initiation by GTP 3',8-cyclase in the molybdenum cofactor biosynthesis. Journal of the American Chemical Society. 137: 3352-9. PMID 25697423 DOI: 10.1021/Ja512997J  0.439
2015 Hover BM, Yokoyama K. C-terminal glycine-gated radical initiation by GTP 3′,8-cyclase in the molybdenum cofactor biosynthesis Journal of the American Chemical Society. 137: 3352-3359. DOI: 10.1021/ja512997j  0.352
2014 Wei Y, Mathies G, Yokoyama K, Chen J, Griffin RG, Stubbe J. A chemically competent thiosulfuranyl radical on the Escherichia coli class III ribonucleotide reductase. Journal of the American Chemical Society. 136: 9001-13. PMID 24827372 DOI: 10.1021/Ja5030194  0.425
2013 Wörsdörfer B, Conner DA, Yokoyama K, Livada J, Seyedsayamdost M, Jiang W, Silakov A, Stubbe J, Bollinger JM, Krebs C. Function of the diiron cluster of Escherichia coli class Ia ribonucleotide reductase in proton-coupled electron transfer. Journal of the American Chemical Society. 135: 8585-93. PMID 23676140 DOI: 10.1021/Ja401342S  0.422
2013 Hover BM, Loksztejn A, Ribeiro AA, Yokoyama K. Identification of a cyclic nucleotide as a cryptic intermediate in molybdenum cofactor biosynthesis. Journal of the American Chemical Society. 135: 7019-32. PMID 23627491 DOI: 10.1021/Ja401781T  0.422
2011 Ando N, Brignole EJ, Zimanyi CM, Funk MA, Yokoyama K, Asturias FJ, Stubbe J, Drennan CL. Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase. Proceedings of the National Academy of Sciences of the United States of America. 108: 21046-51. PMID 22160671 DOI: 10.1073/Pnas.1112715108  0.35
2011 Yokoyama K, Smith AA, Corzilius B, Griffin RG, Stubbe J. Equilibration of tyrosyl radicals (Y356•, Y731•, Y730•) in the radical propagation pathway of the Escherichia coli class Ia ribonucleotide reductase. Journal of the American Chemical Society. 133: 18420-32. PMID 21967342 DOI: 10.1021/Ja207455K  0.357
2010 Yokoyama K, Uhlin U, Stubbe J. A hot oxidant, 3-NO2Y122 radical, unmasks conformational gating in ribonucleotide reductase. Journal of the American Chemical Society. 132: 15368-79. PMID 20929229 DOI: 10.1021/Ja1069344  0.401
2010 Yokoyama K, Uhlin U, Stubbe J. Site-specific incorporation of 3-nitrotyrosine as a probe of pKa perturbation of redox-active tyrosines in ribonucleotide reductase. Journal of the American Chemical Society. 132: 8385-97. PMID 20518462 DOI: 10.1021/Ja101097P  0.337
2009 Artin E, Wang J, Lohman GJ, Yokoyama K, Yu G, Griffin RG, Bar G, Stubbe J. Insight into the mechanism of inactivation of ribonucleotide reductase by gemcitabine 5'-diphosphate in the presence or absence of reductant. Biochemistry. 48: 11622-9. PMID 19899770 DOI: 10.1021/Bi901590Q  0.403
2009 Kudo F, Kawashima T, Yokoyama K, Eguchi T. Enzymatic preparation of neomycin C from ribostamycin. The Journal of Antibiotics. 62: 643-6. PMID 19713992 DOI: 10.1038/Ja.2009.88  0.427
2008 Yokoyama K, Ohmori D, Kudo F, Eguchi T. Mechanistic study on the reaction of a radical SAM dehydrogenase BtrN by electron paramagnetic resonance spectroscopy. Biochemistry. 47: 8950-60. PMID 18672902 DOI: 10.1021/Bi800509X  0.422
2007 Yokoyama K, Numakura M, Kudo F, Ohmori D, Eguchi T. Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin. Journal of the American Chemical Society. 129: 15147-55. PMID 18001019 DOI: 10.1021/Ja072481T  0.47
2005 Kudo F, Yamamoto Y, Yokoyama K, Eguchi T, Kakinuma K. Biosynthesis of 2-deoxystreptamine by three crucial enzymes in Streptomyces fradiae NBRC 12773. The Journal of Antibiotics. 58: 766-74. PMID 16506694 DOI: 10.1038/Ja.2005.104  0.423
2005 Yokoyama K, Kudo F, Kuwahara M, Inomata K, Tamegai H, Eguchi T, Kakinuma K. Stereochemical recognition of doubly functional aminotransferase in 2-deoxystreptamine biosynthesis. Journal of the American Chemical Society. 127: 5869-74. PMID 15839685 DOI: 10.1021/Ja0445948  0.423
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