At Duke
- Nguyen, H.; Kresna, I. D. M.; Böhringer, N.; Ruel, J.; Mora, E. de la; Kramer, J.- C.; Lewis, K.; Nicolet, Y.; Schäberle, T. F.;
Yokoyama, K.*, Characterization of a Radical SAM Oxygenase for the Ether Crosslinking in Darobactin Biosynthesis, J. Am. Chem. Soc. 2022, 144, 41, 18876–18886, doi.org/10.1021/jacs.2c05565
- Ren, Z.#; Chhetri, A.#; Guan, Z.; Suo, Y.; Yokoyama, K.*; Lee, S.-Y.* Structural basis for inhibition and regulation of a chitin synthase from Candida albicans. Nat Struct Mol Biol. 2022 Jul;29(7):653-664. doi: 10.1038/s41594-022-00791-x. (# co-first authorship. * co-correspondence)
- Draelos, M. M.; Thanapipatsiri, A.; Du, Y.;Yokoyama, K.; Cryptic Phosphorylation-Mediated Divergent Biosynthesis of High-Carbon Sugar Nucleoside Antifungals. ACS Chem Biol 2022, 17, 898-907. doi: 10.1021/acschembio.1c00971.
- Cáceres, J. C.; Bailey, C.A.; Yokoyama, K.; Greene B. L.; Selenocysteine substitutions in thiyl radical enzymes. Methods Enzymol 2022, 662, 119-141. doi: 10.1016/bs.mie.2021.10.014.
- Yokoyama, K.; Li, D.#; and 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, 2022 Apr 20;2(2):94-108. (# equal contribution)
- Pang, H.; Walker, L. M.; Silakov, A.; Zhang, P.; Yang, W.; Elliott, S. J.; Yokoyama, K.; Mechanism of Reduction of an Aminyl Radical Intermediate in the Radical SAM GTP 3′,8-Cyclase MoaA. J. Am. Chem. Soc. 2021, 143, 34, 13835–13844. Highlighted in the JACS Spotlight.
- Draelos, M. M.#; 10.1021/acs.biochem.1c00327
- Chhetri, A., Loksztejn, A. and Yokoyama, K. Quantitative Characterization of the Amount and Length of (1,3)-β-D-glucan for Functional and Mechanistic Analysis of Fungal (1,3)-β-D-glucan Synthase. Bio-protocol 2021, 11(8): e3995. DOI: 10.21769/BioProtoc.3995.
- Draelos, M. M.;
- Yokoyama, K., Radical-Mediated Carbon Skeleton Formation in Cofactor and Natural Product Biosynthesis. Comprehensive Natural Products III (Third Ed.) 2020, 5, 70-95, DOI: 10.1016/B978-0-12-409547-2.14745-6.
- Draelos M.; Yokoyama K., Biosynthesis and mechanism of action of antifungal peptidyl nucleoside natural products. Comprehensive Natural Products III (Third Ed.) 2020, 2, 613-641, DOI: 10.1016/B978-0-12-409547-2.14680-3.
- Pang H, Lilla EA, Zhang P, Zhang D, Shields TP, Scott LG, Yang W, Yokoyama K. (2020) Mechanism of rate acceleration of radical C-C bond formation reaction by a radical SAM GTP 3′,8-cyclase. J. Am. Chem. Soc. 2020, 142, 20, 9314–9326.
- Chhetri A, Loksztejn A, Nguyen H, Pianalto KM, Kim MJ, Hong J, Alspaugh JA, Yokoyama K. (2020) Length specificity and polymerization mechanism of (1,3)-β-D-glucan synthase in fungal cell wall biosynthesis. Biochemistry 2020, 59, 5, 682-693.
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Yang H, McDaniel E, Impano S, Byer AS, Jodts RJ, Yokoyama K, Broderick WE, Broderick JB, Hoffman BM. (2019) The Elusive 5′-Deoxyadenosyl Radical: Captured and Characterized by EPR and ENDOR Spectroscopies. J Am Chem Soc 2019, 141(30):12139-12146. doi: 10.1021/jacs.9b05926.
- Nguyen HP, and Yokoyama K (2019). Characterization of Acyl Carrier Protein-Dependent Glycosyltransferase in Mitomycin C Biosynthesis. Biochemistry 2019, 58, 25, 2804–2808.
- Kuhnert E, Li Y, Lan N, Yue Q, Chen L, Cox RJ, An Z, Yokoyama K, Bills GF (2018). Enfumafungin synthase represents a novel lineage of fungal triterpene cyclases. Environ Microbiol 20, 3325-3342. doi: 10.1111/1462-2920.14333.
- Byer, A.; Yang, H.; McDaniel, E.; Kathiresan, V.; Impano, S.; Pagnier, A.; Watts, H.; Denler, C.; Vagstad, A.; Piel, J.; Duschene, K.; Shepard, E.; Shields, T.; Scott, L.; Lilla, E.; Yokoyama, K.; Broderick, W.; Hoffman, B.; Broderick, J. (2018), A paradigm shift for radical SAM reactions: The organometallic intermediate Ω is central to catalysis. J. Am. Chem. Soc, 140, 8634-8638.
- Pang H, and Yokoyama K. (2018) Lessons From the Studies of a C-C Bond Forming Radical SAM Enzyme in Molybdenum Cofactor Biosynthesis. Methods in Enzymology 606, 485-522. doi:10.1016/bs.mie.2018.04.014.
- Yokoyama K, and Lilla EA. (2018). C-C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products. Natural Product Reports 18, 35, 660-694. doi: 10.1039/c8np00006a.
- Yokoyama K. (2018). Radical Breakthroughs in Natural Product and Cofactor Biosynthesis. Biochemistry 57, 390–402. doi:10.1021/acs.biochem.7b00878.
- Lilla EA, Yokoyama K. (2016). Carbon extension in peptidylnucleoside biosynthesis by radical SAM enzymes. Nature Chemical Biology 12, 905-907. doi:10.1038/nchembio.2187.
- Chen L, Li Y, Yue Q, Loksztejn A, Yokoyama K, Felix EA, Liu X, Zhang N, An Z, Bills GF. (2016), Engineering of new pneumocandin side-chain analogues from Glarea lozoyensis by mutasynthesis and evaluation of their antifungal activity, ACS Chem Biol 11, 2724-2733, DOI 10.1021/acschembio.6b00604.
- Hover BM, Lilla EA, Yokoyama K. (2015). Mechanistic Investigation of cPMP Synthase in Molybdenum Cofactor Biosynthesis Using an Uncleavable Substrate Analogue. Biochemistry, 54, 7229-36.
- Hover BM, Tonthat NK, Schumacher MA, Yokoyama K. (2015). Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis. Proc. Natl. Acad. Sci. U. S. A., 112, 6347-52.
- Yokoyama K, Leimkühler S. (2015) The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria. Biochimica et Biophysica Acta. 1853(6):1335-49.
- Hover BM, Yokoyama K. (2015). C-Terminal glycine-gated radical initiation by GTP 3′,8-cyclase in the molybdenum cofactor biosynthesis. J. Am. Chem. Soc. 137(9):3352-9. (Selected for the JACS young investigators virtual issue)
- Hover B. M.; Losztejn, A.; Ribeiro, A. A.; Yokoyama, K., (2013). Identification of a cyclic nucleotide as a cryptic intermediate in molybdenum cofactor biosynthesis, J. Am. Chem. Soc., 135, 7019 – 7032. PMCID: PMC3777439. (Recommended by the F1000Prime)
Prior to Duke
- Ravichandran, K., Minnihan, E. C., Lin, Q., Yokoyama, K., Taguchi, A. T., Shao, J., Nocera, D. G., Stubbe, J., Glutamate 350 plays an essential role in conformational gating of long-range radical transport in Escherichia coli class Ia ribonucleotide reductase, Biochemistry2017, 56, 856-868.
- Wei, Y.; Mathies, G.; Yokoyama, K.; Chen, J.; Griffin R. G.; Stubbe, J. (2014) A chemically competent thiosulfuranyl radical on the Escherichia coli class III ribonucleotide reductase. J Am Chem Soc. 136, 9001-13.
- Wörsdörfer, B.; Conner, D. A.; Yokoyama, K.; Livada, J.; Seyedsayamdost, M.; Jiang, W.; Silakov, A.; Stubbe, J.; Bollinger, J. M. Jr.; Krebs, C., (2013) Function of the Diiron Cluster of Escherichia coli Class Ia Ribonucleotide Reductase in Proton-Coupled Electron Transfer, J. Am. Chem. Soc., DOI: 10.1021/ja401342s. PMID: 23676140
- Ando, N.; Brignole, E.; Zimanyi, C. M.; Funk, M.; Yokoyama, K.; Asturias, F. J.; Stubbe, J.; Drennan, C., (2011). Structural interconversions modulate activity of E. coli ribonucleotide reductase, Proc. Natl. Acad. Sci. U. S. A., 108, 21046–21051. PMCID: PMC3248520
- Yokoyama, K., Smith, A. A., Corzilius, B., Griffin, R. G.; Stubbe, J., (2011). Equilibration of tyrosyl radicals (Y356•, Y731•, Y730•) in the radical propagation pathway of the E. coli class Ia ribonucleotide reductase. J. Am. Chem. Soc., 133, 18420–18432. PMCID: PMC3236566
- Yokoyama, K., Uhlin, U., and Stubbe, J., (2010). A hot oxidant, 3-NO2Y122 radical, unmasks conformational gating in ribonucleotide reductase. J. Am. Chem. Soc., 132, 15368–15379. PMCID: PMC3005585
- Yokoyama, K., Uhlin, U., and Stubbe, J., (2010). Site-specific incorporation of 3-nitrotyrosine as a probe of pKa perturbation of redox active tyrosines in ribonucleotide reductase. J. Am. Chem. Soc., 132, 8385–8397. PMCID: PMC2905227
- Minnihan, E. C., Yokoyama, K., Stubbe, J., (2009). Unnatural amino acid: better than the real thing? F1000 Biology Reports, 1:88, doi: 10.3410/B1-88.
- Artin, E., Wang, J., Lohman, G. J., Yokoyama, K., Yu, G., Griffin, R.G., Bar, G. and Stubbe J., (2009). Insight into the mechanism of inactivation of ribonucleotide reductase by gemcitabine 5’-diphosphate in the presence or absence of reductant. Biochemistry, 48, 11622–11629. PMCID: PMC2917094
- Kudo, F., Kawashima, T., Yokoyama, K., Eguchi, T., (2009). Enzymatic Preparation of Neomycin C from Ribostamycin. J. Antibiot., 62, 643–646.
- Yokoyama, K.; Ohmori, D.; Kudo, F.; Eguchi, T., (2008). Mechanistic Study on the Reaction of a Radical SAM Dehydrogenase BtrN by EPR Spectroscopy. Biochemistry 47, 8950-8960.
- Yokoyama, K.; Yamamoto, Y.; Kudo, F.; Eguchi, T., (2008). Involvement of Two Distinct N-Acetyl Glucosaminyltransferases and a Dual Functional Deacetylase in the Neomycin Biosynthesis. ChemBioChem, 9, 865-869.
- Yokoyama, K., Numakura, M.a, Kudo, F., Ohmori, D.; Eguchi, T., (2007). Characterization and Mechanistic Study of a Radical SAM Dehydrogenase in the Biosynthesis of Butirosin. J. Am. Chem. Soc., 129, 15147-15155.
- Yokoyama, K., Kudo, F., Kuwahara, M., Inomata, K., Tamegai, H., Eguchi, T., Kakinuma, K., (2005) Stereochemical Recognition of Doubly Functional Aminotransferase in 2-Deoxystreptamine Biosynthesis. J. Am. Chem. Soc., 127, 5869-5874.
- Kudo, F., Yamamoto, Y., Yokoyama, K., Eguchi, T., Kakinuma, K., (2005). Biosynthesis of 2-Deoxystreptamine by Three Crucial Enzymes in Streptomyces fradiae NBRC 12773. J. Antibiot., 58, 766-774.
Complete List of Published Work in MyBibliography