Publications

Publications at Duke

  1. 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 Jul 5. doi: 10.1021/jacs.9b05926.

  2. Nguyen HP, and Yokoyama K (2019). Characterization of Acyl Carrier Protein-Dependent Glycosyltransferase in Mitomycin C BiosynthesisBiochemistry, doi.org/10.1021/acs.biochem.9b00379.
  3. 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.
  4. 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.
  5. 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.
  6. 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. 
  7. Yokoyama K. (2018). Radical Breakthroughs in Natural Product and Cofactor Biosynthesis. Biochemistry 57, 390–402. doi:10.1021/acs.biochem.7b00878.
  8. Lilla EA, Yokoyama K. (2016). Carbon extension in peptidylnucleoside biosynthesis by radical SAM enzymesNature Chemical Biology 12, 905-907. doi:10.1038/nchembio.2187.nchembio-2187-toc
  9. 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.cb-2016-00604z_0008
  10. Hover BM, Lilla EA, Yokoyama K. (2015). Mechanistic Investigation of cPMP Synthase in Molybdenum Cofactor Biosynthesis Using an Uncleavable Substrate AnalogueBiochemistry, 54, 7229-36.TOC graphic
  11. 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.PNAS2015
  12. 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.Moco pathway
  13. 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)JACS2015
  14. 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)JACS2013

Publications prior to Duke

  1. 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.
  2. 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.
  3. 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
  4. 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
  5. 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: PMC3236566TOC Y• equilibrium
  6. 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: PMC3005585TOC NO2Y122•
  7. 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:  PMC2905227TOC NO2Y pKa
  8. 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.
  9. 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
  10. Kudo, F., Kawashima, T., Yokoyama, K., Eguchi, T., (2009). Enzymatic Preparation of Neomycin C from Ribostamycin. J. Antibiot., 62, 643–646.
  11. 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.TOC graphic EPR2
  12. 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.neomycin biosynthetic pathway
  13. 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 ButirosinJ. Am. Chem. Soc., 129, 15147-15155.TOC BtrN
  14. 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.TOC BtrS
  15. 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