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User:Shinya Fushinobu

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I am a Professor at Laboratory of Enzymology in Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo located in Tokyo, Japan. Raised in Kure, Hiroshima, Japan. I obtained Ph.D degree in Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo in 1999. My research interests concern structure and function of enzymes, mainly those of Carbohydrate-Active enZymes. My home page is here. I contributed to three-dimensional structure determination of

  • GH1 Phanerochaete chrysosporium β-glucosidase 1B (BGL1B) [1]
  • GH1 Metagenomic β-Glucosidase (Td2F2) [2]
  • GH1 Bacillus sp. pyruvylated galactosidase (PvGal-ase) [3]
  • GH3 Kluyveromyces marxianus β-glucosidase (KmBglI) [4]
  • GH3 Aspergillus aculeatus β-glucosidase (AaBGL1) [5]
  • GH5 Talaromyces trachyspermus β-mannanase (TtMan5A ) [6]
  • GH8 Bacillus halodurans reducing-end xylose-releasing exo-oligoxylanase (Rex) [7]
  • GH9 Photobacterium profundum exo-β-D-glucosaminidase (PpGlcNase) [8]
  • GH10 Clostridium stercorarium xylanase B (XynB) [9]
  • GH11 Aspergillus kawachii xylanase C (XynC) [10]
  • GH13 Arthrobacter globiformis cyclic α-maltosyl-(1→6)-maltose hydrolase (CMMase) [11]
  • GH18 Cordyceps militaris endo-β-N-acetylglucosaminidase (Endo-CoM) [12]
  • GH20 Bifidobacterium bifidum lacto-N-biosidase (BbLNBase) [13]
  • GH20 Bifidobacterium bifidum sulfoglycosidase (BbhII) [14]
  • GH26 β-mannanase from a symbiotic protist of the termite Reticulitermes speratus (RsMan26C) [15]
  • GH29 Bifidobacterium longum subsp. infantis 1,3-1,4-α-L-fucosidase (BiAfcB) [16]
  • GH42 Thermus thermophilus β-galactosidase (A4-β-Gal) Family First [17]
  • GH42 Bifidobacterium animalis subsp. lactis α-L-arabinopyranosidase (BlArap42B) [18]
  • GH42 Bifidobacterium longum subsp. infantis β-galctosidase (BiBga42A) [19]
  • GH45 Phanerochaete chrysosporium endoglucanase (PcCel45A) [20]
  • GH51 Thermotoga maritima α-L-arabinofuranosidase (Tm-AFase) [21]
  • GH54 Aspergillus kawachii α-L-arabinofuranosidase B (AkAbfB) Family First plus identification of CBM42 [22]
  • GH55 Phanerochaete chrysosporium β-1,3-glucanase (Lam55A) Family First [23]
  • GH57 Thermococcus litoralis 4-α-glucanotransferase (TLGT) Family First [24]
  • GH65 Caldicellulosiruptor saccharolyticus kojibiose phosphorylase (CsKP) [25]
  • GH65 Bacillus selenitireducens 2-O-α-glucosylglycerol phosphorylase (GGP) [26]
  • GH79 Fusarium oxysporum 4-O-α-L-rhamnosyl-β-D-glucuronidase (FoBGlcA) [27]
  • GH94 Vibrio proteolyticus chitobiose phosphorylase (ChBP) Family First [28]
  • GH94 Cellvibrio gilvus cellobiose phosphorylase (CBP) [29]
  • GH94 Saccharophagus degradans cellobionic acid phosphorylase (CABP) [30]
  • GH94 Lachnoclostridium phytofermentans 1,2-β-oligoglucan phosphorylase (LpSOGP) [31]
  • GH101 Bifidobacterium longum endo-α-N-acetylgalactosaminidase (EngBF) [32]
  • GH112 Bifidobacterium longum galacto-N-biose/lacto-N-biose I phosphorylase (GLNBP) Family First [33]
  • GH121 Bifidobacterium longum β-L-arabinobiosidase (HypBA2) Family First [34]
  • GH127 Bifidobacterium longum β-L-arabinofuranosidase (HypBA1) Family First [35]
  • GH129 Bifidobacterium bifidum α-N-acetylgalactosaminidase (NagBb) Family First [36]
  • GH130 Listeria innocua β-1,2-mannobiose phosphorylase (Lin0857) [37]
  • GH136 Bifidobacterium longum lacto-N-biosidase (LnbX) Family First [38]
  • GH136 Eubacterium ramulus lacto-N-biosidase (ErLnb136) [39]
  • GH136 Bifidobacterium saguini lacto-N-biosidase (BsaX) [40]
  • GH136 Tyzzerella nexilis lacto-N-biosidase (TnX) [40]
  • GH144 Chitinophaga pinensis endo-β-1,2-glucanase (Cpin_6279) Family First [41]
  • GH172 Bifidobacterium dentium difructose dianhydride I synthase/hydrolase (αFFase1) Family First [42]
  • PL20 Trichoderma reesei endo-β-1,4-glucuronan lyase (TrGL) Family First [43]
  • PL42 Fusarium oxysporum L-rhamnose-α-1,4-D-glucuronate lyase (FoRham1) Family First [44]
  • CBM28 in Clostridium josui Cel5A (CjCBM28) [45]

  1. Nijikken Y, Tsukada T, Igarashi K, Samejima M, Wakagi T, Shoun H, and Fushinobu S. (2007). Crystal structure of intracellular family 1 beta-glucosidase BGL1A from the basidiomycete Phanerochaete chrysosporium. FEBS Lett. 2007;581(7):1514-20. DOI:10.1016/j.febslet.2007.03.009 | PubMed ID:17376440 [Nijikken2007]
  2. Matsuzawa T, Jo T, Uchiyama T, Manninen JA, Arakawa T, Miyazaki K, Fushinobu S, and Yaoi K. (2016). Crystal structure and identification of a key amino acid for glucose tolerance, substrate specificity, and transglycosylation activity of metagenomic β-glucosidase Td2F2. FEBS J. 2016;283(12):2340-53. DOI:10.1111/febs.13743 | PubMed ID:27092463 [Matsuzawa2016]
  3. Higuchi Y, Matsufuji H, Tanuma M, Arakawa T, Mori K, Yamada C, Shofia R, Matsunaga E, Tashiro K, Fushinobu S, and Takegawa K. (2018). Identification and characterization of a novel β-D-galactosidase that releases pyruvylated galactose. Sci Rep. 2018;8(1):12013. DOI:10.1038/s41598-018-30508-4 | PubMed ID:30104607 [Higuchi2018]
  4. Yoshida E, Hidaka M, Fushinobu S, Koyanagi T, Minami H, Tamaki H, Kitaoka M, Katayama T, and Kumagai H. (2010). Role of a PA14 domain in determining substrate specificity of a glycoside hydrolase family 3 β-glucosidase from Kluyveromyces marxianus. Biochem J. 2010;431(1):39-49. DOI:10.1042/BJ20100351 | PubMed ID:20662765 [Yoshida2010]
  5. Suzuki K, Sumitani J, Nam YW, Nishimaki T, Tani S, Wakagi T, Kawaguchi T, and Fushinobu S. (2013). Crystal structures of glycoside hydrolase family 3 β-glucosidase 1 from Aspergillus aculeatus. Biochem J. 2013;452(2):211-21. DOI:10.1042/BJ20130054 | PubMed ID:23537284 [Suzuki2013]
  6. Suzuki K, Michikawa M, Sato H, Yuki M, Kamino K, Ogasawara W, Fushinobu S, and Kaneko S. (2018) Purification, cloning, functional expression, structure, and characterization of a thermostable β-mannanase from Talaromyces trachyspermus B168 and its efficiency in production of mannooligosaccharides from coffee wastes. J. Appl. Glycosci. 65, 13-21. DOI: 10.5458/jag.jag.JAG-2017_018

  7. Fushinobu S, Hidaka M, Honda Y, Wakagi T, Shoun H, and Kitaoka M. (2005). Structural basis for the specificity of the reducing end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125. J Biol Chem. 2005;280(17):17180-6. DOI:10.1074/jbc.M413693200 | PubMed ID:15718242 [Fushinobu2005]
  8. Honda Y, Arai S, Suzuki K, Kitaoka M, and Fushinobu S. (2016). The crystal structure of an inverting glycoside hydrolase family 9 exo-β-D-glucosaminidase and the design of glycosynthase. Biochem J. 2016;473(4):463-72. DOI:10.1042/BJ20150966 | PubMed ID:26621872 [Honda2016]
  9. Nishimoto M, Fushinobu S, Miyanaga A, Kitaoka M, and Hayashi K. (2007). Molecular anatomy of the alkaliphilic xylanase from Bacillus halodurans C-125. J Biochem. 2007;141(5):709-17. DOI:10.1093/jb/mvm072 | PubMed ID:17383976 [Nishimoto2007]
  10. Fushinobu S, Ito K, Konno M, Wakagi T, and Matsuzawa H. (1998). Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH. Protein Eng. 1998;11(12):1121-8. DOI:10.1093/protein/11.12.1121 | PubMed ID:9930661 [Fushinobu1998]
  11. Kohno M, Arakawa T, Ota H, Mori T, Nishimoto T, and Fushinobu S. (2018). Structural features of a bacterial cyclic α-maltosyl-(1→6)-maltose (CMM) hydrolase critical for CMM recognition and hydrolysis. J Biol Chem. 2018;293(43):16874-16888. DOI:10.1074/jbc.RA118.004472 | PubMed ID:30181215 [Kohno2018]
  12. Seki H, Huang Y, Arakawa T, Yamada C, Kinoshita T, Iwamoto S, Higuchi Y, Takegawa K, and Fushinobu S. (2019). Structural basis for the specific cleavage of core-fucosylated N-glycans by endo-β-N-acetylglucosaminidase from the fungus Cordyceps militaris. J Biol Chem. 2019;294(45):17143-17154. DOI:10.1074/jbc.RA119.010842 | PubMed ID:31548313 [Seki2019]
  13. Ito T, Katayama T, Hattie M, Sakurama H, Wada J, Suzuki R, Ashida H, Wakagi T, Yamamoto K, Stubbs KA, and Fushinobu S. (2013). Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum. J Biol Chem. 2013;288(17):11795-806. DOI:10.1074/jbc.M112.420109 | PubMed ID:23479733 [Ito2013]
  14. Katoh T, Yamada C, Wallace MD, Yoshida A, Gotoh A, Arai M, Maeshibu T, Kashima T, Hagenbeek A, Ojima MN, Takada H, Sakanaka M, Shimizu H, Nishiyama K, Ashida H, Hirose J, Suarez-Diez M, Nishiyama M, Kimura I, Stubbs KA, Fushinobu S, and Katayama T. (2023). A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem. Nat Chem Biol. 2023;19(6):778-789. DOI:10.1038/s41589-023-01272-y | PubMed ID:36864192 [Katoh2023]
  15. Tsukagoshi H, Nakamura A, Ishida T, Touhara KK, Otagiri M, Moriya S, Samejima M, Igarashi K, Fushinobu S, Kitamoto K, and Arioka M. (2014). Structural and biochemical analyses of glycoside hydrolase family 26 β-mannanase from a symbiotic protist of the termite Reticulitermes speratus. J Biol Chem. 2014;289(15):10843-10852. DOI:10.1074/jbc.M114.555383 | PubMed ID:24570006 [Tsukagoshi2014]
  16. Sakurama H, Fushinobu S, Hidaka M, Yoshida E, Honda Y, Ashida H, Kitaoka M, Kumagai H, Yamamoto K, and Katayama T. (2012). 1,3-1,4-α-L-fucosynthase that specifically introduces Lewis a/x antigens into type-1/2 chains. J Biol Chem. 2012;287(20):16709-19. DOI:10.1074/jbc.M111.333781 | PubMed ID:22451675 [Sakurama2012]
  17. Hidaka M, Fushinobu S, Ohtsu N, Motoshima H, Matsuzawa H, Shoun H, and Wakagi T. (2002). Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose. J Mol Biol. 2002;322(1):79-91. DOI:10.1016/s0022-2836(02)00746-5 | PubMed ID:12215416 [Hidaka2002]
  18. Viborg AH, Katayama T, Arakawa T, Abou Hachem M, Lo Leggio L, Kitaoka M, Svensson B, and Fushinobu S. (2017). Discovery of α-l-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42. J Biol Chem. 2017;292(51):21092-21101. DOI:10.1074/jbc.M117.792598 | PubMed ID:29061847 [Viborg2017]
  19. Gotoh A, Hidaka M, Sakurama H, Nishimoto M, Kitaoka M, Sakanaka M, Fushinobu S, and Katayama T. (2023) Substrate recognition mode of a glycoside hydrolase family 42 β-galactosidase from Bifidobacterium longum subspecies infantis (BiBga42A) revealed by crystallographic and mutational analyses. Microbiome Res. Rep.2, 20. DOI: 10.20517/mrr.2023.14

  20. Nakamura A, Ishida T, Kusaka K, Yamada T, Fushinobu S, Tanaka I, Kaneko S, Ohta K, Tanaka H, Inaka K, Higuchi Y, Niimura N, Samejima M, and Igarashi K. (2015). "Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography. Sci Adv. 2015;1(7):e1500263. DOI:10.1126/sciadv.1500263 | PubMed ID:26601228 [Nakamura2015]
  21. Im DH, Kimura K, Hayasaka F, Tanaka T, Noguchi M, Kobayashi A, Shoda S, Miyazaki K, Wakagi T, and Fushinobu S. (2012). Crystal structures of glycoside hydrolase family 51 α-L-arabinofuranosidase from Thermotoga maritima. Biosci Biotechnol Biochem. 2012;76(2):423-8. DOI:10.1271/bbb.110902 | PubMed ID:22313787 [Im2012]
  22. Miyanaga A, Koseki T, Matsuzawa H, Wakagi T, Shoun H, and Fushinobu S. (2004). Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose. J Biol Chem. 2004;279(43):44907-14. DOI:10.1074/jbc.M405390200 | PubMed ID:15292273 [Miyanaga2004]
  23. Ishida T, Fushinobu S, Kawai R, Kitaoka M, Igarashi K, and Samejima M. (2009). Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J Biol Chem. 2009;284(15):10100-9. DOI:10.1074/jbc.M808122200 | PubMed ID:19193645 [Ishida2009]
  24. Imamura H, Fushinobu S, Yamamoto M, Kumasaka T, Jeon BS, Wakagi T, and Matsuzawa H. (2003). Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor. J Biol Chem. 2003;278(21):19378-86. DOI:10.1074/jbc.M213134200 | PubMed ID:12618437 [Imamura2003]
  25. Okada S, Yamamoto T, Watanabe H, Nishimoto T, Chaen H, Fukuda S, Wakagi T, and Fushinobu S. (2014). Structural and mutational analysis of substrate recognition in kojibiose phosphorylase. FEBS J. 2014;281(3):778-86. DOI:10.1111/febs.12622 | PubMed ID:24255995 [Okada2013]
  26. Touhara KK, Nihira T, Kitaoka M, Nakai H, and Fushinobu S. (2014). Structural basis for reversible phosphorolysis and hydrolysis reactions of 2-O-α-glucosylglycerol phosphorylase. J Biol Chem. 2014;289(26):18067-75. DOI:10.1074/jbc.M114.573212 | PubMed ID:24828502 [Touhara2014]
  27. Kondo T, Kichijo M, Nakaya M, Takenaka S, Arakawa T, Kotake T, Fushinobu S, and Sakamoto T. (2021). Biochemical and structural characterization of a novel 4-O-α-l-rhamnosyl-β-d-glucuronidase from Fusarium oxysporum. FEBS J. 2021;288(16):4918-4938. DOI:10.1111/febs.15795 | PubMed ID:33645879 [Kondo2021A]
  28. Hidaka M, Honda Y, Kitaoka M, Nirasawa S, Hayashi K, Wakagi T, Shoun H, and Fushinobu S. (2004). Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold. Structure. 2004;12(6):937-47. DOI:10.1016/j.str.2004.03.027 | PubMed ID:15274915 [Hidaka2004]
  29. Hidaka M, Kitaoka M, Hayashi K, Wakagi T, Shoun H, and Fushinobu S. (2006). Structural dissection of the reaction mechanism of cellobiose phosphorylase. Biochem J. 2006;398(1):37-43. DOI:10.1042/BJ20060274 | PubMed ID:16646954 [Hidaka2006]
  30. Nam YW, Nihira T, Arakawa T, Saito Y, Kitaoka M, Nakai H, and Fushinobu S. (2015). Crystal Structure and Substrate Recognition of Cellobionic Acid Phosphorylase, Which Plays a Key Role in Oxidative Cellulose Degradation by Microbes. J Biol Chem. 2015;290(30):18281-92. DOI:10.1074/jbc.M115.664664 | PubMed ID:26041776 [Nam2015]
  31. Nakajima M, Tanaka N, Furukawa N, Nihira T, Kodutsumi Y, Takahashi Y, Sugimoto N, Miyanaga A, Fushinobu S, Taguchi H, and Nakai H. (2017). Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans. Sci Rep. 2017;7:42671. DOI:10.1038/srep42671 | PubMed ID:28198470 [Nakajima2017]
  32. Suzuki R, Katayama T, Kitaoka M, Kumagai H, Wakagi T, Shoun H, Ashida H, Yamamoto K, and Fushinobu S. (2009). Crystallographic and mutational analyses of substrate recognition of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum. J Biochem. 2009;146(3):389-98. DOI:10.1093/jb/mvp086 | PubMed ID:19502354 [Suzuki2009]
  33. Hidaka M, Nishimoto M, Kitaoka M, Wakagi T, Shoun H, and Fushinobu S. (2009). The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: a large deformation of a TIM barrel scaffold. J Biol Chem. 2009;284(11):7273-83. DOI:10.1074/jbc.M808525200 | PubMed ID:19124470 [Hidaka2009]
  34. Saito K, Viborg AH, Sakamoto S, Arakawa T, Yamada C, Fujita K, and Fushinobu S. (2020). Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121. PLoS One. 2020;15(6):e0231513. DOI:10.1371/journal.pone.0231513 | PubMed ID:32479540 [Saito2020]
  35. Ito T, Saikawa K, Kim S, Fujita K, Ishiwata A, Kaeothip S, Arakawa T, Wakagi T, Beckham GT, Ito Y, and Fushinobu S. (2014). Crystal structure of glycoside hydrolase family 127 β-l-arabinofuranosidase from Bifidobacterium longum. Biochem Biophys Res Commun. 2014;447(1):32-7. DOI:10.1016/j.bbrc.2014.03.096 | PubMed ID:24680821 [Ito2014]
  36. Sato M, Liebschner D, Yamada Y, Matsugaki N, Arakawa T, Wills SS, Hattie M, Stubbs KA, Ito T, Senda T, Ashida H, and Fushinobu S. (2017). The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors. J Biol Chem. 2017;292(29):12126-12138. DOI:10.1074/jbc.M117.777391 | PubMed ID:28546425 [Sato2017]
  37. Tsuda T, Nihira T, Chiku K, Suzuki E, Arakawa T, Nishimoto M, Kitaoka M, Nakai H, and Fushinobu S. (2015). Characterization and crystal structure determination of β-1,2-mannobiose phosphorylase from Listeria innocua. FEBS Lett. 2015;589(24 Pt B):3816-21. DOI:10.1016/j.febslet.2015.11.034 | PubMed ID:26632508 [Tsuda2015]
  38. Yamada C, Gotoh A, Sakanaka M, Hattie M, Stubbs KA, Katayama-Ikegami A, Hirose J, Kurihara S, Arakawa T, Kitaoka M, Okuda S, Katayama T, and Fushinobu S. (2017). Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum. Cell Chem Biol. 2017;24(4):515-524.e5. DOI:10.1016/j.chembiol.2017.03.012 | PubMed ID:28392148 [Yamada2017]
  39. Pichler MJ, Yamada C, Shuoker B, Alvarez-Silva C, Gotoh A, Leth ML, Schoof E, Katoh T, Sakanaka M, Katayama T, Jin C, Karlsson NG, Arumugam M, Fushinobu S, and Abou Hachem M. (2020). Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways. Nat Commun. 2020;11(1):3285. DOI:10.1038/s41467-020-17075-x | PubMed ID:32620774 [Pichler2020]
  40. Yamada C, Katayama T, and Fushinobu S. (2022). Crystal structures of glycoside hydrolase family 136 lacto-N-biosidases from monkey gut- and human adult gut bacteria. Biosci Biotechnol Biochem. 2022;86(4):464-475. DOI:10.1093/bbb/zbac015 | PubMed ID:35092420 [Yamada2022]
  41. Abe K, Nakajima M, Yamashita T, Matsunaga H, Kamisuki S, Nihira T, Takahashi Y, Sugimoto N, Miyanaga A, Nakai H, Arakawa T, Fushinobu S, and Taguchi H. (2017). Biochemical and structural analyses of a bacterial endo-β-1,2-glucanase reveal a new glycoside hydrolase family. J Biol Chem. 2017;292(18):7487-7506. DOI:10.1074/jbc.M116.762724 | PubMed ID:28270506 [Abe2017]
  42. Kashima T, Okumura K, Ishiwata A, Kaieda M, Terada T, Arakawa T, Yamada C, Shimizu K, Tanaka K, Kitaoka M, Ito Y, Fujita K, and Fushinobu S. (2021). Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family. J Biol Chem. 2021;297(5):101324. DOI:10.1016/j.jbc.2021.101324 | PubMed ID:34688653 [Kashima2021]
  43. Konno N, Ishida T, Igarashi K, Fushinobu S, Habu N, Samejima M, and Isogai A. (2009). Crystal structure of polysaccharide lyase family 20 endo-beta-1,4-glucuronan lyase from the filamentous fungus Trichoderma reesei. FEBS Lett. 2009;583(8):1323-6. DOI:10.1016/j.febslet.2009.03.034 | PubMed ID:19306878 [Konno2009]
  44. Kondo T, Kichijo M, Maruta A, Nakaya M, Takenaka S, Arakawa T, Fushinobu S, and Sakamoto T. (2021). Structural and functional analysis of gum arabic l-rhamnose-α-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family. J Biol Chem. 2021;297(3):101001. DOI:10.1016/j.jbc.2021.101001 | PubMed ID:34303708 [Kondo2021B]
  45. Tsukimoto K, Takada R, Araki Y, Suzuki K, Karita S, Wakagi T, Shoun H, Watanabe T, and Fushinobu S. (2010). Recognition of cellooligosaccharides by a family 28 carbohydrate-binding module. FEBS Lett. 2010;584(6):1205-11. DOI:10.1016/j.febslet.2010.02.027 | PubMed ID:20159017 [Tsukimoto2010]

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