User:Shinya Fushinobu

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]

---

Error fetching PMID 17376440:
Error fetching PMID 23537284:
Error fetching PMID 15718242:
Error fetching PMID 17383976:
Error fetching PMID 9930661:
Error fetching PMID 23479733:
Error fetching PMID 24570006:
Error fetching PMID 24255995:
Error fetching PMID 16646954:
Error fetching PMID 19502354:
Error fetching PMID 19306878:
Error fetching PMID 20159017:
Error fetching PMID 22313787:
Error fetching PMID 26601228:
Error fetching PMID 26621872:
Error fetching PMID 27092463:
Error fetching PMID 29061847:
Error fetching PMID 30104607:
Error fetching PMID 30181215:
Error fetching PMID 31548313:
Error fetching PMID 33645879:
Error fetching PMID 34303708:
Error fetching PMID 35092420:

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 |

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

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 |
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 |
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 |

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

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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |