Publications & Activities


2017 2016 2015 2014 2013

Enzymology Lab. 2012-2008 2007-2005 2004-2002 2001 - 1999 1998 - 1996 1995 - 1993

Prof. Fushinobu's complete publication list


Original Papers

Crystal structure and substrate specificity modification of acetyl xylan esterase from Aspergillus luchuensis
D. Komiya, A. Hori, T. Ishida, K. Igarashi, M. Samejima, T. Koseki, and S. Fushinobu
Appl. Environ. Microbiol., in press

The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal Co-factors
M. Sato, D. Liebschner, Y. Yamada, N. Matsugaki, T. Arakawa, S. S. Wills, M. Hattie, K. A. Stubbs, T. Ito, T. Senda, H. Ashida, and S. Fushinobu
J. Biol. Chem. 292 (29), 12126-12138 (2017)

Molecular insight into evolution of symbiosis between breast-fed infants and a member of the human gut microbiome Bifidobacterium longum
C. Yamada, A. Gotoh, M. Sakanaka, M. Hattie, K. A. Stubbs, A. Katayama-Ikegami, J. Hirose, S. Kurihara, T. Arakawa, M. Kitaoka, S. Okuda, T. Katayama, and S. Fushinobu
Cell Chem. Biol. 24 (4), 515-524

Biochemical and structural analyses of a bacterial endo-β-1,2-glucanase reveal a new glycoside hydrolase family
K. Abe, M. Nakajima, T. Yamashita, H. Matsunaga, S. Kamisuki, T. Nihira, Y. Takahashi, N. Sugimoto, A. Miyanaga, H. Nakai, T. Arakawa, S. Fushinobu, and H. Taguchi
J. Biol. Chem. 292 (18), 7487-7506 (2017)

Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
M. Nakajima, N. Tanaka, N. Furukawa, T. Nihira, Y. Kodutsumi, Y. Takahashi, N. Sugimoto, A. Miyanaga, S. Fushinobu, H. Taguchi, H. Nakai
Sci Rep. 7, 42671 (2017)

Hydroxylation of compactin (ML-236B) by CYP105D7 (SAV_7469) from Streptomyces avermitilis
Q. Yao, L. Ma, L. Liu, H. Ikeda, S. Fushinobu, S. Li, and L.-H. Xu
J. Microbiol. Biotechnol. 27 (5), 956-964 (2017)


Crystal structures of carbohydrate-active enzymes with potential for practical oligosaccharide synthesis
S. Fushinobu
Int. J. Microgravity Sci. Appl. 34 (1), p340109 (2017)

Metalloenzymes in Denitrification : Applications and Environmental Impacts (Editors: Isabel Moura, José J G Moura, Sofia R Pauleta, Luisa B Maia)
2017, RSC Publishing, Cambridge; ISBN: 978-1-78262-334-2
CHAPTER 14: Denitrification in Fungi
H. Shoun and S. Fushinobu
pp. 331-348.



13th (FY2016) JSPS PRIZE
Structural Bases and Molecular Evolution of Metabolic Enzymes Acting on Sugars and Sugar Phosphates
Shinya Fushinobu

阿部紘一 Koichi Abe

日本応用糖質科学会平成28年度大会(第65回) ポスター賞
阿部紘一 (Koichi Abe)、中島将博、砂川直輝、石田卓也、五十嵐圭日子、鮫島正浩、宮永顕正、中井博之、田口速男、荒川孝俊、伏信進矢

Original Papers

Crystal structures of archaeal 2-oxoacid:ferredoxin oxidoreductases from Sulfolobus tokodaii
Z. Yan, A. Maruyama, T. Arakawa, S. Fushinobu, and T. Wakagi
Sci. Rep. 6, 33061 (2016)

Isolation and characterization of a thermostable lipase from Bacillus thermoamylovorans NB501
C. Yamada, K. Sawano, N. Iwase, M. Matsuoka, T. Arakawa, S. Nishida, and S. Fushinobu
J. Gen. App. Microbiol. 62 (6), 313-319 (2016)

Archaeal Mo-containing glyceraldehyde oxidoreductase isozymes exhibit diverse substrate specificities through unique subunit assemblies
T. Wakagi, H. Nishimasu, M. Miyake, and S. Fushinobu
PLOS ONE 11 (1), e0147333 (2016)

The crystal structure of an inverting glycoside hydrolase family 9 exo-β-D-glucosaminidase and the design of glycosynthase
Y. Honda, S. Arai, K. Suzuki, M. Kitaoka, and S. Fushinobu
Biochem. J. 473 (4), 463-472 (2016)

Crystal structure and identification of a key amino acid for glucose tolerance, substrate specificity and transglycosylation activity of metagenomic β-glucosidase Td2F2
T. Matsuzawa, T. Jo, T. Uchiyama, J. A. Manninen, T. Arakawa, K. Miyazaki, S. Fushinobu, and K. Yaoi
FEBS J. 283 (12), 2340-2353 (2016)

Hydroxylation of flavanones by Cytochrome P450 105D7 from Streptomyces avermitilis
L. Liu, Q. Yao, Z. Ma, H. Ikeda, S. Fushinobu, and L.-H. Xu
J. Mol. Catal. B: Enzymatic 132, 91-97 (2016)


A key enzyme for biofuel production: "Missing link" between oxidative cellulose degradation and ethanol fermentation by microbes
Y.-W. Nam, T. Arakawa, and S. Fushinobu
Photon Factory Activity Report #33 2015 Part A, Highlights and Facility Report [Life Science], pp. 60-61

生活と環境 (日本環境衛生センター) 61 (5) (#721), 67-72 (2016)



伏信 進矢
16th Research Promoted Award on Enzyme Application, Amano's 16th Symposium on Enzyme Applications
Shinya Fushinobu

平成27年度 東京大学大学院農学生命科学研究科長賞
佐藤 真与
Dean's Award from the Graduate School of Agricultural and Life Sciences, The University of Tokyo
Mayo Sato

Original Papers

Characterization and crystal structure determination of β-1,2-mannobiose phosphorylase from Listeria innocua
T. Tsuda, T. Nihira, K. Chiku, E. Suzuki, T. Arakawa, M. Nishimoto, M. Kitaoka, H. Nakai, and S. Fushinobu
FEBS Lett. 589 (24B), 3816-3821 (2015)

Crystal structure and substrate recognition of cellobionic acid phosphorylase, which plays a key role in oxidative cellulose degradation by microbes
Y.-W. Nam, T. Nihira, T. Arakawa, Y. Saito, M. Kitaoka, H. Nakai, and S. Fushinobu
J. Biol. Chem.
290 (30), 18281-18292 (2015)

Open–close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase
M. Sato, T. Arakawa, Y.-W. Nam, M. Nishimoto, M. Kitaoka, and S. Fushinobu
BBA - Proteins Proteom. 1854 (5), 333–340 (2015)

An inverting β-1,2-mannosidase belonging to glycoside hydrolase family 130 from Dyadobacter fermentans
T. Nihira, K. Chiku, E. Suzuki, M. Nishimoto, S. Fushinobu, M. Kitaoka, K. Ohtsubo, and H. Nakai
FEBS Lett. 589 (23), 3604-3610 (2015)

Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis
M. Hattie, T. Ito, A. W. Debowski, T. Arakawa, T. Katayama, K. Yamamoto, S. Fushinobu, and K. A. Stubbs
Chem. Commun. 51 (81), 15008-15011 (2015)

Structural basis for the 4'-hydroxylation of diclofenac by a microbial cytochrome P450 monooxygenase
L.-H. Xu, H. Ikeda, L. Liu, T. Arakawa, T. Wakagi, H. Shoun, and S. Fushinobu
Appl. Microbiol. Biotechnol. 99 (7), 3081-3091 (2015)

" Newton's cradle" proton relay with amide–imidic acid tautomerization in inverting cellulase visualized by neutron crystallography
A. Nakamura, T. Ishida, K. Kusaka, T. Yamada, S. Fushinobu, I. Tanaka, S. Kaneko, K. Ohta, H. Tanaka, K. Inaka, Y. Higuchi, N. Niimura, M. Samejima, and K. Igarashi
Science Adv. 1 (7), e1500263 (2015)

Identification of the flavonoid luteolin as a repressor of the transcription factor hepatocyte nuclear factor 4α
J. Li, J. Inoue, J. M. Choi, S. Nakamura, Z. Yan, S. Fushinobu, H. Kamada, H. Kato, T. Hashidume, M. Shimizu, R. Sato
J. Biol. Chem. 290 (39), 24021-24035 (2015)


生物工学会誌 93 (10), 627 (2015)

Diversity in β-galactosidase Specificities within Bifidobacterium: Towards an Understanding of β-Galactoside Metabolism in the Gut Niche
A. H. Viborg
Trends Glycosi. Glycotechnol. 27 (156), E9-E12/J9-J12 (2015)

クリーンエネルギー 24 (10), 42-46 (2015)

バイオマス分解酵素に新たなスター ― 銅を活性中心にもつ溶解性多糖モノオキシゲナーゼ(最新のトピックス)
月刊化学 70 (1), 68-69 (2015)

53 (1), 45-50 (2015)



日本応用糖質科学会平成26年度大会(第63回) ポスター賞
佐藤 真与、西本 完、荒川 孝俊、北岡 本光、伏信 進矢
Bifidobacterium longum JCM1217由来N-アセチルヘキソサミン 1-キナーゼの構造・機能解析

Original Papers

Crystal structure of a feruloyl esterase belonging to the tannase family: a disulfide bond near a catalytic triad
K. Suzuki, A. Hori, K. Kawamoto, R. R. Thangudu, T. Ishida, K. Igarashi, M. Samejima, C. Yamada, T. Arakawa, T. Wakagi, T. Koseki, and S. Fushinobu
Proteins: Struct. Funct. Bioinform. 82 (10), 2857-2867 (2014)

Structural basis for reversible phosphorolysis and hydrolysis reactions of 2-O-α-glucosylglycerol phosphorylase
K. K. Touhara, T. Nihira, M. Kitaoka, H. Nakai, and S. Fushinobu
J. Biol. Chem. 289 (26), 18067-18075 (2014)

Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum
T. Ito, K. Saikawa, S. Kim, K. Fujita, A. Ishiwata, S. Kaeothip, T. Arakawa, T. Wakagi, G. T. Beckham, Y. Ito, and S. Fushinobu
Biochem. Biophys. Res. Commun. 447 (1), 32-37 (2014)

Mutational and crystallographic analysis of L-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813: Interconversion between oxidase and monooxygenase activities
D. Matsui, D.-H. Im, A. Sugawara, Y. Fukuta, S. Fushinobu, K. Isobe, and Y. Asano
FEBS Open Bio 4, 220-228 (2014)

Engineering the allosteric properties of archaeal non-phosphorylating glyceraldehyde-3-phosphate dehydrogenases
F. Ito, M. Miyake, S. Fushinobu, S. Nakamura, K. Shimizu, and T. Wakagi
BBA - Proteins Proteom. 1844 (4), 759-766 (2014)

Four Cys residues in heterodimeric 2-oxoacid:ferredoxin oxidoreductase are required for CoA-dependent oxidative decarboxylation but not for a non-oxidative decarboxylation
Z. Yan, S. Fushinobu, and T. Wakagi
BBA - Proteins Proteom. 1844 (4), 736-743 (2014)

Structural and mutational analysis of substrate recognition in kojibiose phosphorylase
S. Okada, T. Yamamoto, H. Watanabe, T. Nishimoto, H. Chaen, S. Fukuda, T. Wakagi, and S. Fushinobu
FEBS J. 281 (3), 778-786 (2014)

Sulfolobus tokodaii ST2133 is characterized as a thioredoxin reductase-like ferredoxin:NADP+ oxidoreductase
Z. Yan, Y.-W. Nam, S. Fushinobu, and T. Wakagi
Extremophiles 18 (1), 99-110 (2014)

The core of allosteric motion in Thermus caldophilus L-lactate dehydrogenase
Y. Ikehara, K. Arai, N. Furukawa, T. Ohno, T. Miyake, S. Fushinobu, M. Nakajima, A. Miyanaga, H. Taguchi
J. Biol. Chem. 289 (45), 31550-31564 (2014)

Structural and biochemical analyses of glycoside hydrolase family 26 β-mannanase from a symbiotic protist of the termite Reticulitermes speratus
H. Tsukagoshi, A. Nakamura, T. Ishida, K.K. Touhara, M. Otagiri, S. Moriya, M. Samejima, K. Igarashi, S. Fushinobu, K. Kitamoto, and M. Arioka
J. Biol. Chem. 289 (15), 10843-10852 (2014)


Metalloproteins: A new face for biomass breakdown
S. Fushinobu
Nat. Chem. Biol. 10 (2), 88-89 (2014)

Novel Active Center and Reaction Mechanism of GH127 β-L-Arabinofuranosidase from Bifidobacterium longum
T. Ito
Trends Glycosci. Glycotechnol. 26 (151), 131–140 (2014)
Bifidobacterium longum JCM1217由来GH127β-L-Arabinofuranosidase(HypBA1)の新規な活性中心と反応機構

伊藤佑、片山高嶺、Mitchell Hattie、櫻間晴子、和田潤、鈴木龍一郎、芦田久、若木高善、山本憲二、Keith A. Stubbs、伏信進矢
応用糖質科学 4 (2), 140-146 (2014)
Structure and reaction mechanism of GH20 lacto-N-biosidase from Bifidobacterium bifidum
T. Ito, T. Katayama, M. Hattie, H. Sakurama, J. Wada, R. Suzuki, H. Ashida, T. Wakagi, K. Yamamoto, K. A. Stubbs, and S. Fushinobu
Bull. App. Glycosci. 4 (2), 140-146 (2014)
(Proceedings of the Symposium on Applied Glycoscience, 2013)

Photon Factory News 31 (4), 10-14 (2014)
Crystal structures of GH20 lacto-N-biosidase from Bifidobacterium bifidum
T. Ito and S. Fushinobu



B.B.B.論文賞 (2012年 Vol. 76)
Crystal structures of glycoside hydrolase family 51 α-L-arabinofuranosidase from Thermotoga maritima
D.-H. Im, K. Kimura, F. Hayasaka, T. Tanaka, M. Noguchi, A. Kobayashi, S. Shoda, K. Miyazaki, T. Wakagi, and S. Fushinobu
Biosci. Biotechnol. Biochem. 76 (2), 423-428 (2012)

Original Papers

Archaeal aldehyde dehydrogenase ST0064 from Sulfolobus tokodaii, a paralog of non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase, is a succinate semialdehyde dehydrogenase
F. Ito, H. Chishiki, S. Fushinobu, and T. Wakagi
Biosci. Biotechnol. Biochem. 77 (6), 1344-1348 (2013)

Crystal structures of glycoside hydrolase family 3 β-glucosidase 1 from Aspergillus aculeatus
K. Suzuki, J.-I. Sumitani, Y.-W. Nam, T. Nishimaki, S. Tani, T. Wakagi, T. Kawaguchi, and S. Fushinobu
Biochem. J. 452 (2), 211-221 (2013)

Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum
T. Ito, T. Katayama, M. Hattie, H. Sakurama, J. Wada, R. Suzuki, H. Ashida, T. Wakagi, K. Yamamoto, K. A. Stubbs, and S. Fushinobu
J. Biol. Chem. 288 (17), 11795-11806 (2013)

Preparation of p-nitrophenyl β-L-arabinofuranoside as a substrate of β-L-arabinofuranosidase
S. Kaeothip, A. Ishiwata, T. Ito, S. Fushinobu, K. Fujita K, and Y. Ito
Carbohydr. Res. 382, 95-100 (2013)

Effectiveness of heat treatment to protect introduced denitrifying bacteria from eukaryotic predatory microorganisms in a pilot-scale bioreactor
W. Ikeda-Ohtsubo, M. Miyahara, T. Yamada, A. Watanabe, S. Fushinobu, T. Wakagi, H. Shoun, K. Miyauchi, and G. Endo
J. Biosci. Bioeng. 116 (6), 722-724 (2013)

Bioaugmentation of a wastewater bioreactor system with the nitrous oxide-reducing denitrifier Pseudomonas stutzeri strain TR2
W. Ikeda-Ohtsubo, M. Miyahara, S.-W. Kim, T. Yamada, M. Matsuoka, A. Watanabe, S. Fushinobu, T. Wakagi, H. Shoun, K. Miyauchi, and G. Endo
J. Biosci. Bioeng. 115 (1), 37-42 (2013)


Multiple rewards from a treasure trove of novel glycoside hydrolase and polysaccharide lyase structures: new folds, mechanistic details, and evolutionary relationships
S. Fushinobu, V. D. Alves, and P. M. Coutinho
Curr. Opin. Struct. Biol. 23 (5), 652-659 (2013)

Aldolases - Distinctive Characters in Archaeal Enzymes
T. Wakagi
Trends Glycosci. Glycotechnol. 25 (142), 71-81 (2013)

 108 (4), 204-210 (2013)
Diversity of feruloyl esterases from Koji-Mold and its applications
T. Koseki and S. Fushinobu
J. Brewing Soc. Japan
108 (4), 204-210 (2013) [Japanese]

Phase-diagram-guided method for growth of a large crystal of glycoside hydrolase family 45 inverting cellulase suitable for neutron structural analysis
A. Nakamura, T. Ishida, S. Fushinobu, K. Kusaka, I. Tanaka, K. Inaka, Y. Higuchi, M. Masaki, K. Ohta, S. Kaneko, N. Niimura, K. Igarashi and M. Samajima
J. Synchrotron Rad. 20 (6), 859-863 (2013)