Structural analysis of novel bifidobacterial enzymes degrading human and plant glycans

• Project/Area Number: 24380053
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Applied biochemistry
• Research Institution: The University of Tokyo
• Principal Investigator: FUSHINOBU Shinya 東京大学, 農学生命科学研究科, 教授 (00302589)
• Co-Investigator(Kenkyū-buntansha): ASHIDA Hisashi 近畿大学, 生物理工学部, 教授 (40370987) ; FUJITA Kiyotaka 鹿児島大学, 農学部, 准教授 (20381189) ; 芦田 久 近畿大学, 生物理工学部, 教授 (40379087)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥17,940,000 (Direct Cost: ¥13,800,000、Indirect Cost: ¥4,140,000); Fiscal Year 2014: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000); Fiscal Year 2013: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2012: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
• Keywords: 糖質分解酵素 / ビフィズス菌 / 血液型抗原 / β-アラビノオリゴ糖 / 複合糖鎖

Outline of Final Research Achievements

We determined the crystal structure of GH127 beta-L-arabinofuranosidase (HypBA1). HypBA1 has a Cys residue at its active center and was the first "cysteine glycosidase". We found four new glycosidases from B. bifidum. Moreover, we revealed the transcription regulation mechanism of the beta-arabinooligosaccharide degradation system in B. longum and investigated characteristics of a HypBA1 homolog.

Research Products

• [Journal Article] Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase (2015)
  • Author(s): 佐藤真与、荒川孝俊、伏信進矢ら
  • Journal Title: BBA - Proteins Proteom. Volume: 1854 Pages: 333-340
  • DOI: 10.1016/j.bbapap.2015.01.011
  • Peer Reviewed
• [Journal Article] Structural basis for the 4'-hydroxylation of diclofenac by a microbial cytochrome P450 monooxygenase. (2015)
  • Author(s): L.-H. Xu, H. Ikeda, L. Liu, T. Arakawa, T. Wakagi, H. Shoun, S. Fushinobu
  • Journal Title: Appl. Microbiol. Biotechnol. Volume: 99 Pages: 3081-3091
  • DOI: 10.1007/s00253-014-6148-y
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] α-N-Acetylglucosaminidase from Bifidobacterium bifidum specifically hydrolyzes α-linked N-acetylglucosamine at nonreducing terminus of O-glycan on gastric mucin (2015)
  • Author(s): 芦田久ら
  • Journal Title: Applied Microbiology and Biotechnology Volume: 99 Pages: 3941-3948
  • DOI: 10.1007/s00253-014-6201-x
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Characterization of a β-L-Arabinopyranosidase from <i>Bifidobacterium longum</i> subsp. <i>longum</i> (2015)
  • Author(s): 藤田清貴ら
  • Journal Title: J. Appl. Glycosci. Volume: 62 Issue: 1 Pages: 1-6
  • DOI: 10.5458/jag.jag.jag-2014_006 10.5458/jag.jag.JAG-2014_006
  • NAID: 130004705329
  • ISSN: 1344-7882, 1880-7291
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Crystal structure of a feruloyl esterase belonging to the tannase family: a disulfide bond near a catalytic triad (2014)
  • Author(s): 鈴木健太郎、荒川孝俊、伏信進矢ら
  • Journal Title: Proteins Volume: 82 Pages: 2857-2867
  • DOI: 10.1002/prot.24649
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Structural basis for reversible phosphorolysis and hydrolysis reactions of 2-O-α-glucosylglycerol phosphorylase (2014)
  • Author(s): 東原幸起、荒川孝俊、伏信進矢ら
  • Journal Title: J. Biol. Chem. Volume: 289 Pages: 18067-18075
  • DOI: 10.1074/jbc.m114.573212
  • Peer Reviewed
• [Journal Article] Bifidobacterium longum subsp. longum exo-β-1,3-galactanase, an enzyme for the degradation of type II arabinogalactan (2014)
  • Author(s): 藤田清貴ら
  • Journal Title: Appl. Environ. Microbiol. Volume: 80 Pages: 4577-4584
  • DOI: 10.1128/aem.00802-14
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum (2014)
  • Author(s): 伊藤佑、藤田清貴、伏信進矢ら
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 447 Pages: 32-37
  • DOI: 10.1016/j.bbrc.2014.03.096
  • Peer Reviewed
• [Journal Article] Characterization of a novel β-L-arabinofuranosidase in Bifidobacterium longum: Functional elucidation of a DUF1680 protein family member (2014)
  • Author(s): 藤田清貴ら
  • Journal Title: J. Biol. Chem. Volume: 289 Pages: 5240-5249
  • DOI: 10.1074/jbc.m113.528711
  • Peer Reviewed
• [Journal Article] Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum (2013)
  • Author(s): 伊藤佑、芦田久、伏信進矢ら
  • Journal Title: Journal of Biological Chemistry Volume: 288 Pages: 11795-11806
  • DOI: 10.1074/jbc.m112.420109
  • Peer Reviewed
• [Journal Article] Preparation of p-nitrophenyl β-L-arabinofuranoside as a substrate of β-L-arabinofuranosidase (2013)
  • Author(s): S. Kaeothip、伏信進矢、藤田清貴ら
  • Journal Title: Carbohydr. Res. Volume: 382 Pages: 95-100
  • DOI: 10.1016/j.carres.2013.10.005
  • Peer Reviewed
• [Journal Article] Crystal structures of glycoside hydrolase family 3 β-glucosidase 1 from Aspergillus aculeatus (2013)
  • Author(s): Suzuki, K.
  • Journal Title: Biochem. J. Volume: 452 (2) Pages: 211-221
  • DOI: 10.1042/bj20130054
  • Peer Reviewed
• [Journal Article] Lacto-N-biosidase encoded by a novel gene of Bifidobacterium longum subspecies longum shows unique substrate specificity and requires a designated chaperone for its active expression (2013)
  • Author(s): 櫻間晴子、芦田久ら
  • Journal Title: Journal of Biological Chemistry Volume: 288 Pages: 25194-25206
  • DOI: 10.1074/jbc.m113.484733
  • Peer Reviewed
• [Journal Article] Bifidobacteria! a-galactosidase with unique carbohydrate-binding module specifically acts on blood group B antigen (2013)
  • Author(s): 脇中琢良、芦田久, ら(他8名)
  • Journal Title: Glycobiology Volume: 23 Pages: 232-240
  • Peer Reviewed
• [Journal Article] 1,3-1,4- a ~L_Fucosynthase That Specifically Introduces Lewis a/x Antigens into Type-1/2 Chains (2012)
  • Author(s): 櫻間晴子、伏信進矢、芦田久, ら(他7名)
  • Journal Title: J.Biol. Chem. Volume: 287 Pages: 16709-16719
  • Peer Reviewed
• [Journal Article] Functional Analysis of Degradative Enzymes for Hydroxyproline-linked &beta;-L-Arabinofuranosides in <i>Bifidobacterium longum</i> (2012)
  • Author(s): 藤田清貴, ら(他2名)
  • Journal Title: TIGG Volume: 24 Issue: 139 Pages: 215-224
  • DOI: 10.4052/tigg.24.215
  • NAID: 10031146673
  • ISSN: 0915-7352, 1883-2113
  • Peer Reviewed
• [Journal Article] 新規な糖質関連酵素の構造.機能解析 (2012)
  • Author(s): 伏信進矢
  • Journal Title: 応用糖質科学 Volume: 2 Pages: 44-50
  • NAID: 130005037749
• [Presentation] HRGPの分解に関与するBifidobacterium longum由来α-L-アラビノフラノシダーゼの機能解析 (2015)
  • Author(s): 藤田清貴、坂本彩美、下川倫子、金子 哲、北原兼文
  • Organizer: 日本農芸化学会 2015年度大会
  • Place of Presentation: 岡山
  • Year and Date: 2015-03-28
• [Presentation] ビフィズス菌由来N-アセチルへキソサミン 1-キナーゼのオリゴ糖合成を目指した機能改変 (2015)
  • Author(s): 佐藤真与、荒川孝俊、伏信進矢ら
  • Organizer: 日本農芸化学会 2015年度大会
  • Place of Presentation: 岡山
  • Year and Date: 2015-03-28
• [Presentation] 反転型糖質ホスホリラーゼの立体構造と基質認識 (2015)
  • Author(s): 伏信進矢
  • Organizer: 日本農芸化学会 2015年度大会
  • Place of Presentation: 岡山
  • Year and Date: 2015-03-28
• [Presentation] Sda抗原を分解するビフィズス菌由来のバイファンクショナル酵素 (2015)
  • Author(s): 芦田 久、鈴木 里奈
  • Organizer: 日本農芸化学会 2015年度大会
  • Place of Presentation: 岡山
  • Year and Date: 2015-03-28
• [Presentation] Bifidobacteirum 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 (2014)
  • Author(s): 佐藤真与、西本完、荒川孝俊、北岡本光、伏信進矢
  • Organizer: 日本応用糖質科学会平成２６年度大会（第６３回）
  • Place of Presentation: 新潟
  • Year and Date: 2014-09-24
• [Presentation] Bifidobacterium longumにコードされたβ-L-アラビノフラノシダーゼホモログの機能解析 (2014)
  • Author(s): 藤田清貴、川原由義、下川倫子、伏信進矢、石渡明弘、Sophon Kaeothip、伊藤幸成、北原兼文
  • Organizer: 日本応用糖質科学会平成２６年度大会（第６３回）
  • Place of Presentation: 新潟
  • Year and Date: 2014-09-24
• [Presentation] Bifidobacterium longum由来のβ-1,6-ガラクタン側鎖分解酵素群の機能解析 (2014)
  • Author(s): 坂本彩美、下川倫子、小竹敬久、円谷陽一、北原兼文、藤田清貴
  • Organizer: 日本応用糖質科学会平成２６年度大会（第６３回）
  • Place of Presentation: 新潟
  • Year and Date: 2014-09-24
• [Presentation] チオグリコシド中間体を経由するGH127β-L-アラビノフラノシダーゼの触媒メカニズム (2014)
  • Author(s): 伏信進矢
  • Organizer: 第33回日本糖質学会年会
  • Place of Presentation: 名古屋
  • Year and Date: 2014-08-11
  • Invited
• [Presentation] Bifidobacterium longumのⅡ型アラビノガラクタン分解代謝経路の解析 (2014)
  • Author(s): 藤田清貴、坂本彩美、下川倫子、北原兼文
  • Organizer: 第33回日本糖質学会年会
  • Place of Presentation: 名古屋
  • Year and Date: 2014-08-11
• [Presentation] ビフィズス菌由来 GH127 β-L-アラビノフラノシダーゼの 新規な活性中心 (2014)
  • Author(s): 伏信進矢
  • Organizer: 第28回セルラーゼ研究会
  • Place of Presentation: 千葉
  • Year and Date: 2014-07-11
  • Invited
• [Presentation] ビフィズス菌由来GH127 β-L-アラビノフラノシダ―ゼの新規な活性中心 (2014)
  • Author(s): 伊藤佑、伏信進矢、藤田清貴ら
  • Organizer: 日本農芸化学会2014年度大会
  • Place of Presentation: 明治大学生田キャンパス、神奈川県川崎市
• [Presentation] Bifidobacterium longumにおけるβ-アラビノオリゴ糖鎖分解酵素群の転写解析 (2014)
  • Author(s): 藤田清貴ら
  • Organizer: 日本農芸化学会2014年度大会
  • Place of Presentation: 明治大学生田キャンパス、神奈川県川崎市
• [Presentation] The crystal structure of GH127 β-L-arabinofuranosidase (2013)
  • Author(s): 伏信進矢、藤田清貴ら
  • Organizer: 10th Carbohydrate Bioengineering Meeting
  • Place of Presentation: Prague, Czech Republic
• [Presentation] Crystal structure of lacto-N-biosidase from Bifidobacterium bifidum (2013)
  • Author(s): 伊藤佑、芦田久、伏信進矢ら
  • Organizer: 10th Carbohydrate Bioengineering Meeting
  • Place of Presentation: Prague, Czech Republic
• [Presentation] The crystal structure of GH3 beta-glucosidase 1 from Aspergillus aculeatus (2013)
  • Author(s): 伏信進矢ら
  • Organizer: 4th International Symposium on Diffraction Structure Biology
  • Place of Presentation: 名古屋市中小企業振興会館、愛知県
• [Presentation] 糖とリン酸をあやつる酵素の化学 (2013)
  • Author(s): 伏信進矢
  • Organizer: 第13回日本蛋白質科学会年会
  • Place of Presentation: とりぎん文化会館、鳥取県
• [Presentation] 糖と蛋白質の相互作用 (2013)
  • Author(s): 伏信進矢
  • Organizer: 第53回澱粉研究懇談会
  • Place of Presentation: ホテルラヴィエ川良、静岡県伊東市
  • Invited
• [Presentation] Structure of a glycoside hydrolase with a novel catalytic machinery (2013)
  • Author(s): 伏信進矢
  • Organizer: Gordon Research Conforence: Cellulosomes, Cellulases & Other Carbohydrate Modifying Enzymes
  • Place of Presentation: Proctor Academy, NH
  • Invited
• [Presentation] ビフィズス菌由来GH20ラクト-N-ビオシダーゼの立体構造と反応機構 (2013)
  • Author(s): 伊藤佑、芦田久、伏信進矢ら
  • Organizer: 応用糖質科学シンポジウム
  • Place of Presentation: 鹿児島大学、鹿児島県
• [Presentation] Bifidobacterium longum由来のβ-L-アラビノピラノシダーゼの機能解析 (2013)
  • Author(s): 下川倫子、藤田清貴ら
  • Organizer: 日本応用糖質科学会平成25年度大会
  • Place of Presentation: 鹿児島大学、鹿児島県
• [Presentation] 植物性多糖に作用するBifidobacteirum longum由来の酵素の解析 (2013)
  • Author(s): 芦田久, ら(他2名)
  • Organizer: 日本農芸化学会2013年度大会
  • Place of Presentation: 東北大学川内キャンパス(宮城県)
• [Presentation] Bifidobacteirum longum由来のエキソーβ-1.3-ガラクタナーゼの機能解析 (2013)
  • Author(s): 藤田清貴, ら(他3名)
  • Organizer: 日本農芸化学会2013年度大会
  • Place of Presentation: 東北大学川内キャンパス(宮城県)
• [Presentation] Bifidobacterium longumのハイドロキシプロリンに富む糖タンパク質の分解メカニズムの解明 (2012)
  • Author(s): 藤田清貴, ら(他4名)
  • Organizer: 第2回新潟大学国際糖質科学シンポジウム
  • Place of Presentation: 新潟大学(新潟)(招待講演)
  • Year and Date: 2012-11-13
• [Presentation] ルイスa抗原とルイスx抗原を特異的に認識する1,3-1,4-a-L-フコシダーゼの立体構造 (2012)
  • Author(s): 伏信進矢
  • Organizer: 第10回糖鎖科学コンソーシアムシンポジウム
  • Place of Presentation: 東京コンファレンスセンター(東京)(招待講演)
• [Presentation] ビフィズス菌が生産する植物糖タンパク質糖鎖分解酵素群の解析 (2012)
  • Author(s): 藤田清貴
  • Organizer: 第16回腸内細菌腸内細菌学会
  • Place of Presentation: 神戸市産業振興センター(兵庫県)
• [Book] Glycosidases: inborn errors of glycosphingolipid catabolism (Advances in Neurobiology) (2014)
  • Author(s): 芦田久ら
  • Total Pages: 20
  • Publisher: Springer
• [Remarks] 東京大学大学院農学生命科学研究科応用生命工学専攻酵素学研究室（伏信研）
  • URL: http://enzyme13.bt.a.u-tokyo.ac.jp/index.html
• [Remarks] 芦田久 研究者情報
  • URL: http://researchmap.jp/ashida/
• [Remarks] 藤田清貴 研究ホームページ
  • URL: http://hypba2.jimdo.com/
• [Remarks] 東京大学 大学院農学生命科学研究科 応用生命工学専攻 酵素学研究室
  • URL: http://enzyme13.bt.a.u-tokyo.ac.jp
• [Remarks] 芦田久 研究者情報
  • URL: http://researchmap.jp/ashida/
• [Remarks] 藤田 清貴 鹿児島大学研究者総覧
  • URL: http://kuris.cc.kagoshima-u.ac.jp/408011.html
• [Remarks]
  • URL: http://enzyme13.bt.a.u-tokyo.ac.jp
• [Remarks]
  • URL: http://researchmap.jp/ashida/
• [Remarks]
  • URL: http://kuris.dd.kagoshima-u.ac.jp/408011.html