Elucidation of mobile loop functions in food-related enzymes

• Project/Area Number: 24380054
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Applied biochemistry
• Research Institution: Kyoto University
• Principal Investigator: MIKAMI Bunzo 京都大学, (連合)農学研究科(研究院), 教授 (40135611)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥16,510,000 (Direct Cost: ¥12,700,000、Indirect Cost: ¥3,810,000); Fiscal Year 2014: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2013: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2012: ¥8,710,000 (Direct Cost: ¥6,700,000、Indirect Cost: ¥2,010,000)
• Keywords: 応用構造生物学 / タンパク質工学 / 酵素工学 / X線結晶構造解析 / 酵素反応機構 / タンパク質結晶構造解析 / 構造生物学 / タンパク質構造変化 / 食品関連酵素 / 酵素反応

Outline of Final Research Achievements

The functions of proteins are usually expressed by conformational changes in loop regions. We have investigated the mobile loops in food-related enzymes that are used in food industry. The mobile loops in the active sites of beta-amylase and alginate lyase that are important for incorporation of substrate and release of product are analyzed by X-ray crystal analyses of their mutant enzymes. The x-ray analysis of the mutants of pro protein-glutaminase (A47Q, A47E) showed that this enzyme can catalyze the reverse reaction in its catalytic pocket. The 24mer peptide derived from pro-region of transglutaminase inhibited the enzyme. We have determined the structure of the enzyme/peptide complex by x-ray analysis.

Research Products

• [Journal Article] Preliminary X-ray analysis of the binding domain of the soybean vacuolar sorting receptor complexed with a sorting determinant of a seed storage protein. (2015)
  • Author(s): Maruyama, N., Goshi, T., Sugiyama, S., Niiyama, M., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Matsumura, H., Mikami, B.
  • Journal Title: Acta Crystallogr. F Struct. Biol. Commun. Volume: 71 Issue: 2 Pages: 132-135
  • DOI: 10.1107/s2053230x14027484
  • Peer Reviewed / Open Access
• [Journal Article] Metabolic fate of unsaturated glucuronic/iduronic acids from glycosaminoglycans: molecular identification and structure determination of streptococcal isomerase and dehydrogenase. (2015)
  • Author(s): Maruyama Y., Oiki S., Takase R., Mikami B., Murata K., Hashimoto, W.
  • Journal Title: J. Biol. Chem. Volume: 290 Issue: 10 Pages: 6281-6292
  • DOI: 10.1074/jbc.m114.604546
  • Peer Reviewed / Open Access
• [Journal Article] Crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD⁺-dependent dismutase from Mesorhizobium loti. (2015)
  • Author(s): Mugo, A.N,. Kobayashi, J., Mikami, B., Yoshikane, Y., Yagi, T., Ohnishi, K.
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 456 Issue: 1 Pages: 35-40
  • DOI: 10.1016/j.bbrc.2014.11.028
  • Peer Reviewed / Open Access
• [Journal Article] Structure-based conversion of the coenzyme requirement of a short-chain dehydrogenase/reductase involved in bacterial alginate metabolism. (2015)
  • Author(s): Takase, R., Mikami, B., Kawai, S., Murata, K., Hashimoto, W.
  • Journal Title: J. Biol. Chem. Volume: 289 Issue: 48 Pages: 33198-33214
  • DOI: 10.1074/jbc.m114.585661
  • NAID: 120005690199
  • Peer Reviewed / Open Access
• [Journal Article] Crystal structure of class III chitinase from pomegranate provides the insight into its metal storage capacity. (2015)
  • Author(s): Masuda, T., Zhao, G., Mikami, B..
  • Journal Title: Biosci. Biotechnol. Biochem. Volume: 79 Pages: 45-50
  • Peer Reviewed / Open Access
• [Journal Article] Atomic structure of recombinant thaumatin II reveals flexible conformations in two residues critical for sweetness and three consecutive glycine residues. (2014)
  • Author(s): Masuda, T., Mikami, B., Tani, F.
  • Journal Title: Biochimie. Volume: 106 Pages: 33-38
  • DOI: 10.1016/j.biochi.2014.07.016
  • NAID: 120005682566
  • Peer Reviewed / Open Access
• [Journal Article] The crystal structure of a crustacean prophenoloxidase provides a clue to understanding the functionality of the type 3 copper proteins. (2014)
  • Author(s): Masuda, T., Momoji, K., Hirata, T., Mikami, B.
  • Journal Title: FEBS J. Volume: 281 Issue: 11 Pages: 2659-2673
  • DOI: 10.1111/febs.12812
  • NAID: 120005646484
  • Peer Reviewed / Open Access
• [Journal Article] Structure of 4-pyridoxolactonase from Mesorhizobium loti (2014)
  • Author(s): Kobayashi J, Yoshikane Y, Yagi T, Baba S, Mizutani K, Takahashi N, Mikami B
  • Journal Title: Acta Crystallogr F Struct Biol Commun. Volume: 70 Issue: 4 Pages: 424-432
  • DOI: 10.1107/s2053230x14003926
  • Peer Reviewed / Open Access
• [Journal Article] Crystal structure of a bacterial unsaturated glucuronyl hydrolase with specificity for heparin (2014)
  • Author(s): Yusuke Nakamichi, Bunzo Mikami, Kousaku Murata. and Wataru Hashimoto
  • Journal Title: Journal of Biological Chemistry Volume: 289 Issue: 8 Pages: 4787-4797
  • DOI: 10.1074/jbc.m113.522573
  • Peer Reviewed
• [Journal Article] Purification, crystallization and preliminary crystallographic analysis of soybean mature glycinin A1bB2 (2013)
  • Author(s): Prak K, Mikami B, Itoh T, Fukuda T, Maruyama N, Utsumi S
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun. Volume: 69 Issue: 8 Pages: 937-941
  • DOI: 10.1107/s1744309113019684
  • Peer Reviewed
• [Journal Article] Induced-fit motion of a lid loop involved in catalysis in alginate lyase Al-III. (2012)
  • Author(s): Mikami B.
  • Journal Title: Acta Crystallogr D Biol Crystallogr Volume: 68 Issue: 9 Pages: 1207-1216
  • DOI: 10.1107/s090744491202495x
  • Peer Reviewed
• [Journal Article] Crystal structure of a major seed storage protein, llS proglobulin, from Amaranthus hypochondriacus : insight into its physico-chemical properties (2012)
  • Author(s): Tandang-Silvas MR. Cabanos CS. Carrazco Pena LD. De la Rosa AP, 0suna-Castro JA. Utsumi S. Mikami B, Maruyama N.
  • Journal Title: Food Chem Volume: 135 Issue: 2 Pages: 819-826
  • DOI: 10.1016/j.foodchem.2012.04.135
  • Peer Reviewed
• [Journal Article] Structure of β-1, 4-mannanase from the common sea hare Aplysia kurodai at 1.05 Å resolution (2012)
  • Author(s): Kimihiko Mizutani, Sae Tsuchiya, Mayuko Toyoda, Yuko Naobu, Keiko Tomilaga, Keizo Yuasa, Nobuyuki Takahashi, Akihlko Tsuji and Bunzo Mikmi
  • Journal Title: Acta Crystallographica Section F Volume: 68 Issue: 10 Pages: 1164-1168
  • DOI: 10.1107/s1744309112037074
  • Peer Reviewed
• [Presentation] β-アミラーゼ／マルトース不幸剛体結晶構造のpH変化 (2015)
  • Author(s): 三上文三、河村和広、安達基泰、水谷公彦、高橋延行
  • Organizer: 日本農芸化学会2015年度大会
  • Place of Presentation: 岡山大学
  • Year and Date: 2015-03-28
• [Presentation] 麹菌Aspergillus oryzae由来グルコアミラーゼのX線構造解析 (2015)
  • Author(s): 永吉恵美、水谷公彦、高橋延行、三上文三、瀧井幸男
  • Organizer: 日本農芸化学会2015年度大会
  • Place of Presentation: 岡山大学
  • Year and Date: 2015-03-28
• [Presentation] 甘味タンパク質ソーマチンの連続フェムト秒結晶構造解析 (2015)
  • Author(s): 桝田哲哉、南後恵理子、菅原道泰、鈴木守、登野健介、城地保昌、亀島敬、PARK Jaehyun、SongChangyong、初井宇記、矢橋牧名、大久保喬平、三上文三、北畠直文、谷史人、岩田想
  • Organizer: 日本農芸化学会2015年度大会
  • Place of Presentation: 岡山大学
  • Year and Date: 2015-03-28
• [Presentation] 連鎖球菌による哺乳類細胞外マトリクス（グルコサミノグリカン）の分解：不飽和グルクニルヒドロラーゼの反応機構 (2015)
  • Author(s): 中道優介、老木紗予子、三上文三、村田幸作、橋本渉
  • Organizer: 日本農芸化学会2015年度大会
  • Place of Presentation: 岡山大学
  • Year and Date: 2015-03-28
• [Presentation] イネにおけるジベレリン代謝酵素の構造と機能解析 (2015)
  • Author(s): 竹原清日、三上文三、樫尾徹、松岡信、上口美弥子
  • Organizer: 日本農芸化学会2015年度大会
  • Place of Presentation: 岡山大学
  • Year and Date: 2015-03-27
• [Presentation] 市街吸収分光法とX線結晶構造解析によるリジル‐tRNA合成酵素とL‐リジンの結合の解析およびその融合適合機構に対する洞察 (2015)
  • Author(s): 滝田禎亮、三上文三、井上國世
  • Organizer: 日本農芸化学会2015年度大会
  • Place of Presentation: 岡山大学
  • Year and Date: 2015-03-27
• [Presentation] ダイズβ-アミラーゼのSer297及びIl299変異体の酵素化学的性質と結晶構造 (2014)
  • Author(s): 河村和広、水谷公彦、高橋延行、三上文三
  • Organizer: 2014年度日本農芸化学会関西支部大会（第486回講演会）
  • Place of Presentation: ・奈良先端科学技術大学院大学
  • Year and Date: 2014-09-20
• [Presentation] Structure and Function Analysis of Geobacillus Starch Antistaling Enzyme (SAS) (2014)
  • Author(s): Bunzo Mikami, Hirotaka Bitoh, Yurie Anzai, Kimihiko Mizutani, Nobuyuki Takahashi, Masamichi Okada, Shotaro, Yamaguchi
  • Organizer: 23rd Congress and General Assembly of the International Union of Crystallography
  • Place of Presentation: Montreal, Canada
  • Year and Date: 2014-08-05 – 2014-08-12
• [Presentation] X線結晶構造解析によるダイズβ-アミラーゼの反応機構の解明 (2013)
  • Author(s): 三上文三、姜有那、安達基泰、河村和広、水谷公彦、高橋延行
  • Organizer: 日本農芸化学2013年度大会
  • Place of Presentation: 東北大学川内北キャンパス(宮城県仙台市)
  • Year and Date: 2013-03-25
• [Presentation] X線結晶構造解析による酵素機能の解明 (2012)
  • Author(s): 三上文三
  • Organizer: 日本農芸化学会関西支部第477回講演会
  • Place of Presentation: 神尸大学大農学部(兵庫県神戸市)(招待講演)
  • Year and Date: 2012-12-01
• [Presentation] Crystal Structure of Protein-Glutaminase and Its Pro-Structures Similar to Enzyme- Substrate Complex (2012)
  • Author(s): Mikami B., Hashizume R., Mizutani K., Takahashi N., Matsubara H., Matsunaga A., Yamaguchi S.
  • Organizer: 27th European Crystallographic Meetings
  • Place of Presentation: Bergen, Norway
  • Year and Date: 2012-08-09
• [Presentation] 結晶構造から生化学へ-X線結晶構造解析による酵素機能の解明-機能解析における問題点 (2012)
  • Author(s): 三上文三
  • Organizer: 第59回日本生化学会近畿支部例会シンポジウム
  • Place of Presentation: 京都大学宇治キャンパス(京都府宇治市)
  • Year and Date: 2012-05-19
• [Presentation] 結晶構造から探る食品関連酵素の機能
  • Author(s): 三上文三
  • Organizer: アグリバイオシンポジウム２０１３
  • Place of Presentation: 近畿大学農学部
  • Invited
• [Presentation] 微生物由来トランスグルタミナーゼの活性部位とプロ領域ペプチドとの相互作用
  • Author(s): 森 光平、小林 淳、吉村 卓也、水谷 公彦、高橋 延行、星 由起子、山口 庄太郎、三上 文三
  • Organizer: 日本農芸化学会関西支部第 479 回 講演会
  • Place of Presentation: 京都府立大学
• [Presentation] Ｘ線結晶構造解析によるダイズβ-アミラーゼの反応機構の解明
  • Author(s): 三上文三、姜有那、安達基泰、河村和広、水谷公彦、高橋延行
  • Organizer: 日本農芸化学２０１４年度大会
  • Place of Presentation: 明治大学生田キャンパス
• [Remarks] 応用構造生物学分野
  • URL: http://www.structure.kais.kyoto-u.ac.jp/
• [Remarks] 京都大学農学研究科応用生命科学専攻応用構造生物学分野
  • URL: http://www.applife.kais.kyoto-u.ac.jp/system/fck/11.pdf
• [Remarks] http://www.structure.kais.kyoto-u.ac.jp/
• [Remarks]
  • URL: http://www.structure.kais.kyoto-u.ac.jp/