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Researcher Information

last modified:2024/06/20

Associate Professor YAMASHITA, Satoshi

Laboratory Website

Faculty, Affiliation

Faculty of Chemistry, Institute of Science and Engineering

College and School Educational Field

Division of Material Chemistry, Graduate School of Natural Science and Technology
Division of Material Chemistry, Graduate School of Natural Science and Technology
Course in Chemistry, School of Chemistry, College of Science and Engineering

Laboratory

Biological Chemistry lab

Academic Background

【Academic background(Bachelor's Degree)】
Tohoku University Sch. Biochem. Eng.

Career

Tohoku University(2003/04/01-2005/07/31)
National Institutes of Health NIDDK Visiting Fellow(2005/08/01-2010/08)
Kagawa University Research fellow(2010/10/01-2013/03/31)
Tohoku University Dept. Eng. Assistant professor (2013/04/01-2015/11/30)
Kanazawa University Sch. Nat. Sci. Associate professor(2015/12/01-)

Year & Month of Birth

1975/02

Academic Society


Award




○Japan-Taiwan Plant Biology 2019 Presentation Award(2019/03)
○Japan-Taiwan Plant Biology 2019 Presentation Award(2019/03)

Specialities

Applied biochemistry

Speciality Keywords

enzymology,protein engineering,protein crystallography,Membrane protein

Research Themes

Structural and functional characterizations of natural rubber biosynthetic machinery from Hevea brasiliensis

Structural and functional characterizations of natural rubber biosynthetic machinery from Hevea brasiliensis

Structural and functional analyses of biosynthetic enzymes of lipophilic compounds including flavonoids and lignans

Structural and functional analyses of biosynthetic enzymes of lipophilic compounds including flavonoids and lignans

Books

Papers

  •  Structure-based engineering of a short-chain cis-prenyltransferase to biosynthesize nonnatural all-cis-polyisoprenoids: molecular mechanisms for primer substrate recognition and ultimate product chain-length determination. Ryo Kutsukawa,Riki Imaizumi,Miki Suenaga-Hiromori,Kohei Takeshita,Naoki Sakai,Shuto Misawa,Masaki Yamamoto,Haruhiko Yamaguchi,Yukino Miyagi-Inoue,Toshiyuki Waki,Kunishige Kataoka,Toru Nakayama,Satoshi Yamashita,Seiji Takahashi The FEBS journal 289 15 4602 2022/02/08
  •  Reconstitution of prenyltransferase activity on nanodiscs by components of the rubber synthesis machinery of the Para rubber tree and guayule. Fu Kuroiwa,Akira Nishino,Yasuko Mandal,Masataka Honzawa,Miki Suenaga-Hiromori,Kakeru Suzuki,Yukie Takani,Yukino Miyagi-Inoue,Haruhiko Yamaguchi,Satoshi Yamashita,Seiji Takahashi,Yuzuru Tozawa Scientific reports 12 1 3734 2022/03/08
  •  Identification and reconstitution of the rubber biosynthetic machinery on rubber particles from Hevea brasiliensis Satoshi Yamashita,Haruhiko Yamaguchi,Toshiyuki Waki,Yuichi Aoki,Makie Mizuno,Fumihiro Yanbe,Tomoki Ishii,Ayuta Funaki,Yuzuru Tozawa,Yukino Miyagi-Inoue,Kazuhisa Fushihara,Toru Nakayama,Seiji Takahashi ELIFE 5 2016/10
  •  Molecular mechanisms of natural rubber biosynthesis YAMASHITA Satoshi,TAKAHASHI Seiji Annual Review of Biochemistry 89 in press 2020/03
  •  A conserved strategy of chalcone isomerase-like protein to rectify promiscuous chalcone synthase specificity. Toshiyuki Waki,Ryo Mameda,Takuya Nakano,Sayumi Yamada,Miho Terashita,Keisuke Ito,Natsuki Tenma,Yanbing Li,Naoto Fujino,Kaichi Uno,Satoshi Yamashita,Yuichi Aoki,Konstantin Denessiouk,Yosuke Kawai,Satoko Sugawara,Kazuki Saito,Keiko Yonekura-Sakakibara,Yasumasa Morita,Atsushi Hoshino,Seiji Takahashi,Toru Nakayama Nature communications 11 1 870 2020/02/13

show all

  •  Product chain-length determination mechanism of short-chain cis-prenyltransferase from Mycobacterium tuberculosis Motoyoshi Noike,Takanori Ambo,Sayaka Mkuchi,Satoshi Yamashita,Seiji Takahashi,Hirofurm Kurokawa,Tanetoshi Koyama JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC 48 3-4 111 2007/09
  •  Manipulation of prenyl chain length determination mechanism of cis-prenyltransferases Y Kharel,S Takahashi,S Yamashita,T Koyama FEBS JOURNAL 273 3 647 2006/02
  •  Cloning, expression, and characterization of cis-polyprenyl diphosphate synthase from the thermoacidophilic archaeon Sulfolobus acidocaldarius H Hemmi,S Yamashita,T Shimoyama,T Nakayama,T Nishino JOURNAL OF BACTERIOLOGY 183 1 401 2001/01
  •  Quantitative analyses of the behavior of exogenously added bacteria during an acidulocomposting process Takatoshi Suematsu,Satoshi Yamashita,Hisashi Hemmi,Ayaka Yoshinari,Takefumi Shimoyama,Toru Nakayama,Tokuzo Nishino JOURNAL OF BIOSCIENCE AND BIOENGINEERING 114 1 70 2012/07
  •  Catalytic mechanism of type 2 isopentenyl diphosphate : dimethylailyl diphosphate isomerase: verification of a redox role of the flavin cofactor in a reaction with no net redox change H Hemmi,Y Ikeda,S Yamashita,T Nakayama,T Nishino BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 322 3 905 2004/09
  •  Novel fluorescent analogues for transmembrane movement study of polyprenyl phosphates Koichi Koseki,Satoshi Yamashita,Seiji Takahashi,Tanetoshi Koyama BIOORGANIC & MEDICINAL CHEMISTRY LETTERS 17 4 946 2007/02
  •  Novel sugar phosphotransferase system applicable to the efficient labeling of the compounds synthesized via the non-mevalonate pathway in Escherichia coli H Hemmi,S Yamashita,T Nakayama,T Nishino JOURNAL OF BIOSCIENCE AND BIOENGINEERING 93 5 515 2002/05
  •  X-ray structure of a protease-resistant mutant form of human galectin-8 with two carbohydrate recognition domains Hiromi Yoshida,Satoshi Yamashita,Misa Teraoka,Aiko Itoh,Shin-ichi Nakakita,Nozomu Nishi,Shigehiro Kamitori FEBS JOURNAL 279 20 3937 2012/10
  •  Structural Insights into Ail-Mediated Adhesion in Yersinia pestis Satoshi Yamashita,Petra Lukacik,Travis J. Barnard,Nicholas Noinaj,Suleyman Felek,Tiffany M. Tsang,Eric S. Krukonis,B. Joseph Hinnebusch,Susan K. Buchanan STRUCTURE 19 11 1672 2011/11
  •  Structure of L-rhamnose isomerase in complex with L-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site Hiromi Yoshida,Akihide Yoshihara,Misa Teraoka,Satoshi Yamashita,Ken Izumori,Shigehiro Kamitori FEBS OPEN BIO 3 35 2013
  •  New Role of Flavin as a General Acid-Base Catalyst with No Redox Function in Type 2 Isopentenyl-diphosphate Isomerase Hideaki Unno,Satoshi Yamashita,Yosuke Ikeda,Shin-ya Sekiguchi,Norie Yoshida,Tohru Yoshimura,Masami Kusunoki,Toru Nakayama,Tokuzo Nishino,Hisashi Hemmi JOURNAL OF BIOLOGICAL CHEMISTRY 284 14 9160 2009/04
  •  Purification, characterization, and primary structure of a novel N-acyl-D-amino acid amidohydrolase from Microbacterium natoriense TNJL143-2 Jian Liu,Yu Asano,Keiko Ikoma,Satoshi Yamashita,Yoshihiko Hirose,Takefumi Shimoyama,Seiji Takahashi,Toru Nakayama,Tokuzo Nishino JOURNAL OF BIOSCIENCE AND BIOENGINEERING 114 4 391 2012/10
  •  Characterization of cis-prenyltransferases from the rubber producing plant Hevea brasiliensis heterologously expressed in yeast and plant cells Seiji Takahashi,Hye-Jin Lee,Satoshi Yamashita,Tanetoshi Koyama PLANT BIOTECHNOLOGY 29 4 411 2012
  •  In vivo interaction between the human dehydrodolichyl diphosphate synthase and the Niemann-Pick C2 protein revealed by a yeast two-hybrid system Y Kharel,S Takahashi,S Yamashita,T Koyama BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 318 1 198 2004/05
  •  Type 2 isopentenyl diphosphate isomerase from a thermoacidophilic archaeon Sulfolobus shibatae S Yamashita,H Hemmi,Y Ikeda,T Nakayama,T Nishino EUROPEAN JOURNAL OF BIOCHEMISTRY 271 6 1087 2004/03
  •  Product chain-length determination mechanism of Z,E-farnesyl diphosphate synthase Motoyoshi Noike,Takanori Arnbo,Sayaka Kikuch,Toshihide Suzuki,Satoshi Yamashita,Seiji Takahashi,Hirofumi Kurokawa,Sebabrata Mahapatra,Dean C. Crick,Tanetoshi Koyama BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 377 1 17 2008/12
  •  Novel medium-chain prenyl diphosphate synthase from the thermo acidophilic archaeon Sulfolobus solfataticus H Hemmi,S Ikejiri,S Yamashita,T Nishino JOURNAL OF BACTERIOLOGY 184 3 615 2002/02
  •  Structural Insights into the Low pH Adaptation of a Unique Carboxylesterase from Ferroplasma ALTERING THE pH OPTIMA OF TWO CARBOXYLESTERASES Kazuhiro Ohara,Hideaki Unno,Yasuhiro Oshima,Miho Hosoya,Naoto Fujino,Kazutake Hirooka,Seiji Takahashi,Satoshi Yamashita,Masami Kusunoki,Toru Nakayama JOURNAL OF BIOLOGICAL CHEMISTRY 289 35 24499 2014/08
  •  Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean. Riki Imaizumi,Ryo Mameda,Kohei Takeshita,Hiroki Kubo,Naoki Sakai,Shun Nakata,Seiji Takahashi,Kunishige Kataoka,Masaki Yamamoto,Toru Nakayama,Satoshi Yamashita,Toshiyuki Waki Proteins 2020/07/29
  •  Alpha/beta-hydrolases: A unique structural motif coordinates catalytic acid residue in 40 protein fold families Polytimi S. Dimitriou,Alexander Denesyuk,Seiji Takahashi,Satoshi Yamashita,Mark S. Johnson,Toru Nakayama,Konstantin Denessiouk PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 85 10 1845 2017/10
  •  パラゴムノキの天然ゴム生合成酵素の試験管内再構成 山下哲,高橋征司 機能材料 37 4 66‐72 2017/04/05 
  •  Identification of protein-protein interactions of isoflavonoid biosynthetic enzymes with 2-hydroxyisoflavanone synthase in soybean (Glycine max (L.) Merr.) Toshiyuki Waki,DongChan Yoo,Naoto Fujino,Ryo Mameda,Konstantin Denessiouk,Satoshi Yamashita,Reiko Motohashi,Tomoyoshi Akashi,Toshio Aoki,Shin-ichi Ayabe,Seiji Takahashi,Toru Nakayama BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 469 3 546 2016/01
  •  Roles of the indole ring of Trp396 covalently bound with the imidazole ring of His398 coordinated to type I copper in bilirubin oxidase. Kataoka K,Ito T,Okuda Y,Sakai Y,Yamashita S,Sakurai T Biochemical and biophysical research communications 2019/10
  •  (+)-Sesamin, a sesame lignan, is a potent inhibitor of gut bacterial tryptophan indole-lyase that is a key enzyme in chronic kidney disease pathogenesis. Daiki Oikawa,Satoshi Yamashita,Seiji Takahashi,Toshiyuki Waki,Koichi Kikuchi,Takaaki Abe,Takane Katayama,Toru Nakayama Biochemical and biophysical research communications 590 158 2022/01/29
  •  Toward Total Elucidation of Biosynthetic Mechanism of Natural Rubber 高橋 征司,山下 哲,伏原 和久 高分子 = High polymers, Japan : polymers 66 6 278 2017/06
  •  Physical interactions among flavonoid enzymes in snapdragon and torenia reveal the diversity in the flavonoid metabolon organization of different plant species Naoto Fujino,Natsuki Tenma,Toshiyuki Waki,Keisuke Ito,Yuki Komatsuzaki,Keigo Sugiyama,Tatsuya Yamazaki,Saori Yoshida,Masayoshi Hatayama,Satoshi Yamashita,Yoshikazu Tanaka,Reiko Motohashi,Konstantin Denessiouk,Seiji Takahashi,Toru Nakayama Plant Journal 94 2 372 2018/04/01
  •  Purification and characterization of small and large rubber particles from Hevea brasiliensis. Yamashita S,Mizuno M,Hayashi H,Yamaguchi H,Miyagi-Inoue Y,Fushihara K,Koyama T,Nakayama T,Takahashi S Bioscience, biotechnology, and biochemistry 82 6 1011 2018/06
  •  Identification of a Highly Specific Isoflavone 7-O-glucosyltransferase in the soybean (Glycine max (L.) Merr.) Ayuta Funaki,Toshiyuki Waki,Akio Noguchi,Yosuke Kawai,Satoshi Yamashita,Seiji Takahashi,Toru Nakayama PLANT AND CELL PHYSIOLOGY 56 8 1512 2015/08
  •  触媒機能を指標にした自然界からの酵素探索研究:セサミノール配糖体分解酵素の探索を例として 山下哲,下山武文,高橋征司,山口雅篤,中山亨 日本生物工学会誌 92 8 3 2014 
  •  明らかになりつつある天然ゴム生合成の分子機構 高橋征司,山下哲 バイオサイエンスとインダストリー 75 4 292‐298 2017/07/10 
  •  Catalytic promiscuity of rice 2-oxoglutarate/Fe(II)-dependent dioxygenases supports xenobiotic metabolism. Natsuki Takamura,Akihiko Yamazaki,Nozomi Sakuma,Sakiko Hirose,Motonari Sakai,Yukie Takani,Satoshi Yamashita,Masahiro Oshima,Makoto Kuroki,Yuzuru Tozawa Plant physiology 187 2 816 2021/10/05
  •  Identification and characterization of a novel bacterial β-glucosidase that is highly specific for the β-1,2-glucosidic linkage of sesaminol triglucoside. Sakurai A,Hongo S,Nair A,Waki T,Oikawa D,Nishio T,Shimoyama T,Takahashi S,Yamashita S,Nakayama T Bioscience, biotechnology, and biochemistry 82 9 1518 2018/09
  •  cDNA cloning and characterization of chalcone isomerase-fold proteins from snapdragon (Antirrhinum majus L.) flowers Naoto Fujino,Tatsuya Yamazaki,Yanbing Li,Kota Kera,Erika Furuhashi,Satoshi Yamashita,Yasumasa Morita,Masayoshi Nakayama,Seiji Takahashi,Toru Nakayama PLANT BIOTECHNOLOGY 31 2 105 2014
  •  Acidulocomposting, an Accerated Composting Process of Garbage under Thermoacidophilic Conditions for Prolonged Periods Tokuzo Nishino,Toru Nakayama,Hisashi Hemmi,Takefumi Shimoyama,Satoshi Yamashita,Minoru Akai,Takahiro Kanagawa,Katsuji Hoshi Journal of Environmental Biotechnology 3 1 33 2003
  •  Carbohydrate recognition mechanism of HA70 from Clostridium botulinum deduced from X-ray structures in complexes with sialylated oligosaccharides Satoshi Yamashita,Hiromi Yoshida,Noboru Uchiyama,Yukari Nakakita,Shin-ichi Nakakita,Takashi Tonozuka,Keiji Oguma,Atsushi Nishikawa,Shigehiro Kamitori FEBS LETTERS 586 16 2404 2012/07
  •  X-ray structure of a stable protease-resistant glectin-9 with short linker H. Yoshida,N. Nishi,M. Teraoka,S. Yamashita,S. Kamitori FEBS JOURNAL 280 531 2013/07

Conference Presentations

  • Identification and in vitro reconstitution of natural rubber biosynthetic complex from the Para rubber tree(conference:The 13th International Meeting on Biosynthesis, Function and Synthetic Biology of Isoprenoids)(2017/07)
  • Reconstitution of natural rubber biosynthetic enzyme from the Para rubber tree(conference:Baltic conference on Plastics and Rubber)(2018/05)
  • In vitro synthesis of natural rubber and its derivatives by enzymes introduced into rubber particles(conference:12th Annual World Protein & Peptide Conference)(2019/06)

Others

Arts and Fieldwork

Patent

Theme to the desired joint research

Grant-in-Aid for Scientific Research

○「植物の有用物質生産に関与する膜酵素複合体のコア構造と膜上ダイナミクスの解明」(2021-2023) 
○「反応中間体の構造解析によるマルチ銅オキシダーゼの酸素還元機構の解明と応用」(2018-2020) 
○「ゴマ搾り粕から高効率な有用物質生産を可能にする新規酵素の分子解析と応用」(2015-2017) 

Competitive research funding,Contribution

Collaborative research,Consignment study

Classes (Bachelors)

○Experiments in Fundamental Chemistry(2021)
○Experiments in Basic Chemistry C(2021)
○Introduction of Chemistry B(2021)
○Experiments in Basic Chemistry A(2020)
○Experiments in Basic Chemistry C(2017)
○Biochemistry II(2017)
○Experiments in Basic Chemistry C(2016)
○Biochemistry II(2016)

Classes (Graduate Schools)

○Seminar in Material Creation(2021)
○Molecular Enzyme Chemistry(2021)
○Biochemistry for Education(2021)
○Material Creation Chemistry IV(2021)
○Functions of Proteins(2021)
○Functions of Proteins(2017)
○Functions of Proteins(2017)
○Functions of Proteins(2017)
○Functions of Proteins(2017)
○Material Creation Chemistry IV(2017)
○Seminar in Material Creation(2017)
○Molecular Enzyme Chemistry(2017)
○Seminar in Material Creation(2017)
○Seminar in Material Creation(2016)
○Functions of Proteins(2016)
○Seminar in Material Creation(2016)
○Material Creation Chemistry IV(2016)
○Molecular Enzyme Chemistry(2016)

International Project

International Students

Lecture themes

Others (Social Activities)

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