Koji Nagata

Profile Information

Affiliation: Professor, Graduate School of Agricultural and Life SciencesApplied Biological Chemistry, The University of Tokyo

Degree: Ph.D. (Agriculture)(The University of Tokyo)

Researcher number: 30280788
ORCID ID: https://orcid.org/0000-0002-4704-0603
J-GLOBAL ID: 200901040510243820
researchmap Member ID: 1000229485

External link: https://park-ssl.itc.u-tokyo.ac.jp/fbsb/

Research Interests

Research Areas

Research History

Apr, 2020 - Present

Graduate School of Agricultural and Life Sciences Applied Biological Chemistry, The University of Tokyo
Apr, 2007 - Mar, 2020

Graduate School of Agricultural and Life Sciences Applied Biological Chemistry, The University of Tokyo
Dec, 2005 - Mar, 2007

Graduate School of Agricultural and Life Sciences Applied Biological Chemistry, The University of Tokyo
Oct, 2002 - Dec, 2005

Graduate School of Agricultural and Life Sciences Applied Biological Chemistry, The University of Tokyo
Apr, 1997 - Sep, 2002

Biotechnology Research Center, The University of Tokyo
Oct, 2000 - Mar, 2002

Research Associate, Imperial College London
Apr, 2000 - Mar, 2002

Overseas Research Fellow, Japan Society for the Promotion of Science
Apr, 2000 - Sep, 2000

Postdoctoral Fellow, Uppsala University
Apr, 1997 - Mar, 1998

非常勤研究員, 東京都臨床医学総合研究所
Apr, 1995 - Mar, 1997

東京都臨床医学総合研究所研究員
1993 - 1995

日本学術振興会特別研究員DC2

Awards

Jul, 2021

日本生化学会 2021年(第29回）JB論文賞, Crystal structure of the complex of the interaction domains of Escherichia coli DnaB helicase and DnaC helicase loader: structural basis implying a distortion-accumulation mechanism for the DnaB ring opening caused by DnaC binding

Koji Nagata, Akitoshi Okada, Jun Ohtsuka, Takatoshi Ohkuri, Yusuke Akama, Yukari Sakiyama, Erika Miyazaki, Shoichiro Horita, Tsutomu Katayama, Tadashi Ueda, Masaru Tanokura
Mar, 2007

2007年農芸化学奨励賞, 発生・分化に関わるペプチド・タンパク質の立体構造解析と構造・機能相関
1999

日本ペプチド学会平成11年度奨励賞, カイコのインスリン族ペプチド、ボンビキシン-IIの立体構造と受容体認識部位
1998

井上科学振興財団第14回（平成 9年度）井上研究奨励賞, カイコのインスリン族ペプチド、ボンビキシン-IIの立体構造と受容体認識部位

Papers

171

Structural model for ligand binding and channel opening of an insect gustatory receptor

Satoshi Morinaga, Koji Nagata, Sayoko Ihara, Tomohiro Yumita, Yoshihito Niimura, Koji Sato, Kazushige Touhara

Journal of Biological Chemistry, Oct, 2022
Lactic acid bacteria-derived γ-linolenic acid metabolites are PPARδ ligands that reduce lipid accumulation in human intestinal organoids.

Makoto Noguchi, Makoto Shimizu, Peng Lu, Yu Takahashi, Yoshio Yamauchi, Shintaro Sato, Hiroshi Kiyono, Shigenobu Kishino, Jun Ogawa, Koji Nagata, Ryuichiro Sato

Journal of Biological Chemistry, 102534-102534, Sep, 2022
Analysis of Purine Metabolism to Elucidate the Pathogenesis of Acute Kidney Injury in Renal Hypouricemia

Miyamoto, D., Sato, N., Nagata, K., Sakai, Y., Sugihara, H., Ohashi, Y., Stiburkova, B., Sebesta, I., Ichida, K., Okamoto, K.

Biomedicines, 10(7), 2022
Adsorption kinetics and thermodynamics of toxic metal ions onto chitosan nanoparticles extracted from shrimp shells

Abomosallam, M., Elalfy, M., Zheng, Z., Nagata, K., Suzuki, M.

Nanotechnology for Environmental Engineering, 7(1), 2022
NMR and HPLC profiling of bee pollen products from different countries

Lu, P., Takiguchi, S., Honda, Y., Lu, Y., Mitsui, T., Kato, S., Kodera, R., Furihata, K., Zhang, M., Okamoto, K., Itoh, H., Suzuki, M., Kono, H., Nagata, K.

Food Chemistry: Molecular Sciences, 5, 2022
Rosmarinic Acid and Sodium Citrate Have a Synergistic Bacteriostatic Effect against Vibrio Species by Inhibiting Iron Uptake.

Peng Lu, Miaomiao Sui, Mimin Zhang, Mengyao Wang, Takehiro Kamiya, Ken Okamoto, Hideaki Itoh, Suguru Okuda, Michio Suzuki, Tomiko Asakura, Toru Fujiwara, Koji Nagata

International journal of molecular sciences, 22(23), Dec 1, 2021
A glutamine sensor that directly activates TORC1

Mirai Tanigawa, Katsuyoshi Yamamoto, Satoru Nagatoishi, Koji Nagata, Daisuke Noshiro, Nobuo N. Noda, Kouhei Tsumoto, Tatsuya Maeda

Communications Biology, 4(1), Dec, 2021
Quercetin 3,5,7,3′,4′-pentamethyl ether from Kaempferia parviflora directly and effectively activates human SIRT1

Mimin Zhang, Peng Lu, Tohru Terada, Miaomiao Sui, Haruka Furuta, Kilico Iida, Yukie Katayama, Yi Lu, Ken Okamoto, Michio Suzuki, Tomiko Asakura, Kentaro Shimizu, Fumihiko Hakuno, Shin-Ichiro Takahashi, Norimoto Shimada, Jinwei Yang, Tsutomu Ishikawa, Jin Tatsuzaki, Koji Nagata

Communications Biology, 4(1), Dec, 2021
Fermented food Tempeh induces interleukin 12 and enhances macrophage phagocytosis.

Yoshihito Hosaka, Kei Itoh, Shun Matsutani, Shinya Kawate, Atsuko Miura, Yukaze Mizoura, Sayumi Yamada, Hiroshi Konno, Ewa Grave, Koji Nagata, Hideki Wakui, Hideaki Itoh

Journal of food biochemistry, 45(11) e13958, Nov, 2021
Oxidative deamination of lysine residues by polyphenols generates an equilibrium of aldehyde and 2-piperidinol products.

Kosuke Yamaguchi, Masanori Itakura, Roma Kitazawa, Sei-Young Lim, Koji Nagata, Takahiro Shibata, Mitsugu Akagawa, Koji Uchida

The Journal of Biological Chemistry, 297(3) 101035-101035, Jul 31, 2021
Functional analyses of chitinolytic enzymes in the formation of calcite prisms in Pinctada fucata.

Hiroyuki Kintsu, Alberto Pérez-Huerta, Shigeru Ohtsuka, Taiga Okumura, Shinsuke Ifuku, Koji Nagata, Toshihiro Kogure, Michio Suzuki

Micron (Oxford, England : 1993), 145 103063-103063, Jun, 2021
Identification and functional analysis of cadmium-binding protein in the visceral mass of Crassostrea gigas.

Zehua Zheng, Kazuhiro Kawakami, Dingkun Zhang, Lumi Negishi, Mohamed Abomosallam, Tomiko Asakura, Koji Nagata, Michio Suzuki

Scientific reports, 11(1) 11306-11306, May 28, 2021
Gut microbiome of indonesian adults associated with obesity and type 2 diabetes: A cross-sectional study in an asian city, yogyakarta

Phatthanaphong Therdtatha, Yayi Song, Masaru Tanaka, Mariyatun Mariyatun, Maisaroh Almunifah, Nancy Eka Putri Manurung, Siska Indriarsih, Yi Lu, Koji Nagata, Katsuya Fukami, Tetsuo Ikeda, Yuan Kun Lee, Endang Sutriswati Rahayu, Jiro Nakayama

Microorganisms, 9(5), May, 2021
Application of 2,2′-dipyridyl disulfide-mediated thiazolidine ring-opening reaction to glycoprotein synthesis: Total chemical synthesis of evasin-3

Hidekazu Katayama, Koji Nagata

Journal of Peptide Science, 27(2), Feb, 2021
Purification, crystallization and X-ray analysis of Pf-SCP (sarcoplasmic Ca-binding protein), related to storage and transport of calcium in mantle of Pinctada fucata

Lingxiao Zhu, Liying Wang, Akihiro Matsuura, Mimin Zhang, Peng Lu, Kurin Iimura, Koji Nagata, Michio Suzuki

Protein Expression and Purification, 178 105781-105781, Feb, 2021
Mechanism of self/nonself-discrimination in Brassica self-incompatibility

Kohji Murase, Yoshitaka Moriwaki, Tomoyuki Mori, Xiao Liu, Chiho Masaka, Yoshinobu Takada, Ryoko Maesaki, Masaki Mishima, Sota Fujii, Yoshinori Hirano, Zen Kawabe, Koji Nagata, Tohru Terada, Go Suzuki, Masao Watanabe, Kentaro Shimizu, Toshio Hakoshima, Seiji Takayama

Nature Communications, 11(1), Dec, 2020
Identification of methionine -rich insoluble proteins in the shell of the pearl oyster, Pinctada fucata.

Hiroyuki Kintsu, Ryo Nishimura, Lumi Negishi, Isao Kuriyama, Yasushi Tsuchihashi, Lingxiao Zhu, Koji Nagata, Michio Suzuki

Scientific reports, 10(1) 18335-18335, Oct 27, 2020
Characterization of the chalky layer-derived EGF-like domain-containing protein (CgELC) in the pacific oyster, Crassostrea gigas.

Shihori Iwamoto, Keisuke Shimizu, Lumi Negishi, Nobuo Suzuki, Koji Nagata, Michio Suzuki

Journal of structural biology, 212(1) 107594-107594, Oct 1, 2020
Crystal structure of the complex of the interaction domains of E. coli DnaB helicase and DnaC helicase loader: Structural basis implying a distortion-accumulation mechanism for the DnaB ring opening caused by DnaC binding.

Nagata K, Okada A, Ohtsuka J, Ohkuri T, Akama Y, Sakiyama Y, Miyazaki E, Horita S, Katayama T, Ueda T, Tanokura M

J. Biochem., 167, Feb, 2020 Peer-reviewed
Modified forearm ischemic test in hypouricemic patients.

Ivan Sebesta, Daisuke Miyamoto, Blanka Stiburkova, Sarka Blahova, Nana Sato, Koji Nagata, Ken Okamoto, Shuichi Tsuruoka, Kimiyoshi Ichida

Nucleosides, nucleotides & nucleic acids, 39(10-12) 1432-1439, 2020

Misc.

119

Identification and mechanism analysis of a plant peptide that inhibits the growth of Porphyromonas gingivalis

小澤友弥, ZHANG Mimin, LU Peng, 岡本研, 伊藤英晃, 鈴木道生, 花田耕介, 柘植尚志, 中曽根光, 米倉円佳, 永田宏次

日本農芸化学会大会講演要旨集(Web), 2021, 2021
カキ(Crassostrea gigas)軟体部におけるカドミウム結合タンパク質の同定と機能解析

鄭澤華, 川上和宏, 根岸瑠美, 朝倉富子, 永田宏次, 鈴木道生

マリンバイオテクノロジー学会大会講演要旨集, 21st, 2021
Structural and functional analyses of ACC binding protein in the shell of Pinctada fucata

岩橋晴香, 荒城綾香, 根岸瑠美, 降旗一夫, 永田宏次, 鈴木道生

日本農芸化学会大会講演要旨集(Web), 2020, 2020
黒生姜由来フラボノイドKPMF-8によるSIRT1活性化機構解析

張迷敏, 陸鵬, 隋苗苗, 飯田季里子, 片山幸江, 鈴木道生, 楊金緯, 石川勉, 立崎仁, 永田宏次

植物化学シンポジウム, 56th (CD-ROM), 2019
ダイズ由来ペプチド,ルナシンの抗がん作用機構の解析

飯田季里子, 鈴木友璃葉, ZHANG Mimin, 片山幸江, LU Yi, 岡本研, 鈴木道生, 名倉敬仁, 西宏起, 伯野史彦, 片岡直行, 高橋伸一郎, 川上浩, 永田宏次

日本農芸化学会大会講演要旨集(Web), 2019, 2019
エチレン受容体の全長とリガンド結合領域の組換えタンパク質の発現

長谷川恵一, LU Peng, 高橋郁夫, 片山幸江, LU Yi, 岡本研, 鈴木道生, 中村英光, 中嶋正敏, 浅見忠男, 永田宏次

日本農芸化学会大会講演要旨集(Web), 2019, 2019
アコヤガイ貝殻内のACC結合タンパク質の構造・機能解析

岩橋晴香, 荒城綾香, 永田宏次, 根岸瑠美, 降旗一夫, 鈴木道生

日本農芸化学会大会講演要旨集(Web), 2019, 2019
共役ポリケトン還元酵素の基質特異性の構造基盤

宮川拓也, 秦慧民, 山村昭裕, 片岡道彦, 片岡道彦, 永井貴大, 北村苗穂子, 浦野信行, 浦野信行, 丸岡慎太郎, 大塚淳, 永田宏次, 清水昌, 田之倉優

バイオイメージング, 22(2), 2013
水酸化アミノ酸の立体選択的合成に有用なアルドラーゼ(asHPAL)-第一基質複合体の結晶構造決定と変異導入による反応機構解析

GUO Linjun, 岡井公彦, 間瀬朋子, IMAI Fabiana Lica, 永田宏次, 日比慎, 宮川拓也, 小川順, 田之倉優

日本農芸化学会大会講演要旨集(Web), 2013, 2013
水酸化アミノ酸の合成に有用なアルドラーゼ(asHPAL)の基質特異性に関する分子機構の解明

GUO Linjun, 岡井公彦, 間瀬朋子, IMAI FABIANA Lica, 永田宏次, 日比慎, 宮川拓也, 小川順, 田之倉優

日本蛋白質科学会年会プログラム・要旨集, 13th, 2013
構造生物学を利用した機能未知タンパク質の機能解明

石橋純, 逸見光, 永田宏次, 田之倉優

蚕糸・昆虫バイオテック = Sanshi-konchu biotec, 81(2) 125-129, Aug 1, 2012
日本農芸化学会大会

野田陽一, 新井博之, 井上順, 森直紀, 永田晋治, 伏信進矢, 加藤久典, 中嶋正敏, 野尻秀昭, 永田宏次

バイオサイエンスとインダストリー = Bioscience & industry, 70(4) 285-293, Jul 1, 2012
B320 NMR solution structure of an insecticidal toxin LaIT 1 from the venom of scorpion Liocheles australasiae

Miyashita Masahiro, Horita Shoichiro, Miyakawa Takuya, Nakagawa Yoshiaki, Nagata Koji, Tanokura Masaru, Miyagawa Hisashi

(37) 135-135, Mar 14, 2012
Identification of the Amino-Acid Residues Important for the Recognition of Silkmoth Pheromone Biosynthesis-Activating Neuropeptide by Its Receptor

NAGATA Koji, KAWAI Takeshi, EBISAWA Tatsuki, HAYAKAWA Kou, LEE Jae Min, HULL J. Joe, MATSUMOTO Shogo, NAGASAWA Hiromichi, TANOKURA Masaru

2011 181-182, Mar 1, 2012
Structure-Activity Relationship Study of the C-Terminal Part of Pheromone Biosynthesis-Activating Neuropeptide

KAWAI Takeshi, LEE Jae Min, NAGATA Koji, HULL J. Joe, MATSUMOTO Shogo, TANOKURA Masaru, NAGASAWA Hiromichi

2011 175-178, Mar 1, 2012
Solution Structure and Functional Residues of a Short-Chain Insecticidal Toxin LaIT1 from the Venom of Scorpion Liocheles australasiae

MIYASHITA Masahiro, HORITA Shoichiro, MIYAKAWA Takuya, NAKAGAWA Yoshiaki, NAGATA Koji, MIYAGAWA Hisashi, TANOKURA Masaru

2011 169-170, Mar 1, 2012
Agrobacterium tumefaciens由来キヌクリジノン還元酵素の高活性に関する構造基盤

HOU Feng, 宮川拓也, 片岡道彦, 片岡道彦, 熊代祥子, 竹下大二郎, 永田宏次, 清水昌, 清水昌, 田之倉優

日本農芸化学会大会講演要旨集(Web), 2012, 2012
腸球菌のクオラムセンシング阻害剤ZBzl-YAA5911の創製とその抗感染症剤としての効果検証

中山二郎, 横畑綾治, 松藤貴久, 鈴木崇, 永田宏次, 園元謙二

日本分子生物学会年会プログラム・要旨集(Web), 35th, 2012
Structure-activity relationship studies of the pheromone biosynthesis activating neuropeptide of the silkmoth, Bombyx mori

KAWAI Takeshi, NAGATA Koji, OKADA Akitoshi, HAYAKAWA Koh, HULL J. Joe, LEE Jae Min, MATSUMOTO Shogo, TANOKURA Masaru, NAGASAWA Hiromichi

2010 126-126, Mar 1, 2011
Structure-based Functional Characterization of Oryctin, a Hemolymph Protein from the Coconut Rhinoceros Beetle, Oryctes Rhinoceros, As a Novel Serine Protease Inhibitor

HORITA Shoichiro, ISHIBASHI Jun, NAGATA Koji, MIYAKAWA Takuya, YAMAKAWA Minoru, TANOKURA Masaru

2010 142-142, Mar 1, 2011

Books and Other Publications

ミクロの世界を可視化する in 科学の技法東京大学「初年次ゼミナール理科」テキスト (東京大学教養教育高度化機構初年次教育部門, 増田建, 坂口菊恵編)

永田宏次, 木下滋晴 (Role: Contributor, pp. 126-129,)

東京大学出版会 (東京), 2017
溶液構造解析法 in 21世紀のバイオサイエンス実験農芸化学 (東京大学大学院農学生命科学研究科応用生命化学専攻・応用生命工学専攻編)

永田宏次, 宮川拓也 (Role: Contributor, pp. 150-151,)

朝倉書店 (東京)., 2013
ゲル濾過クロマトグラフィー in 21世紀のバイオサイエンス実験農芸化学 (東京大学大学院農学生命科学研究科応用生命化学専攻・応用生命工学専攻編),

永田宏次 (Role: Contributor, pp. 136-138,)

朝倉書店 (東京)., 2013
タンパク質試料の定量, 純度検定, 一次構造確認 in タンパク質の結晶化－回折構造生物学のために (坂部知平監修，相原茂夫編著)

永田宏次, 田之倉優 (Role: Joint author, pp. 58-68,)

京都大学学術出版会 (京都), 2005
クロマトグラフィーによる試料の分離精製 in タンパク質の結晶化－回折構造生物学のために (坂部知平監修，相原茂夫編著)

永田宏次, 田之倉優 (Role: Joint author, pp. 51-58,)

京都大学学術出版会 (京都)., 2005
タンパク質の発現 in ゲノミクス・プロテオミクスの新展開－生物情報の解析と応用－(今中忠行編)

永田宏次, 田之倉優 (Role: Joint author, pp. 534-538,)

エヌ・ティー・エス (東京), 2004
タンパク質工学 in 分子生物学 (田沼靖一編)

田之倉優, 永田宏次 (Role: Joint author, pp. 274-288,)

丸善(東京), 1999
X線およびNMRによる三次元構造解析 in 魚介類筋肉タンパク質－その構造と機能 (西田清義編)

田之倉優, 永田宏次, 佐々木宏 (Role: Joint author, pp. 38-45,)

恒星社厚生閣(東京), 1999
Three-dimensional structure and receptor-recognition site of bombyxin-II, an insulin-like brain-secretory peptide of the silkmoth Bombyx mori. (共著)

Molecular Mechanisms of Insect Metamorphosis and Diapause(Industrial Publishing & Consulting, Inc. , Tokyo), 1995

Professional Memberships

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Industrial Property Rights

特開P2008-137961A タンパク質結晶化方法.

株式会社テクノメデイカ, 発明者, 鳥居徹, アルハックムハマッドイムラン, ルブラッスルエリック, 山崎浩樹, 永田宏次, 田之倉優
特開WO2007/063898 タンパク質結晶化方法及び装置並びにタンパク質結晶化処理装置

株式会社テクノメデイカ, 発明者, 鳥居徹, アルハックムハマッドイムラン, ルブラッスルエリック, 山崎浩樹, 永田宏次, 田之倉優
特開2005-289898 平滑筋弛緩剤とその有効成分の抽出方法

小濱一弘, 田之倉優, 発明者, 小濱一弘, 中村彰男, 吉山伸司, 田之倉優, 永田宏次

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