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Komori Hirofumi

  • Faculty of Education
  • Teacher Training Courses
  • Graduate School of Science for Creative Emergence
  • Division of Science for Creative Emergence
  • Professor
Last Updated :2025/04/24

Researcher Information

J-Global ID

Research Interests

  • 構造生物学   タンパク質結晶学   Structural biology   Protein crystallography   

Research Areas

  • Life sciences / Structural biochemistry

Academic & Professional Experience

  • 2021/04 - Today  Kagawa UniversityFaculty of Education教授
  • 2017 - Today  Kagawa Prefectural College of Health Sciences
  • 2014/04 - 2021/03  Kagawa UniversityFaculty of Education准教授
  • 2004 - 2016  理化学研究所, 客員研究員
  • 2013 - 2014  Kagawa UniversityFaculty of Education
  • 2004 - 2013  University of Hyogo
  • 2012  - 大阪大学蛋白質研究所, 共同研究員
  • 2002 - 2004  スタンフォード大学, ヒューマン・フロンティア・サイエンス・プログラム博士研究員
  • 2004  University of Hyogo
  • 1999 - 2002  日本学術振興会, 特別研究員

Education

  •        - 2002  Kyoto University  Graduate School, Division of Natural Science
  •        - 2002  Kyoto University  理学研究科
  •        - 1997  Kyoto University  Faculty of Science

Association Memberships

  • 日本化学会   日本生物高分子学会   日本蛋白質科学会   日本結晶学会   日本生化学会   

Published Papers

Conference Activities & Talks

  • Conversion of a Monomeric Protein into a Domain-swapped Dimer by Utilizing a Tight Hydrogen Bond Network at the Hinge Region for Myoglobin  [Not invited]
    Cheng Xie; Hiromitsu Shimoyama; Masaru Yamanaka; Satoshi Nagao; Hirofumi Komori; Naoki Shibata; Yoshiki Higuchi; Yasuteru Shigeta; Shun Hirota
    10th Asian Biological Inorganic Chemistry Conference  2022/11
  • ヒスタミン合成酵素Y334変異体の構造解析  [Not invited]
    小森博文; 新田陽子
    生化学会2022年度大会  2022/11
  • Construction and structural characterization of a unique dimer of ferredoxin from Thermotoga maritima
    Nur Afiqah; BINTI AZMI; Tsuyoshi MASHIMA; Hideaki OGATA; Hirofumi KOMORI; Tomoshige ANDO; Masaru YAMANAKA; Shun HIROTA
    日本化学会第102春季年会（2022)  2022/03
  • Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge region  [Not invited]
    Cheng Xie; Hiromitsu Shimoyama; Masaru Yamanaka; Satoshi Nagao; Hirofumi Komori; Naoki Shibata; Yoshiki Higuchi; Yasuteru Shigeta; Shun Hirota
    日本化学会第102春季年会（2022)  2022/03
  • ヒスタミン生成酵素の1アミノ酸置換による触媒能変換について  [Not invited]
    竹島 大貴; 小森 博文; 植野 洋志; 新田 陽子
    日本ヒスタミン学会  2022/01
  • エラジタンニンによるヒスチジンデカルボキシラーゼ活性阻害機構の検討  [Not invited]
    竹島 大貴; 菊崎 泰枝; 伊東 秀之; 小森 博文; 植野 洋志; 新田 陽子
    日本ビタミン学会  2021/06

MISC

  • ヒスタミン合成酵素変異体の過酸化水素生成
    竹島大貴; 小森博文; 植野洋志; 新田陽子  生物高分子  18-  (2)  37  2018/09
  • ヒスタミン合成酵素とヒスタミンアナログ阻害剤の構造解析
    松村瑶子; 西田理央; JIMENEZ Francisca Sanchez; 新田陽子; 小森博文  生物高分子  17-  (2)  34  2017/09
  • イチゴ品種‘桃薫’のヒスチジンデカルボキシラーゼ活性阻害物質の単離と同定
    森美幸; 菊崎泰枝; 山下慶子; 宇野雄一; 野口裕司; 小森博文; 植野洋志; 新田陽子  生物高分子  17-  (2)  35  2017/09
  • アミノオキシメチルイミダゾールによるヒスタミン合成酵素の阻害機構
    西田理央; 松村瑶子; JIMENEZ Francisca; 新田陽子; 小森博文  日本生化学会大会(Web)  90th-  ROMBUNNO.2LBA‐001 (WEB ONLY)  2017
  • イチゴ品種‘桃薫’のヒスチジン脱炭酸酵素の活性阻害
    森美幸; 菊崎泰枝; 宇野雄一; 野口裕司; 小森博文; 植野洋志; 新田陽子  生物高分子  16-  (1)  36  2016/09
  • ガロタンニン,エラジタンニンによるヒスチジン脱炭酸酵素の活性阻害の解析
    森美幸; 菊崎泰枝; 植野洋志; 小森博文; 新田陽子  ビタミン  90-  (4)  184  2016/04
  • 芳香族アミノ酸脱炭酸酵素の基質認識
    新田陽子; 小森博文; 小森博文; 植野洋志  生物高分子  15-  (1)  75  2015/09
  • A critical examination of recent science textbooks for Japanese elementary school with focus on practical works
    笠 潤平; 礒田 誠; 高橋 尚志; 青木 高明; 大浦みゆき; 佐々木 信行; 高木 由美子; 小森 博文; 高橋智香; 松本 一範; 篠原 渉; 稗田美嘉; 松村雅文; 寺尾 徹; 北林 雅洋  Memoirs of the Faculty of Education, Kagawa University  65-  (2)  53-66  -66  2015/09
  • Change in structure and ligand binding properties of hyperstable cytochrome c555 from Aquifex aeolicus by domain swapping
    Yamanaka Masaru; Nagao Satoshi; Komori Hirofumi; Higuchi Yoshiki; Hirota Shun  2015/03
  • ヒスタミン合成酵素のX線結晶構造解析
    小森博文; 新田陽子; 植野洋志; 樋口芳樹  生物高分子  14-  (2)  116  2014/09
  • 中学校理科の新教科書の研究： 理科教員養成をめぐる新しい課題の明確化
    松村 雅文; 寺尾 徹; 礒田 誠; 高橋 尚志; 青木 高明; 大浦みゆき; 佐々木 信行; 高木 由美子; 小森 博文; 高橋智香; 松本 一範; 篠原 渉; 稗田美嘉; 北林 雅洋; 笠 潤平  香川大学教育学部研究報告第Ⅱ部  64-  (1)  5  2014/03
  • ヒスチジン脱炭酸反応における触媒ループの役割
    小森博文; 新田陽子; 植野洋志; 樋口芳樹  日本生化学会大会(Web)  87th-  2P-194 (WEB ONLY)  2014
  • ヒスタミン合成酵素の構造解析
    小森博文; 新田陽子; 植野洋志; 樋口芳樹  日本結晶学会年会講演要旨集  2013-  29  2013/10
  • αフルオロメチルヒスチジンによるヒスタミン合成酵素の阻害機構の解明
    小森博文; 新田陽子; 植野洋志; 樋口芳樹  日本生化学会大会(Web)  86th-  2T18A-03(2P-122) (WEB ONLY)  2013
  • ヒト由来ヒスチジンデカルボキシラーゼの基質特異性と触媒機構の研究
    新田陽子; 小森博文; 樋口芳樹; 植野洋志  生物高分子  12-  (2)  66  2012/09
  • ヒト由来ヒスチジン脱炭酸酵素の構造解析
    小森博文; 新田陽子; 植野洋志; 樋口芳樹  日本生化学会大会(Web)  85th-  3P-289 (WEB ONLY)  2012
  • Nagao Satoshi; Kataoka Mikio; Higuchi Yoshiki; Hirota Shun; Hattori Yoko; Ueda Mariko; Taketa Midori; Osuka Hisao; Komori Hirofumi; Kamikubo Hironari; Negi Shigeru; Sugiura Yukio  Seibutsu Butsuri  51-  (0)  S22  -S23  2011
  • 酸化型ウマシトクロムcの多量体構造とポリマー化機構
    廣田俊; 服部洋子; 長尾聡; 竹田翠; 小森博文; 上久保裕生; 根木滋; 杉浦幸雄; 片岡幹雄; 樋口芳樹  生体分子科学討論会講演要旨集  37th-  2010
  • Hirota Shun; Sugiura Yukio; Kataoka Mikio; Higuchi Yoshiki; Hattori Yoko; Nagao Satoshi; Taketa Midori; Komori Hirofumi; Kamikubo Hironari; Wang Zhonghua; Takahashi Isao; Negi Shigeru  Seibutsu Butsuri  50-  (2)  S149  2010
  • メタゲノム由来ラッカーゼのX線結晶構造解析
    小森博文; 宮崎健太郎; 樋口芳樹  生体分子科学討論会講演要旨集  36th-  16-17  2009/06
  • メタゲノム由来ラッカーゼの結晶構造
    小森博文; 小森博文; 宮崎健太郎; 樋口芳樹; 樋口芳樹  日本結晶学会年会講演要旨集  2009-  106  2009
  • II X-ray Structural Biology of Proteins Functioning Brain and Neuron(Molecular Biophysics I,Graduate School of Life Science)
    Shomura Y.; Komori H.; Shibata N.; Higuchi Y.  Annual review, Graduate School of Material Science and Graduate School of Life Science, University of Hyogo  18-  112  -112  2006/04
  • I X-ray Structural Chemistry of Proteins in Metabolic Systems(Molecular Biophysics I,Graduate School of Life Science)
    Shomura Y.; Komori H.; Shibata N.; Higuchi Y.  Annual review, Graduate School of Material Science and Graduate School of Life Science, University of Hyogo  18-  112  -112  2006/04
  • X-ray Structural Biology of Proteins Functioning in Brain and Neuron(Molecular Biophysics I)
    Komori H.; Shibata N.; Higuchi Y.  Annual review, Graduate School of Material Science and Graduate School of Life Science, University of Hyogo  16-  113  -113  2005/10
  • X-ray Structural Chemistry of Proteins in Metabolic Systems(Molecular Biophysics I)
    Komori H.; Shibata N.; Higuchi Y.  Annual review, Graduate School of Material Science and Graduate School of Life Science, University of Hyogo  16-  113  -113  2005/10

Research Grants & Projects

  • Elucidation of the molecular mechanism of histidine decarboxylase
    Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
    Date (from‐to) : 2016/04 -2020/03 
    Author : Komori Hirofumi
     
    We have processed the X-ray diffraction data and determined the crystal structure of human histidine decarboxylase (HDC) in complex with a novel inhibitor, aminooxy analog of histamine. By comparing it with the HDC complex with histidine methyl ester, we confirmed that the tyrosine (Y334) existing on the catalytic loop plays an important role in decarboxylation reaction. The Y334F mutant were crystallized under the same crystallization conditions used for wild type HDC-inhibitor complex. By soaking the substrate histidine into the crystal of Y334F mutant, the structure of the reaction intermediate has been determined. Furthermore, by comparing with the structures of vitamin B6 dependent enzymes, we suggest that the corresponding tyrosine residue of all decarboxylases has a common catalytic function.
  • Study on Dioxygen Reduction Mechanism by Multicopper Oxidases and Application of Function Modulated Mutants as Electrode Catalyst
    Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2014/04 -2017/03 
    Author : Sakurai Takeshi; KOMORI Hirofumi; TSUJIMURA Seiya; IDA Tomonori
     
    Studies on the three-domain multicopper oxidases such as CueO and bilirubin oxidase by the mutations at the type I copper ligand and/or the acidic amino acid located in the proton transport pathway revealed that the four-electron reduction of dioxygen proceeds according to a common reaction pathway. Amino acids located in the outer-sphere of the trinuclear copper center were found not to play a role as the fourth electron donor. From the finding that an acetate ion from buffer solution was bound to type II copper, it was found that this exogenous anion reaches deep inside protein molecule and enhances enzymatic activities. Further, we performed crystallization of CueO in heavy water for neutral diffraction to reveal the reaction mechanism. We also succeeded in enhancing enzymatic activities by performing mutations at the amino acids located in the outer-coordination spheres of type I copper and obtained excellent electrochemical responses suitable as cathodic enzyme for biofuel cell.
  • Structural analysis of transcription factor TFIIH subcomplex
    Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)
    Date (from‐to) : 2010/04 -2014/03 
    Author : KOMORI Hirofumi
     
    The purpose of this study is to determine the three-dimensional structures of transcription factors by X-ray crystallographic analysis, in order to understand the molecular mechanism of the DNA transcriptional regulation with RNA polymerase II. Transcription factors function as a complex of various kinds of proteins. To prepare the sample suitable for crystallization, the purification of the significant protein complex involved in transcriptional regulation was performed by using a co-expression system of E. coli and insect cells.
  • Structural analysis of CO-sensing transcription factor
    Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)
    Date (from‐to) : 2006 -2008 
    Author : KOMORI Hirofumi
     
    生物は環境に適応するために外界のシグナルを受容し,生体内へ伝達する仕組みを持っている.一酸化炭素(CO)以外の気体分子のシグナルセンサーとして働くタンパク質も多数発見されているが,CooAタンパク質はその分子中にヘムを含むとてもユニークな転写制御因子であり,ヘムタンパク質としても全く新規なものである.本研究は、COによる転写制御のメカニズムを明らかにすることを目的として、嫌気性微生物C.hydrogenoformans由来CooAタンパク質の構造解析を行った。CooAタンパク質は、C末端にhis-tagの付いた組換えタンパク質として発現、精製し、ポリエチレングリコールを沈殿剤として用いた条件で結晶化に成功した。ヘム鉄の異常分散を利用してSAD法による位相決定を行い、最終的に2.2A分解能で結晶構造を決定した。明らかとなった不活性型CooAの結晶構造と同じ転写制御因子ファミリーに属する活性型CRPの結晶構造を比較した結果、活性化によってDNA結合ドメインが大きく構造変化をすることが示唆された。
  • Activation mechanism of the Active Site of [NiFe] hydrogenas
    Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Priority Areas
    Date (from‐to) : 2004 -2007 
    Author : HIGUCHI Yoshiki
     
    [NiFe] hydrogenase is composed of two subunits and has a Ni-Fe active site in the large subunit. Ni is coordinated by four cysteine sulfurs (two of them form a bridge between Fe and Ni). Fe has additional non-protein diatomic ligands, and a third bridge in the oxidized form. The as-purified (inactive-oxidized), Ni-C (active-reduced) and CO-inhibited forms of the [NiFe] hydrogenase from D. v. Miyazaki F were already reported. Recently, it was found that the oxidized form is a mixture of Ni-A and Ni-B, and the enzyme is activated from Ni-A to Ni-C through Ni-B. 1. In this project, we have discovered the protocol to prepare pure Ni-A from Ni-B by using 50 mM Na_2S and exposure to O_2, and elucidated the crystal structures of Ni-A and Ni-B. We found that Ni-B has a monatomic non-protein bridging ligand (X_), whereas the Ni-A has a diatomic species (X_-X_). In addition, the sulfurs of cysteines are found to have a modified atomic species (X_<546>) in both Ni-A and Ni-B. 2. In order to clarify the activation mechanism of H_2 at the active site, we have succeeded in preparing the large single crystal (1.0 mm^3) of the enzyme in D_2O solution. Neutron diffraction experiments showed that- the crystal diffract about 10 A. The crystallization condition for the larger crystals is being improved. 3. The Ni-Fe active site is matured by a series of the proteins coded in the hyp operon. HypE is involved in the biosynthesis of CN which is coordinated to Fe. We determined the crystal structures of HypE in the absence and presence of ATP at 2.0 and 2.6 A resolution, respectively. Comparison of the structures reveals that the binding of ATP does not entail an overall structural change. The residue Cys341 at the C-terminus, whose thiol group is supposed to be carbamoylated prior to the nitrile group synthesis, is completely buried within the protein, and is located in the vicinity of the ・-phosphate group of the bound ATP. The obtained structure suggests that the catalytic reaction occurs in this configuration but that a conformational change is required for the carbamoylation of Cys341. 4. CooA is a transcription factor, and is responsible for the expression of CO-tolerant hydrogenases in some bacteria. We have determined the crystal structure of an imidazole (Im)-bound CooA from C. hydrogenoformans (Ch-CooA) at 2.2 A. The structure of Ch-CooA reveals that Im binds to the heme Fe, and replaces the N-terminus, as does CO. Even though the ligand exchange, Im-bound Ch-CooA remains in the inactive form. These results indicate that the release of the N-terminus resulting from Im-binding is not sufficient to activate CooA. The structure provides new insights into the structural changes required to achieve activation.
  • X線結晶構造に基づくDNA複製開始の分子機構に関する研究
    日本学術振興会：科学研究費助成事業 特別研究員奨励費
    Date (from‐to) : 1999 -2001 
    Author : 小森 博文

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