シヨウムラ ヤスヒト庄村 康人准教授Yasuhito SHOMURA
■研究者基本情報
学歴
経歴
■研究活動情報
論文
- An ependymin-related blue carotenoprotein decorates marine blue sponge
Shinji Kawasaki; Takayuki Kaneko; Tomomi Asano; Takashi Maoka; Shinichi Takaichi; Yasuhito Shomura, 責任著者, ELSEVIER
Journal of Biological Chemistry, 2023年09月, ［査読有り］ - NAD+-reducing [NiFe]-hydrogenase
Y. Shomura; Y. Higuchi
Encyclopedia of Inorganic and Bioinorganic Chemistry, 2019年12月, ［査読有り］, ［招待有り］ - Complete Genome Sequence of a Moderately Thermophilic Facultative Chemolithoautotrophic Hydrogen-Oxidizing Bacterium, Hydrogenophilus thermoluteolus TH-1
Arai H; Shomura Y; Higuchi Y; Ishii M
Microbiol. Resour. Announc., 2018年, ［査読有り］ - Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2
Noor N.D.M; Matsuura H; Nishikawa K; Tai H; Hirota S; Kim J; Kang J; Tateno M; Yoon K-S; Ogo S; Kubota S; Shomura Y; Higuchi Y,
, Royal Society of Chemistry (RSC)
Citrobacter sp. S-77 [NiFe]-hydrogenase harbors a standard [4Fe–4S] cluster proximal to the Ni–Fe active site.
Chem. Commun., 2018年, ［査読有り］ - Rational Design of Domain-Swapping-Based c-Type Cytochrome Heterodimers by Using Chimeric Proteins
Mohan Zhang; Tsukasa Nakanishi; Masaru Yamanaka; Satoshi Nagao; Sachiko Yanagisawa; Yasuhito Shomura; Naoki Shibata; Takashi Ogura; Yoshiki Higuchi; Shun Hirota, The design of protein oligomers with multiple active sites has been gaining interest, owing to their potential use for biomaterials, which has encouraged researchers to develop a new design method. Three-dimensional domain swapping is the unique phenomenon in which protein molecules exchange the same structural region between each other. Herein, to construct oligomeric heme proteins with different active sites by utilizing domain swapping, two c-type cytochrome-based chimeric proteins have been constructed and the domains swapped. According to X-ray crystallographic analysis, the two chimeric proteins formed a domain-swapped dimer with two His/Met coordinated hemes. By mutating the heme coordination structure of one of the two chimeric proteins, a domainswapped heterodimer with His/Met and His/H2O coordinated hemes was formed. Binding of an oxygen molecule to the His/H2O site of the heterodimer was confirmed by resonance Raman spectroscopy, in which the Fe-O-2 stretching band was observed at 580cm(-1) for the reduced/oxygenated heterodimer (at 554cm(-1) under an O-18(2) atmosphere). These results show that domain swapping is a useful method to design multiheme proteins., WILEY-V C H VERLAG GMBH
CHEMBIOCHEM, 2017年09月, ［査読有り］ - Structural basis of the redox switches in the NAD+-reducing soluble [NiFe]-hydrogenase
Shomura Y.; Taketa M.; Nakashima H.; Tai H.; Nakagawa H.; Ikeda Y.; Ishii M.; Igarashi Y.; Nishihara H.; Yoon K-S.; Ogo S.; Hirota S.; Higuchi Y., 筆頭著者, NAD(+) (oxidized form of NAD: nicotinamide adenine dinucleotide)-reducing soluble [ NiFe]hydrogenase (SH) is phylogenetically related to NADH (reduced form of NAD(+)): quinone oxidoreductase (complex I), but the geometrical arrangements of the subunits and Fe-S clusters are unclear. Here, we describe the crystal structures of SH in the oxidized and reduced states. The cluster arrangement is similar to that of complex I, but the subunits orientation is not, which supports the hypothesis that subunits evolved as prebuilt modules. The oxidized active site includes a six-coordinate Ni, which is unprecedented for hydrogenases, whose coordination geometry would prevent O-2 from approaching. In the reduced state showing the normal active site structure without a physiological electron acceptor, the flavin mononucleotide cofactor is dissociated, which may be caused by the oxidation state change of nearby Fe-S clusters and may suppress production of reactive oxygen species., AMER ASSOC ADVANCEMENT SCIENCE
Science, 2017年, ［査読有り］ - Construction of Zn-SO4 Cluster-encapsulating Protein Nanocage by Domain Swapping
Takaaki Miyamoto; Mai Kuribayashi; Satoshi Nagao; Yasuhito Shomura; Yoshiki Higuchi; Shun Hirota, WILEY-BLACKWELL
PROTEIN SCIENCE, 2016年10月, ［査読有り］ - Synthesis and Reactivity of a Water-soluble NiRu Monohydride Complex with a Tethered Pyridine Moiety
Takahiro Matsumoto; Koji Yoshimoto; Chunbai Zheng; Yasuhito Shomura; Yoshiki Higuchi; Hidetaka Nakai; Seiji Ogo, We report the synthesis, characterization, and reactivity of a NiRu monohydride complex with a pyridine-bound hexamethylbenzene ligand. We investigate the mechanistic insights it provides on the H-2-activation of [NiFe]hydrogenase., CHEMICAL SOC JAPAN
CHEMISTRY LETTERS, 2016年02月, ［査読有り］ - Formation of Cytochrome cb562 Oligomers by Domain Swapping
Miyamoto Takaaki; Kuribayashi Mai; Nagao Satoshi; Shomura Yasuhito; Higuchi Yoshiki; Hirota Shun
PROTEIN SCIENCE, 2015年10月, ［査読有り］ - Refined Regio- and Stereoselective Hydroxylation of L-Pipecolic Acid by Protein Engineering of L-Proline cis-4-Hydroxylase Based on the X-ray Crystal Structure
Kento Koketsu; Yasuhito Shomura; Kei Moriwaki; Mikiro Hayashi; Satoshi Mitsuhashi; Ryotaro Hara; Kuniki Kino; Yoshiki Higuchi, Enzymatic regio- and stereoselective hydroxylation are valuable for the production of hydroxylated chiral ingredients. Pro line hydroxylases are representative members of the nonheme Fe2+/alpha-ketoglutarate-dependent dioxygenase family. These enzymes catalyze the conversion of L-proline into hydroxy-L-prolines (Hyps). L-Proline cis-4-hydroxylases (cis-P4Hs) from Sinorhizobium rneliloti and Mesorhizobium loti catalyze the hydroxylation of L-proline, generating cis-4-hydroxy-L-proline, as well as the hydroxylation of L-pipecolic acid (L-Pip), generating two regioisomers, cis-5-Hypip and cis-3-Hypip. To selectively produce cis-5-Hypip without simultaneous production of two isomers, protein engineering of cis-P4Hs is required. We therefore carried out protein engineering of cis-P4H to facilitate the conversion of the majority of L-Pip into the cis-5-Hypip isomer. We first solved the X-ray crystal structure of cis-P4H in complex with each of L-Pro and L-Pip. Then, we conducted three rounds of directed evolution and successfully created a cis-P4H triple mutant, V97F/V95W/E114G, demonstrating the desired regioselectivity toward cis-5-Hypip., AMER CHEMICAL SOC
ACS Synthetic Biology, 2015年04月, ［査読有り］ - Rational Design of Heterodimeric Protein using Domain Swapping for Myoglobin
Lin Y.W.; Nagao S.; Zhang M.; Shomura Y.; Higuchi Y.; Hirota S., Protein design is a useful method to create novel artificial proteins. A rational approach to design a heterodimeric protein using domain swapping for horse myoglobin (Mb) was developed. As confirmed by X-ray crystallographic analysis, a heterodimeric Mb with two different active sites was produced efficiently from two surface mutants of Mb, in which the charges of two amino acids involved in the dimer salt bridges were reversed in each mutant individually, with the active site of one mutant modified. This study shows that the method of constructing heterodimeric Mb with domain swapping is useful for designing artificial multiheme proteins., Wiley Online Library
Angew. Chem. Int. Ed. Engl., 2015年, ［査読有り］ - Crystallization and preliminary X-ray analysis of the NAD(+)-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus TH-1
Midori Taketa; Hanae Nakagawa; Mao Habukawa; Hisao Osuka; Kiyohito Kihira; Hirofumi Komori; Naoki Shibata; Masaharu Ishii; Yasuo Igarashi; Hirofumi Nishihara; Ki-Seok Yoon; Seiji Ogo; Yasuhito Shomura; Yoshiki Higuchi, NAD(+)-reducing [NiFe] hydrogenases catalyze the oxidoreduction of dihydrogen concomitant with the interconversion of NAD(+) and NADH. Here, the isolation, purification and crystallization of the NAD(+)-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus TH-1 are reported. Crystals of the NAD(+)-reducing [NiFe] hydrogenase were obtained within one week from a solution containing polyethylene glycol using the sitting-drop vapour-diffusion method and micro-seeding. The crystal diffracted to 2.58 angstrom resolution and belonged to space group C2, with unit-cell parameters a = 131.43, b = 189.71, c = 124.59 angstrom, = 109.42 degrees. Assuming the presence of two NAD(+)-reducing [NiFe] hydrogenase molecules in the asymmetric unit, V-M was calculated to be 2.2 angstrom(3)Da(-1), which corresponds to a solvent content of 43%. Initial phases were determined by the single-wavelength anomalous dispersion method using the anomalous signal from the Fe atoms., WILEY-BLACKWELL
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2015年01月, ［査読有り］ - Oligomerization enhancement and two domain swapping mode detection for thermostable cytochrome c(552) via the elongation of the major hinge loop
Chunguang Ren; Satoshi Nagao; Masaru Yamanaka; Hirofumi Komori; Yasuhito Shomura; Yoshiki Higuchi; Shun Hirota, High-order oligomers of Hydrogenobacter thermophilus cytochrome c(552) increased with the insertion of more Gly residues between Ala18 and Lys19 at the major hinge loop of the wild-type protein. N-Terminal domain swapping and C-terminal domain swapping were elucidated by using X-ray crystallography for the mutant with the insertion of three Gly residues at the hinge loop., ROYAL SOC CHEMISTRY
MOLECULAR BIOSYSTEMS, 2015年, ［査読有り］ - Domain-swapped cytochrome cb(562) dimer and its nanocage encapsulating a Zn-SO4 cluster in the internal cavity
Takaaki Miyamoto; Mai Kuribayashi; Satoshi Nagao; Yasuhito Shomura; Yoshiki Higuchi; Shun Hirota, Protein nanostructures have been gaining in interest, along with developments in new methods for construction of novel nanostructures. We have previously shown that c-type cytochromes and myoglobin form oligomers by domain swapping. Herein, we show that a four-helix bundle protein cyt cb(562), with the cyt b(562) heme attached to the protein moiety by two Cys residues insertion, forms a domain-swapped dimer. Dimeric cyt cb(562) did not dissociate to monomers at 4 degrees C, whereas dimeric cyt b(562) dissociated under the same conditions, showing that heme attachment to the protein moiety stabilizes the domain-swapped structure. According to X-ray crystallographic analysis of dimeric cyt cb(562), the two helices in the N-terminal region of one protomer interacted with the other two helices in the C-terminal region of the other protomer, where Lys51-Asp54 served as a hinge loop. The heme coordination structure of the dimer was similar to that of the monomer. In the crystal, three domain-swapped cyt cb(562) dimers formed a unique cage structure with a Zn-SO4 cluster inside the cavity. The Zn-SO4 cluster consisted of fifteen Zn2+ and seven SO42- ions, whereas six additional Zn2+ ions were detected inside the cavity. The cage structure was stabilized by coordination of the amino acid side chains of the dimers to the Zn2+ ions and connection of two four-helix bundle units through the conformation-adjustable hinge loop. These results show that domain swapping can be applied in the construction of unique protein nanostructures., ROYAL SOC CHEMISTRY
CHEMICAL SCIENCE, 2015年, ［査読有り］ - Structural and Ligand Binding Properties of Dimeric Horse Myoglobin
Satoshi Nagao; Hisao Osuka; Takuya Yamada; Takeshi Uni; Yasuhito Shomura; Kiyohiro Imai; Yoshiki Higuchi; Shun Hirota, WILEY-BLACKWELL
PROTEIN SCIENCE, 2014年07月, ［査読有り］ - Structural aspects of [NiFe]-hydrogenases
Shomura Yasuhito; Higuchi Yoshiki
REVIEWS IN INORGANIC CHEMISTRY, 2013年12月, ［査読有り］ - Photosensitivity of the Ni-A state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F with visible light.
Osuka H; Shomura Y; Komori H; Shibata N; Nagao S; Higuchi Y; Hirota S
Biochemical and biophysical research communications, 2013年01月, ［査読有り］ - Crystal structure analysis of the translation factor RF3 (release factor 3).
Kihira K; Shimizu Y; Shomura Y; Shibata N; Kitamura M; Nakagawa A; Ueda T; Ochi K; Higuchi Y
FEBS letters, 2012年10月, ［査読有り］ - Structural and oxygen binding properties of dimeric horse myoglobin.
Nagao S; Osuka H; Yamada T; Uni T; Shomura Y; Imai K; Higuchi Y; Hirota S; Dalton transactions; Cambridge, Engl, Nagao S, Osuka H, Yamada T, Uni T, Shomura Y, Imai K, Higuchi Y, Hirota S, Dalton transactions (Cambridge, England : 2003), 2012, vol. 41, no. 37, pp. 11378-11385, 2012
2012年10月, ［査読有り］ - Structural Basis for the Reaction Mechanism of S-Carbamoylation of HypE by HypF in the Maturation of [NiFe]-Hydrogenases
Shomura Yasuhito; Higuchi Yoshiki
JOURNAL OF BIOLOGICAL CHEMISTRY, 2012年08月17日, ［査読有り］ - Structural and enzymatic characterization of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis.
Shomura Y; Hinokuchi E; Ikeda H; Senoo A; Takahashi Y; Saito J; Komori H; Shibata N; Yonetani Y; Higuchi Y
Protein science : a publication of the Protein Society, 2012年05月, ［査読有り］ - 3B0912 [NiFe]ヒドロゲナーゼ成熟化因子HypE,HypFのX線結晶構造解析(蛋白質-構造機能相関III:動態,生体リズム,口頭発表,日本生物物理学会第50回年会(2012年度))
Shomura Yasuhito; Higuchi Yoshiki, 一般社団法人 日本生物物理学会
生物物理, 2012年 - Crystallographic characterization of the DIX domain of the Wnt signalling positive regulator Ccd1
Shin-ichi Terawaki; Koumei Yano; Takuya Katsutani; Kensuke Shiomi; Kazuko Keino-Masu; Masayuki Masu; Yasuhito Shomura; Hirofumi Komori; Naoki Shibata; Yoshiki Higuchi, Coiled-coil DIX1 (Ccd1) is a positive regulator that activates the canonical Wnt signalling pathway by inhibiting the degradation of the key signal transducer beta-catenin. The C-terminal DIX domain of Ccd1 plays an important role in the regulation of signal transduction through homo-oligomerization and protein complex formation with other DIX domain-containing proteins, i. e. axin and dishevelled proteins. Here, the expression, purification, crystallization and X-ray data collection of the Ccd1 DIX domain are reported. The crystals of the Ccd1 DIX domain belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 72.9, b = 75.7, c = 125.6 angstrom. An X-ray diffraction data set was collected at 3.0 angstrom resolution., WILEY-BLACKWELL
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 2011年07月, ［査読有り］ - Crystallization and preliminary X-ray diffraction analysis of membrane-bound respiratory [NiFe] hydrogenase from Hydrogenovibrio marinus.
Shomura, Y; Hagiya, K; Yoon, K. S; Nishihara, H; Higuchi, Y
Acta Cryst., 2011年, ［査読有り］ - Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase
Shomura, Y; Yoon, K. S; Nishihara, H; Higuchi, Y
Nature, 2011年, ［査読有り］ - Purification, crystallization and preliminary X-ray analysis of the dissimilatory sulfite reductase from Desulfovibrio vulgaris Miyazaki F
Hideaki Ogata; Yasuhito Shomura; Aruna Goenka Agrawal; Amrit Pal Kaur; Wolfgang Gärtner; Yoshiki Higuchi; Wolfgang Lubitz, Dissimilatory sulfite reductase (Dsr) plays an important role in sulfate respiration in many sulfate-reducing bacteria. Dsr from Desulfovibrio vulgaris Miyazaki F has been purified and crystallized at 277 K using the sitting-drop vapour-diffusion method with PEG 3350 and potassium thiocyanate as precipitants. A data set was collected to 3.7 Å resolution from a single crystal at 100 K using synchrotron radiation. The Dsr crystal belonged to space group P41212, with unit-cell parameters a = b = 163.26, c = 435.32 Å. The crystal structure of Dsr was determined by the molecular-replacement method based on the three-dimensional structure of Dsr from D. vulgaris Hildenborough. The crystal contained three 2β22 units per asymmetric unit, with a Matthews coefficient (V M) of 2.35 Å3 Da-1; the solvent content was estimated to be 47.7%. © 2010 International Union of Crystallography All rights reserved.
Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 2010年11月, ［査読有り］ - Crystal Structures of Ethanolamine Ammonia-lyase Complexed with Coenzyme B-12 Analogs and Substrates
Naoki Shibata; Hiroko Tamagaki; Naoki Hieda; Keita Akita; Hirofumi Komori; Yasuhito Shomura; Shin-ichi Terawaki; Koichi Mori; Noritake Yasuoka; Yoshiki Higuchi; Tetsuo Toraya, N-terminal truncation of the Escherichia coli ethanolamine ammonia-lyase beta-subunit does not affect the catalytic properties of the enzyme (Akita, K., Hieda, N., Baba, N., Kawaguchi, S., Sakamoto, H., Nakanishi, Y., Yamanishi, M., Mori, K., and Toraya, T. (2010) J. Biochem. 147, 83-93). The binary complex of the truncated enzyme with cyanocobalamin and the ternary complex with cyanocobalamin or adeninylpentylcobalamin and substrates were crystallized, and their x-ray structures were analyzed. The enzyme exists as a trimer of the (alpha beta)(2) dimer. The active site is in the (alpha/beta)(8) barrel of the alpha-subunit; the beta-subunit covers the lower part of the cobalamin that is bound in the interface of the alpha- and beta-subunits. The structure complexed with adeninylpentylcobalamin revealed the presence of an adenine ring-binding pocket in the enzyme that accommodates the adenine moiety through a hydrogen bond network. The substrate is bound by six hydrogen bonds with active-site residues. Arg alpha(160) contributes to substrate binding most likely by hydrogen bonding with the O1 atom. The modeling study implies that marked angular strains and tensile forces induced by tight enzyme-coenzyme interactions are responsible for breaking the coenzyme Co-C bond. The coenzyme adenosyl radical in the productive conformation was modeled by superimposing its adenine ring on the adenine ring-binding site followed by ribosyl rotation around the N-glycosidic bond. A major structural change upon substrate binding was not observed with this particular enzyme. Glu alpha(287), one of the substrate-binding residues, has a direct con-tact with the ribose group of the modeled adenosylcobalamin, which may contribute to the substrate-induced additional labilization of the Co-C bond., AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
JOURNAL OF BIOLOGICAL CHEMISTRY, 2010年08月, ［査読有り］ - Expression, crystallization and preliminary X-ray crystallographic study of ethanolamine ammonia-lyase from Escherichia coli
Naoki Shibata; Hiroko Tamagaki; Shungo Ohtsuki; Naoki Hieda; Keita Akita; Hirofumi Komori; Yasuhito Shomura; Shin-ichi Terawaki; Tetsuo Toraya; Noritake Yasuoka; Yoshiki Higuchi, Ethanolamine ammonia-lyase (EAL) catalyzes the adenosylcobalamindependent conversion of ethanolamine to acetaldehyde and ammonia. The wild-type enzyme shows a very low solubility. N-terminal truncation of the Escherichia coli EAL beta-subunit dramatically increases the solubility of the enzyme without altering its catalytic properties. Two deletion mutants of the enzyme [EAL(beta Delta 4-30) and EAL(beta Delta 4-43)] have been overexpressed, purified and crystallized using the sitting-drop vapour-diffusion method. Crystals of EAL(beta Delta 4-30) and EAL(beta Delta 4-43) diffracted to approximately 8.0 and 2.1 angstrom resolution, respectively., WILEY-BLACKWELL
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 2010年06月, ［査読有り］ - Crystal structure of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum: a key component of the dioxygen scavenging system in obligatory anaerobes.
Nishikawa K; Shomura Y; Kawasaki S; Niimura Y; Higuchi Y, 絶対嫌気性菌のClostridium acetobutylicum（アセトンブタノール発酵菌）で新規に同定されたO2代謝の中心的役割を担う酵素(NRFA)の結晶解析と構造解析を行った。結晶解析にあたり多量の酵素が必要であったことから、その精製に関する技術的な指導や精製酵素の提供を行った。
Proteins, 2010年05月, ［査読有り］ - Crystallization and preliminary X-ray analysis of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum
Koji Nishikawa; Yasuhito Shomura; Shinji Kawasaki; Youichi Niimura; Yoshiki Higuchi, NADH: rubredoxin oxidoreductase (NROR), an O(2)-inducible protein, is a versatile electron donor for scavengers of O(2) and reactive oxygen species (ROS) in Clostridium acetobutylicum. Recombinant NROR was overexpressed in Escherichia coli and purified to homogeneity; it was subsequently crystallized using the sitting-drop vapour-diffusion method at 293 K. Preliminary crystallographic analysis revealed that the crystals belonged to space group P4(1)22 or P4(3)22, with unit-cell parameters a = b = 98.6, c = 88.3 angstrom, and diffracted to 2.1 angstrom resolution. Assuming that the crystals contained one molecule per asymmetric unit, the Matthews coefficient was calculated to be 2.7 angstrom(3) Da(-1) and the solvent content to be 54.1%., WILEY-BLACKWELL PUBLISHING, INC
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 2010年01月, ［査読有り］ - 1SP5-05 [NiFe]ヒドロゲナーゼのX線結晶構造解析と赤外分光測定(1SP5 若手研究者による生体金属分子分光学の新展開,第47回日本生物物理学会年会)
大須賀 久織; 寺脇 慎一; 庄村 康人; 小森 博文; 柴田 直樹; 廣田 俊; 樋口 芳樹, 一般社団法人 日本生物物理学会
生物物理, 2009年 - Crystallization and preliminary X-ray analysis of a class II release factor RF3 from a sulfate-reducing bacterium.
Kihira K; Numata S; Kitamura M; Kondo J; Terawaki S; Shomura Y; Komori H; Shibata N; Higuchi Y
Acta crystallographica. Section F, Structural biology and crystallization communications, 2008年07月, ［査読有り］ - 2P-048 翻訳終結因子RF3のX線結晶解析(蛋白質・構造機能相関(2),第46回日本生物物理学会年会)
Kihira Kiyohito; Numata Shuko; Kitamura Masaya; Kondo Jun; Terawaki Shinichi; Shomura Yasuhito; Komori Hirofumi; Shibata Naoki; Higuchi Yoshiki, 一般社団法人 日本生物物理学会
生物物理, 2008年 - 2P-016 アデノシルコバラミンを補酵素とするエタノールアミンアンモニアリアーゼの構造化学的研究(蛋白質・構造(2),第46回日本生物物理学会年会)
Shibata Naoki; Tamagaki Hiroko; Komori Hirofumi; Shomura Yasuhito; Hieda Naoki; Akita Keita; Mori Koichi; Toraya Tetsuo; Yasuoka Noritake; Higuchi Yoshiki, 一般社団法人 日本生物物理学会
生物物理, 2008年 - 2P-032 [NiFe]ヒドロゲナーゼのFT-IRによる研究(蛋白質・構造(2),第46回日本生物物理学会年会)
Osuka Hisao; Terawaki Shin-ichi; Shomura Yasuhito; Komori Hirofumi; Shibata Naoki; Hirota Shun; Higuchi Yoshiki, 一般社団法人 日本生物物理学会
生物物理, 2008年 - Crystal structures of hydrogenase maturation protein HypE in the Apo and ATP-bound forms.
Shomura Y; Komori H; Miyabe N; Tomiyama M; Shibata N; Higuchi Y
Journal of molecular biology, 2007年09月, ［査読有り］ - Crystallization and preliminary X-ray crystallographic studies of the axin DIX domain
Naoki Shibata; Yusuke Tomimoto; Toru Hanamura; Ryo Yamamoto; Mai Ueda; Yasufumi Ueda; Nobuhiro Mizuno; Hideaki Ogata; Hirofumi Komori; Yasuhito Shomura; Michihiko Kataoka; Sakayu Shimizu; Jun Kondo; Hideki Yamamoto; Akira Kikuchi; Yoshiki Higuchi, Axin is a negative regulator of the canonical Wnt signalling pathway that mediates the phosphorylation of beta-catenin by glycogen synthase kinase 3 beta. The DIX domain of rat axin, which is important for its homooligomerization and interactions with other regulators in the Wnt pathway, was purified and crystallized by the sitting-drop vapour-diffusion technique using polyethylene glycol 6000 and lithium sulfate as crystallization agents. Crystals belong to space group P6(1) or P6(5), with unit-cell parameters a = b = 91.49, c = 84.92 angstrom. An X-ray diffraction data set has been collected to a nominal resolution of 2.9 angstrom., INT UNION CRYSTALLOGRAPHY
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2007年06月, ［査読有り］ - Crystallization and preliminary X-ray crystallographic studies of the axin DIX domain
Naoki Shibata; Yusuke Tomimoto; Toru Hanamura; Ryo Yamamoto; Mai Ueda; Yasufumi Ueda; Nobuhiro Mizuno; Hideaki Ogata; Hirofumi Komori; Yasuhito Shomura; Michihiko Kataoka; Sakayu Shimizu; Jun Kondo; Hideki Yamamoto; Akira Kikuchi; Yoshiki Higuchi, Axin is a negative regulator of the canonical Wnt signalling pathway that mediates the phosphorylation of β-catenin by glycogen synthase kinase 3β. The DIX domain of rat axin, which is important for its homooligomerization and interactions with other regulators in the Wnt pathway, was purified and crystallized by the sitting-drop vapour-diffusion technique using polyethylene glycol 6000 and lithium sulfate as crystallization agents. Crystals belong to space group P61 or P65, with unit-cell parameters a = b = 91.49, c = 84.92 Å. An X-ray diffraction data set has been collected to a nominal resolution of 2.9 Å. © International Union of Crystallography 2007.
Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 2007年05月, ［査読有り］ - 1P018 DIXドメインを介するWntタンパク質の可逆的ポリマー化の構造基盤とWntシグナル制御モデル(蛋白質(構造・構造機能相関),口頭発表,第45回日本生物物理学会年会)
柴田 直樹; Schwarz-Romond Thomas; Fiedler Marc; Butler P. Jonathan G.; 小森 博文; 庄村 康人; 山本 英樹; 菊池 章; Bienz Mariann; 樋口 芳樹, 一般社団法人 日本生物物理学会
生物物理, 2007年 - Crystal structure of stilbene synthase from Arachis hypogaea
Yasuhito Shomura; Ichiro Torayama; Dae‐Yeon Suh; Ting Xiang; Akiko Kita; Ushio Sankawa; Kunio Miki, Wiley
Proteins: Structure, Function, and Bioinformatics, 2005年07月18日, ［査読有り］ - Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms
Yasuhito Shomura; Takao Yoshida; Ryo Iizuka; Tadashi Maruyama; Masafumi Yohda; Kunio Miki, The crystal structures of the group II chaperonins consisting of the α subunit with amino acid substitutions of G65C and/or I125T from the hyperthermophilic archaeum Thermococcus strain KS-1 were determined. These mutants have been shown to be active in ATP hydrolysis but inactive in protein folding. The structures were shown to be double-ring hexadecamers in an extremely closed form, which was consistent with the crystal structure of native α8β8-chaperonin from Thermoplasma acidophilum. Comparisons of the present structures with the atomic structures of the GroEL14-GroES7-(ADP)7 complex revealed that the deficiency in protein-folding activity with the G65C amino acid substitution is caused by the steric hindrance of the local conformational change in an equatorial domain. We concluded that this mutant chaperonin with G65C substitution is deprived of the smooth conformational change in the refolding-reaction cycle. We obtained a new form of crystal with a distinct space group at a lower concentration of sulfate ion in the presence of nucleotide. The crystal structure obtained at the lower concentration of sulfate ion tilts outward, and has much looser inter-subunit contacts compared with those in the presence of a higher concentration of sulfate ion. Such subunit rotation has never been characterized in group II chaperonins. The crystal structure obtained at the lower concentration of sulfate ion tilts outward, and has much looser inter-subunit contacts compared with those in the presence of a higher concentration of sulfate ion. © 2003 Elsevier Ltd. All rights reserved.
Journal of Molecular Biology, 2004年01月30日, ［査読有り］ - ATP Binding Is Critical for the Conformational Change from an Open to Closed State in Archaeal Group II Chaperonin
Ryo Iizuka; Takao Yoshida; Yasuhito Shomura; Kunio Miki; Tadashi Maruyama; Masafumi Odaka; Masafumi Yohda, Group II chaperonins, found in archaea and in eukaryotic cytosol, do not have a co-chaperonin corresponding to GroES. Instead, it is suggested that the helical protrusion extending from the apical domain acts as a built-in lid for the central cavity and that the opening and closing of the lid is regulated by ATP binding and hydrolysis. However, details of this conformational change remain unclear. To investigate the conformational change associated with the ATP-driven cycle, we conducted protease sensitivity analyses and tryptophan fluorescence spectroscopy of α-chaperonin from a hyperthermophilic archaeum, Thermococcus strain KS-1. In the nucleotide-free or ADP-bound state, the chaperonin, especially in the helical protrusion region, was highly sensitive to proteases. Addition of ATP and ammonium sulfate induced the transition to the relatively protease-resistant form. The fluorescence intensity of the tryptophan residue introduced at the tip of the helical protrusion was enhanced by the presence of ATP or ammonium sulfate. We conclude that ATP binding induces the conformational change from the lid-open to lid-closed form in archaeal group II chaperonin.
Journal of Biological Chemistry, 2003年11月07日, ［査読有り］ - Crystallization and preliminary X-ray characterization of archaeal group II chaperonin alpha-subunit from Thermococcus strain KS-1.
Yasuhito Shomura; Takao Yoshida; Tadashi Maruyama; Masafumi Yohda; Kunio Miki, The archaeal group II chaperonin from Thermococcus strain KS-1 is composed of two kinds of subunits (alpha and beta). Each of the recombinant subunits was individually expressed in Escherichia coli and purified as homo-hexadecamers of each subunit. Both homo-oligomers facilitate the refolding of denatured proteins in vitro in an ATP-dependent manner. A mutant alpha-subunit homo-oligomer with two amino-acid substitutions, which has the ability to capture the unfolded protein but lacks the ability to refold the unfolded protein, was crystallized in two different conditions. One crystal form was obtained from a high-concentration solution of ammonium sulfate and grew to maximum dimensions of 0.15 x 0.15 x 0.4 mm. The crystals of this form belonged to the tetragonal space group P42(1)2, with unit-cell parameters a = b = 209.3, c = 156.1 A, and diffracted X-rays to 2.4 A resolution with synchrotron radiation. The other form was crystallized from a polyethylene glycol 6000 solution and belonged to the tetragonal space group, with unit-cell parameters a = b = 220.8, c = 182.4 A. This form only diffracts X-rays to 6 A resolution. Diffraction data collected from the former crystal enabled initial successful phases to be obtained by the molecular-replacement method.
Acta crystallographica. Section D, Biological crystallography, 2002年10月, ［査読有り］ - Glycine at the 65th position plays an essential role in ATP-dependent protein folding by archael group II chaperonin
Ryo Iizuka; Takao Yoshida; Tadashi Maruyama; Yasuhito Shomura; Kunio Miki; Masafumi Yohda, In the previous study, we have found that G65C and I125T double mutant of a chaperonin homo-oligomer from a hyperthermophilic archaeum, Thermococcus sp. strain KS-1, lacks ATP-dependent protein refolding activity despite showing ATPase activity and the ability to bind the denatured proteins. In this study, we have characterized several mutant Thermococcus chaperonin homo-oligomers with the amino acid substitutions of Gly-65 or Ile-125. The results showed that amino acid residue at 65th position should be a small amino acid such as glycine or alanine for the ATP-dependent refolding activity. The a chaperonin homooligomers with amino acid substitution of Gly-65 by amino acids whose side chains are larger than the methyl group did not have ATP-dependent protein refolding activity, but exhibited an increase of the binding affinity for unfolded proteins in the presence of ATP or AMP-PNP. © 2001 Elsevier Science.
Biochemical and Biophysical Research Communications, 2001年12月21日, ［査読有り］
MISC
- Crystal structures of the NAD+-reducing soluble [NiFe]-hydrogenase
庄村康人; 樋口芳樹
SPring-8 SACLA リサーチフロンティア 2017, 2018年08月, ［査読有り］, ［招待有り］ - [NiFe]ヒドロゲナーゼがもつ鉄硫黄クラスターによる酸素防御機構
庄村康人,樋口芳樹
生物物理, 2018年, ［査読有り］, ［招待有り］
筆頭著者 - Rational Design of Heterodimeric Protein using Domain Swapping for Myoglobin
Lin Ying-Wu; Nagao Satoshi; Zhang Mohan; Shomura Yasuhito; Higuchi Yoshiki; Hirota Shun
2014年11月04日 - Preparation of single crystals of Multicopper oxidases for neutron diffraction study
Y. Higuchi; M. Akter; C. Inoue; Y. Shomura; N. Shibata; K. Inaka; K. Kataoka; T. Sakurai; K. Komori
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 2014年03月 - Crystal structure of O2-tolerant [NiFe] hydrogenase reveals the mechanism of O2-tolerance attributable to a redox-dependent conformational change of [4Fe-3S] cluster
SHOMURA Yasuhito; HIGUCHI Yoshiki
SPring-8 リサーチフロンティア 2011, 2012年07月, ［査読有り］, ［招待有り］ - 酸素耐性ヒドロゲナーゼの構造化学的研究 －酵素分子に見出された活性保護機構－
樋口芳樹; 庄村康人
燃料電池, 2012年04月, ［招待有り］ - ヒドロゲナーゼの新規酸素耐性機構 -膜結合型[NiFe]ヒドロゲナーゼ
庄村康人; 樋口芳樹
化学, 2012年04月, ［招待有り］ - 4Fe-3S］クラスターによる［NiFe］ヒドロゲナーゼの酸素耐性機構の構造基盤
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SPring-8利用者情報誌, 2012年04月, ［査読有り］, ［招待有り］ - Structural study of H2O2 reductase, rubperoxin
Koji Nishikawa; Yasuhito Shomura; Shinji Kawasaki; Yu Sakai; Youichi Niimura; Shinichi Terawaki; Hirofumi Komori; Naoki Shibata; Yoshiki Higuchi
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2008年 - I 代謝系に関わるタンパク質・酵素群のX線構造化学(生体物質構造学I)
庄村 康人; 小森 博文; 柴田 直樹; 樋口 芳樹
兵庫県立大学大学院物質理学研究科・生命理学研究科研究一覧, 2006年10月10日 - I 代謝系に関わるタンパク質・酵素群のX線構造化学(生体物質構造学I,生命理学研究科)
庄村 康人; 小森 博文; 柴田 直樹; 樋口 芳樹
兵庫県立大学大学院物質理学研究科・生命理学研究科研究一覧, 2006年04月 - An engineered chaperonin caging a guest protein: Structural insights and potential as a protein expression tool
Masahiro Furutani; Jun Ichi Hata; Yasuhito Shomura; Keisukeitami; Takao Yoshida; Yoshitaka Izumoto; Akiko Togi; Akira Ideno; Takuo Yasunaga; Kunio Miki; Tadashi Maruyama
Protein Science, 2005年02月
書籍等出版物
- ADVANCES IN BIOORGAOMETALLIC CHEMISTRY,Chapter 18 "Structural Insights into the Protective Mechanisms against O2 in the [NiFe]-Hydrogenases"
共著
ELSEVIER, 2019年 - Encyclopedia of Inorganic and Bioinorganic Chemistry,Standard Article "NAD+-reducing [NiFe]-Hydrogenase"
Shomura Y.; Higuchi Y., 単著
Wiely, 2019年 - ADVANCES IN BIOORGAOMETALLIC CHEMISTRY Chapter 18 "Structural Insights into the Protective Mechanisms against O2 in the [NiFe]-Hydrogenases"
共著
ELSEVIER, 2019年 - Encyclopedia of Inorganic and Bioinorganic Chemistry Standard Article "NAD+-reducing [NiFe]-Hydrogenase"
Shomura Y; Higuchi Y, 単著
Wiely, 2019年
講演・口頭発表等
- Mn-カタラーゼにおける過酸化水素不均化反応機構の解明に向けて
庄村康人
2022年度iBIX-JAXA-KEK物構研-QST 合同タンパク質研究会, 2023年02月27日, ［招待有り］
20230227, 20230227 - 偏性嫌気性細菌由来Mn-カタラーゼ様タンパク質の構造解析
野村 葵、門倉 佳輝、庄村 康人
第22回日本蛋白質科学年会, 2022年06月07日
20220607, 20220609 - Ni 置換型ルブレドキシン変異体の構造機能相関の解明
遠藤 啓貴、横山 優花、松井 眞美、飯塚 夏海、庄村 康人
第22回日本蛋白質科学年会, 2022年06月07日
20220607, 20220609 - Ni置換型ルブレドキシン変異体のX線・中性子結晶子構造解析
遠藤啓貴; 庄村康人
2021年度量子ビームサイエンスフェスタ, 2022年03月08日 - X-ray crystal structure analysis of the Ni-substituted rubredoxin mutant
Keiki Endo; Yuka Yokoyama; Mami Matsui; Natsumi Iitsuka; Yasuhito Shomura
6th International Symposium of Quantum Beam Science at Ibaraki University, 2022年02月22日 - 還元型Mn-カタラーゼのX線・中性子結晶構造解析
鈴井美羽,高木夕里圭,高野紗和,高橋果林,山田太郎,庄村康人
令和3年度 日本結晶学会年会, 2021年11月19日 - Clostridium acetobutylicum由来Rubrerythrinの構造解析
伊藤拓未,川崎信治,庄村康人
2020年度量子ビームサイエンスフェスタ, 2021年03月10日 - 高度好熱菌由来Mn-カタラーゼの結晶構造解析
高木夕里圭,高野紗和,高橋果林,山田太郎,庄村康人
2020年度量子ビームサイエンスフェスタ, 2021年03月10日 - Structure analyses of Rubrerythrin from Clostridium acetobutylicum
Takumi Itoh; Yasuhito Shomura
5th International Symposium of Quantum Beam Science at Ibaraki University, 2020年11月19日 - Ni結合型ルブレドキシンの物性・機能相関の解明
庄村康人
2020年度iBIX-JAXA-KEK 物構研-QST 合同タンパク質研究会, 2020年11月09日, ［招待有り］ - Improved hydrogen evolution activity of the Ni-substituted rubredoxin by site-directed mutagenesis
Yasuhito Shomura; Yuka Yokoyama
The 70th JSCC Conference, 2020年09月28日, 錯体化学会, ［招待有り］
20200928, 20200930 - Mn-カタラーゼへの部位特異的変異導入とその酵素学的解析
高野紗和,高橋果林,山田太郎,庄村康人
第19回日本蛋白質科学年会, 2019年06月24日 - Ni置換型ルブレドキシンのX線・中性子結晶構造解析
横山優花,庄村康人
2018年度量子ビームサイエンスフェスタ, 2019年03月12日 - L-アミノ酸リガーゼを用いた生理活性ペプチドのin vivo合成系の確立
清野里々花,矢ヶ崎誠,庄村康人
日本農芸化学会関東支部2018年度大会, 2018年10月03日 - 放線菌由来シトクロムP450の基質特異性の解明
樋澤芽依,纐纈健人,庄村康人
日本農芸化学会関東支部2018年度大会, 2018年10月03日 - [NiFe]ヒドロゲナーゼがもつ鉄硫黄クラスターの新規機能
庄村康人
第56回日本生物物理学会, 2018年09月15日, ［招待有り］ - Oxidation-induced conformational change at the active site of the soluble NAD+-reducing [NiFe]-hydrogenase
Yasuhito Shomura
43rd International Conference on Coordination Chemistry, 2018年07月30日, ［招待有り］ - X線小角散乱法による コラーゲンプロリンtrans-4-水酸化酵素の構造解析
宗田善久,庄村康人
第18回日本蛋白質科学会年会, 2018年06月26日 - In vivo synthesis of physiologically active peptides using the protein-engineered L-amino acid ligase
Ririka Seino; Makoto Yagasaki; Yasuhito Shomura
3rd International Symposium of Quantum Beam Science at Ibaraki University, 2018年05月30日 - Quaternary structure prediction of collagen prolyl trans-4-hydroxylase by SAXS analysis
Yoshihisa Soda; Yasuhito Shomura
3rd International Symposium of Quantum Beam Science at Ibaraki University, 2018年05月30日 - Crystal structure analysis of the nickel-Substituted rubredoxin from Caldanaerobacter subterraneus
Yuka Yokoyama; Yasuhito Shomura
3rd International Symposium of Quantum Beam Science at Ibaraki University, 2018年05月30日 - Structural studies on [NiFe]-hydrogenases
Yasuhito Shomura
3rd International Symposium of Quantum Beam Science at Ibaraki University, 2018年05月30日, ［招待有り］ - X線小角散乱法によるコラーゲンプロリンtrans-4-水酸化酵素の構造解析
宗田善久,庄村康人
2017年度量子ビームサイエンスフェスタ, 2018年03月02日 - Small angle X-ray scattering analysis of collagen prolyl trans-4-hydroxylase
Yoshihisa Soda; Yasuhito Shomura
2nd International Symposium of Quantum Beam Science at Ibaraki University, 2017年12月08日 - X-ray structure analysis of cytochrome P450 from Stackebrandtia nassauensis
Mei Hizawa; Kento Koketsu; Yasuhito Shomura
2nd International Symposium of Quantum Beam Science at Ibaraki University, 2017年12月08日 - Biosynthesis of the organometallic compound: the maturation processes of [NiFe]-hydrogenases
Yasuhito Shomura
The International Symposium of Quantum Beam Science at Ibaraki University, 2016年11月20日, ［招待有り］ - X-ray structure analysis of the HypCD complex in the metal-bound forms
Masashi Sawabe; Yoshiki Higuchi; Yasuhito Shomura
The International Symposium of Quantum Beam Science at Ibaraki University, 2016年11月18日 - X-ray structure analysis of the dipeptide synthetase RSp1486a
Mei Hizawa; Makoto Yagasaki; Yoshiki Higuchi; Yasuhito Shomura
The International Symposium of Quantum Beam Science at Ibaraki University, 2016年11月18日 - Fe(CN)2CO 錯体の生合成に関与するHypCD複合体の二価金属結合型構造
澤辺大嗣,樋口芳樹,庄村康人
平成28年度 日本結晶学会年会, 2016年11月17日 - ジペプチド合成酵素RSp1486aのX線結晶構造解析
樋澤芽依,矢ケ崎誠,樋口芳樹,庄村康人
平成28年度 日本結晶学会年会, 2016年11月17日 - ヒドロゲナーゼがもつ鉄硫黄クラスターの構造的多様性
庄村康人; Noor Dina Binti Muhd Noor; 西川幸志; 樋口芳樹
第88回 日本生化学会大会, 2015年12月01日, ［招待有り］ - Fe(CN)2CO 錯体の生合成に関与するHypCD複合体のFe結合型構造
庄村康人,樋口芳樹,Robert Szilagyi
平成27年度 日本結晶学会年会, 2015年10月17日 - X-ray structure analysis of the [NiFe]-hydrogenase from Citrobacter sp. S-77
Yasuhito Shomura
I2CNER International Workshop 2015, 2015年02月04日, ［招待有り］ - Ni-Fe型水素分解酵素の構造化学的研究
庄村康人
異分野融合若手研究者Science & Technology クラブ, 2015年01月26日, ［招待有り］ - Development of the Heterologous Expression System of the Group IV [NiFe]-hydrogenase
Yasuhito Shomura
ICARP(International Conference on Artficial Photosynthesis), 2014年11月26日 - 膜結合型[NiFe]-ヒドロゲナーゼの酸素耐性機構の解明
庄村康人,尹基石,西原宏史,樋口芳樹
２１世紀播磨科学技術フォーラム, 2014年07月24日 - X線結晶構造解析によるL-プロリンcis-4-水酸化酵素の位置選択性の解明
庄村康人; 纐纈健人; 樋口芳樹
第6回日本生物物理学会 中国四国支部大会, 2014年05月17日 - [NiFe]ヒドロゲナーゼのX線結晶構造解析
庄村康人
第27回 日本放射光学会年会放射光科学合同シンポジウム, 2014年01月11日, ［招待有り］
