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構造生物学を通して、
生命現象の詳細な理解と、
高度利用を目指しています。 |
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構造生物学研究室
（生物化学研究室）では |
「遺伝子工学」による
蛋白質、ＤＮＡ、ＲＮＡの合成、
「生化学」による
生体分子の精製と機能解析、
「Ｘ線結晶構造解析」による
立体構造解析、
これらの情報と技術を融合させた
酵素の高機能化、
などを行っています。 |
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２０１６年
Jiang D, Izumi K, Ueda T, Oshima K, Nakashima T, Kimura M.
Functional characterization of archaeal homologs of human nuclear RNase P proteins Rpp21 and Rpp29 provides insights into the molecular basis of their cooperativity in catalysis.
Biochem Biophys Res Commun. 2016 Nov 1.
Oshima K, Kakiuchi Y, Tanaka Y, Ueda T, Nakashima T, Kimura M, Yao M.
Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38.
Biochem Biophys Res Commun. 2016 Jun 3;474(3):541-6.
Hamasaki M, Hazeyama K, Iwasaki F, Ueda T, Nakashima T, Kakuta Y, Kimura MFunctional implication of archaeal homologues of human RNase P protein pair Pop5 and Rpp30.
Biochem. 2016 Jan;159(1):31-40.
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２０１５年
Ueda T, Ishino S, Suematsu K, Nakashima T, Kakuta Y, Kawarabayasi Y, Ishino Y, Kimura M.
Mutation of the gene encoding the ribonuclease P RNA in the hyperthermophilic archaeon Thermococcus kodakarensis causes decreased growth rate and impaired processing of tRNA precursors.
Biochem Biophys Res Commun. 2015 Dec 25;468(4):660-5.
Suematsu K, Ueda, T, Nakashima T, Kakuta Y, and Kimura M,
On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the
hyperthermophilic archaeon Thermococcus kodakarensis.
Biosci. Biotechnol. Biochem., 79, 6, 952-959., 2015.
Miyanoshita M, Nakashima T, Kakuta Y, Kimura M.
Archaeal ribonuclease P proteins have potential for biotechnological applications
where precise hybridization of nucleic acids is needed.
Biosci Biotechnol Biochem. 2015;79(12):2014-7.
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２０１４年
Imai T, Nakamura T, Nakayama K, Maeda T, Nakashima T, Kakuta Y, and Kimura
M, Pentatricopeptide repeat motifs in the processing enzyme, PRORP1, in
Arabidopsis thaliana play a crucial role in recognition of nucleotides
at TψC-loop in precursor tRNAs.
Biochem. Biophys. Res. Commun., 450, 1541-1546., 2014.
Hino M, Takagi H, Miyoshi T, Uchiumi T, Nakashima T, Kakuta Y, and Kimura
M, Characterization of putative toxin-antitoxin systems in Vibrio parahaemolyticus.
J. App. Microbiol., 117, 185-195., 2014.
Furutani T, Hazeyama K, Tomita S, Ueda T, Imai T, Nakashima T, Kakuta
K, and Kimura M, Enhancement of RNA annealing and strand displacement found
in archaeal ribonulease P proteins is conserved in Escherichia coli protein
C5 and yeast protein Rpr2. Biosci. Biotechnol. Biochem., 78, 1700-1702.,
2014.
Ueda T, Yamaguchi H, Miyanoshita M, Nakashima T, Kakuta Y, Kimura M.
Characterization of the peripheral structures of archaeal RNase P RNA from
Pyrococcus horikoshii OT3.
J Biochem. 155(1):25-33., 2014.
Takakura Y, Suzuki J, Oka N, Kakuta Y.
Tamavidin 2-HOT, a highly thermostable biotin-binding protein.
J Biotechnol., 169, 1-8., 2014.
２０１３年
Kawaguchi Y, Sugiura N, Kimata K, Kimura M, Kakuta Y.
The crystal structure of novel chondroitin lyase ODV-E66, a baculovirus
envelope protein.
FEBS lett., 587(24), 3943-3948., 2013.
Shimasaki Y, Tsuyama M, Tasmin R, Qiu X, Shimizu M, Sato Y, Yamasaki Y, Kato-Unoki Y, Nukata A, Nakashima T, Ichinose H, Wariishi H, Honjo T, Oshima Y.
Thiobencarb herbicide reduces growth, photosynthetic activity, and amount of Rieske iron-sulfur protein in the diatom Thalassiosira pseudonana.
J Biochem Mol Toxicol. 27(9):437-44., 2013.
Qiu X, Shimasaki Y, Tsuyama M, Yamada T, Kuwahara R, Kawaguchi M, Honda
M, Gunjikake H, Tasmin R, Shimizu M, Sato Y, Kato-Unoki Y, Nakashima T,
Matsubara T, Yamasaki Y, Ichinose H, Wariishi H, Honjo T, Oshima Y.
Growth-phase dependent variation in photosynthetic activity and cellular protein expression profile in the harmful raphidophyte Chattonella antiqua.
Biosci Biotechnol Biochem. 77(1):46-52., 2013.
Hazeyama K, Ishihara M, Ueda T, Nishimoto E, Nakashima T, Kakuta Y, Kimura
M.
Extra-structural elements in the RNA recognition motif in archaeal Pop5
play a crucial role in the activation of RNase P RNA from Pyrococcus horikoshii
OT3.
Biochem. Biophys. Res. Commun., 440, 594-598., 2013.
Teramoto T, Fujikawa Y, Kawaguchi Y, Kurogi K, Soejima M, Adachi R, Nakanishi Y, Mishiro-Sato E, Liu MC, Sakakibara Y, Suiko M, Kimura M, Kakuta Y.
Crystal structure of human tyrosylprotein sulfotransferase-2 reveals the mechanism of protein tyrosine sulfation reaction.
Nat Commun., 4:1572. 2013.
２０１２年
Ishihara M, Nishimoto E, Yamashita S, Kakuta Y, Kimura M.
A distinct binding mode of archaeal ribonuclease p proteins to RNA.
Biosci Biotechnol Biochem., 76(12), 2335-2337., 2012.
Oshima K, Nakashima T, Kakuta Y, Tsumoto K, Kimura M.
Thermodynamic Analysis of a Multifunctional RNA-Binding Protein, PhoRpp38, in the Hyperthermophilic Archaeon Pyrococcus horikoshii OT3.
Biosci Biotechnol Biochem., 76(6), 1252-1255., 2012.
Chaen K, Noguchi J, Omori T, Kakuta Y, Kimura M.
Crystal structure of the rice branching enzyme I (BEI) in complex with maltopentaose.
Biochem Biophys Res Commun., 424, 508-511., 2012.
Yamamoto K, Usuda K, Kakuta Y, Kimura M, Higashiura A, Nakagawa A, Aso
Y, Suzuki M.
Structural basis for catalytic activity of a silkworm Delta-class glutathione transferase.
Biochim Biophys Acta., 1820(10), 1469-1474., 2012.
Kawaguchi Y, Sugiura N, Onishi M, Kimata K, Kimura M, and Kakuta Y.,
Crystallization and X-ray diffraction analysis of chondroitin lyase from
baculovirus: envelope protein ODV-E66.
Acta Cryst. F68, 190-192., 2012.
Kimura M and Kakuta Y.,
Structural biology of the ribonuclease P in the hyperthermophilic archaeon
Pyrococcus horikoshii OT3.,
In Microorganisms in Sustainable Agriculture and Biotechnology.
T. Satyanarayana et al. (eds.)
Springer Science+Business Media B.V. Part 2, 487-508., 2012.
Hossain MM, Moriizumi Y, Tanaka S, Kimura M, Kakuta Y.,
Crystal structure of sulfotransferase STF9 from Mycobacterium avium.
Mol Cell Biochem., 361(1-2), 97-104., 2012.
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２０１1年
Zwieb C, Nakao Y, Nakashima H, Takagi H, Goda S, Andersen E.S, Kakuta
Y, and Kimura M.,
Structural modeling of RNase P RNA from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.,
Biochem. Biophys. Res.Commun., 414, 517-522., 2011.
Kakuta Y, Usuda K, Nakashima T, Kimura M, Aso Y, Yamamoto K.,
Crystallographic survey of active sites of an unclassified glutathione transferase from Bombyx mori.
Biochim Biophys Acta., 1810(12), 1355-60., 2011.
Hossain MM, Moriizumi Y, Tanaka S, Kimura M, Kakuta Y.,
Molecular cloning, expression, and functional analysis of a predicted sulfotransferase
STF9 from Mycobacterium avium.
Mol Cell Biochem. 350(1-2):155-62. 2011
Noguchi J, Chaen K, N.T. Vu, Akasaka T, Shimada H, Nakashima T, Nishi A,
Satoh H, Omori T, Kakuta Y, and Kimura M.,
Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with
implications for catalysis and substrate binding.,
Glycobiology, 21(8), 1108-1116., 2011.
Hara T, Terada A, Yamaguchi H, Nakashima T, Kakuta Y, and Kimura M.,
Contribution of peripheral stem-loops to catalytic activity of archaeal
RNase P RNA from Pyrococcus horikoshii OT3.,
Biosci Biotechnol Biochem., 75(4), 816-819.,2011.
Yamamoto K, Ichinose H, Aso Y, Banno Y, Kimura M, and Nakashima T.,
Molecular characterization of an insecticide-induced novel glutathione
transferase in silkworm.,
Biochem Biophys Acta., 1810, 420-426., 2011.
２０１０年
Shinohara M, Guo JX, Mori M, Nakashima T, Takagi H, Nishimoto E, Yamashita
S, Tsumoto K, Kakuta Y, Kimura M.,
The structural mechanism of the inhibition of archaeal RelE toxin by its
cognate RelB antitoxin.,
Biochem Biophys Res Commun., 400, 346-351.,2010.
Katekaew S, Kuaprasert B, Torikata T, Kakuta Y, Kimura M, Yoneda K, Araki
T.,
Structure of the newly found green turtle egg-white ribonuclease.
Acta. Crystallogr. Sect F, 66, 755-759.,2010.
Liu TA, Bhuiyan S, Liu MY, Sugahara T, Sakakibara Y, Suiko M, Yasuda S,
Kakuta Y, Kimura M, Williams FE, Liu MC.,
Zebrafish as a model for the study of the phase II cytosolic sulfotransferases.,
Curr. Drug Metab., 6, :538-546., 2010.
Honda T, Hara T, Nan J, Zhang X, Kimura M.,
Archaeal homologs of human RNase P protein pairs Pop5 with Rpp30 and Rpp21
with Rpp29 word on distinct functional domains of the RNA subunit.,
Biosci. Biotechnol. Biochem., 74, 266-273.,2010.
Kosaka S, Hada K, Nakashima T, and Kimura M.,
Structural change of ribonuclease P RNA in the hyperthermophilic archaeon
Pyrococcus horikoshii OT3, as induced upon interaction with proteins.,
Biosci. Biotechnol. Biochem., 74, 394-396.,2010.
Sugiura N, Baba Y, Kawaguchi Y, Iwatani T, Suzuki K, Kusakabe T, Yamagishi
K, Kimata K, Kakuta Y, Watanabe H.,
Glucuronyltransferase activity of KfiC from Escherichia coli strain K5 requires association of KfiA: KfiC and KfiA are essential enzymes for production of K5 polysaccharide, N-acetylheparosan.,
J Biol Chem., 285(3):1597-1606.,2010.
２００９年
木村 誠
超好熱アーキアリボ核タンパク質酵素の構造機能相関と耐熱性
生化学,81(12):1038-1048. ,2009.
Kikutake T, Shinohara M, Takagi H, Nakashima T, Kimura M.,
The C-terminal portion of an archaeal toxin aRelE plays a crucial role
in protein synthesis inhibition.,
Biosci. Biotechnol. Biochem., 73:2766-2768. 2009.
Akasaka T, Vu NT, Chaen K, Nishi A, Satoh H, Ida H, Omori T, Kimura M.,
The action of rice branching enzyme I (BEI) on starch.,
Biosci. Biotechnol. Biochem., 73:2516-2518.,2009.
Hossain MM, Kawarabayasi Y, Kimura M, Kakuta Y.,
Expression and functional analysis of a predicted AtsG arylsulphatase identified
from Mycobacterium tuberculosis genomic data.,
J Biochem., 146(6):767-769.,2009.
Teramoto T, Adachi R, Sakakibara Y, Liu MC, Suiko M, Kimura M, Kakuta Y.,
On
the similar spatial arrangement of active site residues in PAPS-dependent and
phenolic sulfate-utilizing sulfotransferases.,
FEBS Lett., 583(18):3091-3094.,2009.
Doi-Kawano K, Nishimoto E, Kouzuma Y, Takahashi D, Yamashita S, Kimura M.,
Steady-state and time-resolved fluorescence spectroscopic studies on interaction
of the N-terminal region with the hairpin loop of the phytocystatin Scb.,
J. Fluoresc., 19:631-639.,2009.
Yamamoto K, Shigeoka Y, Aso Y, Banno Y, Kimura M, Nakashima T.,
Molecular and biochemical characterization of a zeta-class glutathione
S-transferase of the silkmoth,
Pest. Biochem. Physiol., 94:30-35.,2009.
Iwatani T, Okino N, Sakakura M, Kajiwara H, Takakura Y, Kimura M, Ito M, Yamamoto T, Kakuta Y.,
Crystal structure of alpha/beta-galactoside alpha2,3-sialyltransferase from a luminous marine bacterium, Photobacterium phosphoreum.,
FEBS Lett.,583(12):2083-2087.,2009.
Teramoto T, Sakakibara Y, Liu MC, Suiko M, Kimura M, Kakuta Y.,
Snapshot of a Michaelis
complex in a sulfuryl transfer reaction: Crystal structure of a
mouse sulfotransferase, mSULT1D1, complexed with donor substrate and accepter
substrate.,
Biochem Biophys Res Commun.,383(1):83-87.,2009.
Inoue T, Okino N, Kakuta Y, Hijikata A, Okano H, Goda HM, Tani M, Sueyoshi
N, Kambayashi K, Matsumura H, Kai Y, Ito M.,
Mechanistic insights into the hydrolysis and
synthesis of ceramide by neutral ceramidase.,
J Biol Chem. ,284(14):9566-9577.,2009.
Takakura Y, Tsunashima M, Suzuki J, Usami S, Kakuta Y, Okino N, Ito M, Yamamoto T.,
Tamavidins--novel avidin-like
biotin-binding proteins from the Tamogitake mushroom.,
FEBS J.
,276(5):1383-1397.,2009.
Teramoto T, Sakakibara Y, Liu MC, Suiko M, Kimura M, Kakuta Y.,
Structural basis for the broad range substrate
specificity of a novel mouse cytosolic sulfotransferase--mSULT1D1.,
Biochem
Biophys Res Commun.,379(1):76-80.,2009.
Osawa T, Sugiura N, Shimada H, Hirooka R, Tsuji A, Shirakawa T, Fukuyama
K, Kimura M, Kimata K, Kakuta Y.,
Crystal structure of chondroitin polymerase from Escherichia coli
K4.,
Biochem Biophys Res Commun.,378(1):10-14.,2009.
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２００８年
Honda T, Kakuta Y, Kimura K, Saho J, Kimura M.,
Structure of an archaeal
homolog of the human protein complex Rpp21-Rpp29 that is a key core component
for the assembly of active ribonuclease P.,
J Mol Biol.,384(3):652-662.,2008.
Satone H, Oshima Y, Shimasaki Y, Tawaratsumida T, Oba Y,
Takahashi E, Kitano T, Kawabata S, Kakuta Y, Honjo T.,
Tributyltin-binding
protein type 1 has a distinctive lipocalin-like structure and is involved in the
excretion of tributyltin in Japanese flounder, Paralichthys olivaceus.,
Aquat
Toxicol. ,90(4):292-299.,2008.
Sobhany M, Kakuta Y, Sugiura N, Kimata K,
Negishi M.,
The Chondroitin Polymerase K4CP and the Molecular Mechanism of
Selective Bindings of Donor Substrates to Two Active Sites.,
J Biol
Chem.,283(47):32328-32333.,2008.
Teramoto T, Sakakibara Y, Inada K,
Kurogi K, Liu MC, Suiko M, Kimura M, Kakuta Y.,
Crystal structure of
mSULT1D1, a mouse catecholamine sulfotransferase.,
FEBS Lett. ,582(28):3909-3914.,2008.
Vu NT, Shimada H, Kakuta Y, Nakashima T, Ida H,
Omori T, Nishi A, Satoh H, Kimura M.,
Biochemical and Crystallographic
Characterization of the Starch Branching Enzyme I (BEI) from Oryza sativa
L.,
Biosci Biotechnol Biochem.,72(11):2858-2866.,2008.
Noguchi J,
Hayashi Y, Baba Y, Okino N, Kimura M, Ito M, Kakuta Y.,
Crystal structure of the covalent intermediate of human cytosolic beta-glucosidase.,
Biochem Biophys Res Commun.,374(3):549-552.,2008.
Matsushima A, Teramoto T,
Okada H, Liu X, Tokunaga T, Kakuta Y, Shimohigashi Y.,
ERRgamma tethers
strongly bisphenol A and 4-alpha-cumylphenol in an induced-fit
manner.,
Biochem Biophys Res Commun. ,373(3):408-413.,2008.
Hada K,
Nakashima T, Osawa T, Shimada H, Kakuta Y, Kimura M.,
Crystal structure and
functional analysis of an archaeal chromatin protein Alba from the
hyperthermophilic archaeon Pyrococcus horikoshii OT3.,
Biosci Biotechnol
Biochem.,72(3):749-758.,2008.
Kakuta Y, Okino N, Kajiwara H, Ichikawa M, Takakura Y,Ito M, Yamamoto T.,
Crystal structure of Vibrionaceae
Photobacterium sp. JT-ISH-224 alpha-2,6-sialyltransferase in a ternary complex
with donor product CMP and acceptor substrate lactose: catalytic mechanism and
substrate recognition.,
Glycobiology,18, 66-73.,2008.
Zhang X,
Nakashima T, Kakuta Y, Yao M, Tanaka I, Kimura M.,
Crystal structure of an
archaeal Ski2p-like protein from Pyrococcus horikoshii OT3.,
Protein Sci.,17:136-145.,2008.
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２００７年
Hayashi Y, Okino N, Kakuta Y, Shikanai T, Tani M, Narimatsu H, Ito M.,
Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase.,
J Biol Chem., 282, 30889-30900.,2007.
Matsushima A, Kakuta Y, Teramoto T, Koshiba T, Liu X, Okada H, Tokunaga
T, Kawabata S, Kimura M, Shimohigashi Y.,
Structural evidence for endocrine disruptor bisphenol A binding to human
nuclear receptor ERR gamma.,
J Biochem., 142, 517-524.,2007.
Goto T, Abe Y, Kakuta Y, Takeshita K, Imoto T, Ueda T.,
Crystal structure of Tapes japonica Lysozyme with substrate analogue: structural
basis of the catalytic mechanism and manifestation of its chitinase activity
accompanied by quaternary structural change.,
J Biol Chem. 282, 27459-27467.,2007.
Terada A, Yoshida T, Kimura M.,
Identification of nucleotide residues essential for RNase P activity from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.,
Biosci Biotechnol Biochem. 71, 1940-1945.,2007.
Okino N, Kakuta Y, Kajiwara H, Ichikawa M, Takakura Y, Ito M, Yamamoto
T.,
Purification, crystallization and preliminary crystallographic characterization
of the alpha 2,6-sialyltransferase from Photobacterium sp. JT-ISH-224.,
Acta Crystallogr Sect F Struct Biol Cryst Commun. 63, 662-664.,2007.
Yamamoto K, Kimura M, Aso Y, Banno Y and Koga K.,
Characterization of superoxide dismutase from the fall webworm, Hyphantria cunea : comparison of its properties to superoxide dismutase from the silkworm Bombyx mori.,
Appl. Entomol. Zool., 42, 465-472.,2007.
角田佳充，木村誠，
古細菌リボヌクレアーゼP構成タンパク質の結晶構造解析，
日本結晶学会誌，49, 255-258.,2007.
高木久徳，菊竹智恵，木村誠，
タンパク質合成抑制因子RelEの作用機構
RelEはリボソーム依存性のリボヌクレアーゼか？，
生物と化学，45, 530-532.,2007.
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２００６年
Terada A, Honda T, Fukuhara H, Hada K, Kimura M.,
Characterization of the archaeal ribonuclease P proteins from Pyrococcus
horikoshii OT3.,
J Biochem., 140(2):293-298.,2006.
Fukuhara H, Kifusa M, Watanabe M, Terada A, Honda T, Numata T, Kakuta Y,
Kimura M.,
A fifth protein subunit Ph1496p elevates the optimum temperature for the
ribonuclease P activity from Pyrococcus horikoshii OT3.,
Biochem Biophys Res Commun.,343(3):956-964.,2006.
Kawano S, Kakuta Y, Nakashima T, Kimura M. ,
Crystal structures of the Nicotiana glutinosa ribonuclease NT in complex
with nucleoside monophosphates.,
J Biochem (Tokyo). ,140(3):375-81.,2006.
Kawano S, Nakashima T, Kakuta Y, Tanaka I, Kimura M.,
Crystal structure of protein Ph1481p in complex with protein Ph1877p of
archaeal RNase P from Pyrococcus horikoshii OT3: implication of dimer formation
of the holoenzyme.,
J. Mol Biol.,357, 583-591.,2006.
Nomura T, Nakano K, Maki Y, Naganuma T, Nakashima T, Tanaka I, Kimura M,
Hachimori A, Uchiumi T.,
In vitro reconstitution of the GTPase-associated centre of the archaebacterial
ribosome: the functional features observed in a hybrid form with Escherichia
coli 50S subunits.,
Biochem J.,396(3):565-571.,2006.
木村 誠
タンパク質合成抑制因子ＲｅｌＥとその調節の構造基盤，
生物物理４６（５），２７９−２８２.,２００６.
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