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publications

‚Q‚O‚P‚V”N

Jiang D, Izumi K, Ueda T., Oshima K, Nakashima K, and Kimura M, Functional characterization of archaeal homologues of a human nuclear RNase P proteins Rpp21 and Rpp29 provides insights into the molecular basis of their cooperativity in catalysis. Biochem. Biophys. Res. Commun., 482, 68-74 (2017).

Zhang J, Ito H, Hino M, and Kimura M, A RelE/ParE superfamily toxin in Vibrio parahaemolyticus has DNA nicking endonuclease activity. Biochem. Biophys. Res. Commun., 489, 29-34 (2017).

Zhang J, Taniguchi S, Ito H, Iiyama K, Hino M, Katayama T, and Kimura M, Expression of the Vibrio parahaemolyticus toxin in Escherichia coli results in chromosomal DNA degradation. Biosci. Biotechnol. Biochem., 81, 1937-1940 (2017).

Gao X, Oshima K, Ueda T, Nakashima T, and Kimura M, A three-dimensional model of RNase P of the hyperthermophilic archaeon Pyrococcus horikoshii OT3. Biochem. Biophys. Res. Commun., 493, 1063-1068 (2017).

–Ø‘º½AƒA[ƒLƒA‚Ì“]ŽÊŒãCüERNAƒvƒƒZƒVƒ“ƒOAƒA[ƒLƒA‚̶•¨ŠwAi“ú–{ƒA[ƒLƒAŒ¤‹†‰ïŠÄCAΖì—ǃAÕŒ©°K@•ÒjA‹¤—§o”ÅApp. 107-113i2017j.

Kimura M, Oshima K, Gao X, Jiang D, Nakashima T, and Ueda T, Structure and function of archaeal ribonuclease P. In Nucleic Acids and Molecular Biology Vol. 32, RNA Metabolism and Gene Expression in Archaea, B. Clouet-d'Orval (Eds) Springer Nature, pp. 159-175 (2017).
https://link.springer.com/chapter/10.1007/978-3-319-65795-0_7

Kimura M, Structural basis for activation of an archaeal ribonuclease P RNA by protein cofactors. Biosci. Biotechnol. Biochem., 81, 1670-1680 (2017).



‚Q‚O‚P‚U”N

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 M

Functional implication of archaeal homologues of human RNase P protein pair Pop5 and Rpp30.
Biochem. 2016 Jan;159(1):31-40.




‚Q‚O‚P‚T”N

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.

‚Q‚O‚P‚S”N

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 TƒÕC-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.



‚Q‚O‚P‚R”N

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.



‚Q‚O‚P‚Q”N

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.


‚Q‚O‚P1”N

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.

‚Q‚O‚P‚O”N

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.


‚Q‚O‚O‚X”N



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¶‰»Šw,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.


‚Q‚O‚O‚W”N


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.


‚Q‚O‚O‚V”N


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.

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“ú–{Œ‹»Šw‰ïŽC49, 255-258.,2007.

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¶•¨‚Ɖ»ŠwC45, 530-532.,2007.


‚Q‚O‚O‚U”N


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.

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