研究领域

Structural Biology/ Protein Crystallography

Function of biological macromolecules elucidated by their three-dimensional structures Molecular mechanism of formation and maturation of three-dimensional structures of proteins Methodology in protein crystallography

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Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0 Å. S. Niwa, L.-J. Yu, K. Takeda, Y. Hirano, T. Kawakami, ZY. Wang-Otomo, and K. Miki Nature, in press pubmed PDBID:3WMM, 3WMN, 3WMO Roles of the protruding loop of factor B essential for the localization of lipoproteins (LolB) in the anchoring of bacterial triacylated proteins to the outer membrane. Y. Hayashi, R. Tsurumizu, J. Tsukahara, K. Takeda, SI. Narita, M. Mori, K. Miki, and H. Tokuda J. Biol. Chem., in press. pubmed PDBID:3WJT, 3WJU, 3WJV Crystal Structure of Phosphopantothenate Synthetase from Thermococcus kodakarensis. A. Kishimoto, A. Kita, T Ishibashi, H. Tomita, Y. Yokooji, T. Imanaka, H. Atomi, and K. Miki Proteins: Struct., Funct., Bioinfo., in press pubmed PDBID:3WDK, 3WDL, 3WDM Structural characterization of a ligand-bound form of Bacillus subtilis FadR involved in the regulation of fatty acid degradation. M. Fujihashi, T. Nakatani, K. Takeda, K. Hirooka, H. Matsuoka, Y. Fujita, and K. Miki Proteins: Struct., Funct., Bioinfo., in press. pubmed PDBID:3WHB, 3WHC Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation. T. Tominaga, S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, and K. Miki Proc. Natl. Acad. Sci. USA, 110, 20485-20490 (2013). pubmed PDBID:3WJP, 3WJQ, 3WJR Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. M. Fujihashi, T. Ishida, S. Kuroda, L. P. Kotra, E. F. Pai, and K. Miki J. Am. Chem. Soc., 135, 17432-17443 (2013). pubmed PDBID:3WJW, 3WJX, 3WJY, 3WJZ, 3WK0, 3WK1, 3WK2, 3WK3 Elucidations of the Catalytic Cycle of NADH-cytochrome b5 reductase by X-Ray Crystallography: New Insights into Regulation of Efficient Election Transfer. M. Yamada, T. Tamada, K. Takeda, F. Matsumoto, H. Ohno, M. Kosugi, K. Takaba, Y. Shoyama, S. Kimura, R. Kuroki, and K. Miki J. Mol. Biol., 425, 4295-4306 (2013). pubmed PDBID:3W2E, 3W2F, 3W2G, 3W2H, 3W2I, 3W5H An uncharacterized member of the ribokinase family in Thermococcus kodakarensis exhibits myo-inositol kinase activity. T. Sato, M. Fujihashi, Y. Miyamoto, K. Kuwata, E. Kusaka, H. Fujita, K. Miki, and H. Atomi J. Biol. Chem., 288, 20856-20867 (2013). pubmed PDBID:3W4S Structure Analysis of Archaeal AMP Phosphorylase Reveals Two Unique Modes of Dimerization. Y. Nishitani, R. Aono, A. Nakamura, T. Sato, H. Atomi, T. Imanaka, and K. Miki J. Mol. Biol., 425, 2709-2721 (2013). pubmed PDBID:4GA4, 4GA5, 4GA6 Origin of Asymmetry at the Inter-subunit Interfaces of V1-ATPase from Thermus thermophilus. Y. Nagamatsu, K. Takeda, T. Kuranaga, N. Numoto, and K. Miki J. Mol. Biol., 425, 2699-2708 (2013). pubmed PDBID:3W3A Identification and structure of a novel archaeal HypB for [NiFe] hydrogenase maturation. D. Sasaki, S. Watanabe, R. Matsumi, T. Shoji, A. Yasukochi, K. Tagashira, W. Fukuda, T. Kanai, H. Atomi, T. Imanaka, and K. Miki J. Mol. Biol., 425, 1627-1640 (2013). pubmed PDBID:3VX3 Atomic-resolution structure of the orotidine 5'-monophosphate decarboxylase product complex combined with surface plasmon resonance analysis: Implications for the catalytic mechanism. M. Fujihashi, K. Mito, E. F. Pai, and K. Miki J. Biol. Chem., 288, 9011-9016 (2013). pubmed PDBID:3W07 Observation of the orientation of membrane protein crystals grown in high magnetic force fields. N. Numoto, K. Shimizu, K. Matsumoto, K. Miki, and A. Kita J. Cryst. Growth, 367, 53-56 (2013). Nonequivalence Observed for the 16-Meric Structure of a Small Heat Shock Protein, SpHsp16.0, from Schizosaccharomyces pombe. Y. Hanazono, K. Takeda, T. Oka, T. Abe, T. Tomonari, N. Akiyama, Y. Aikawa, M. Yohda, and K. Miki Structure, 21, 220-228 (2013). pubmed PDBID:3W1Z Crystal Structures of the HypCD Complex and the HypCDE Ternary Complex: Transient Intermediate Complexes during [NiFe] Hydrogenase Maturation. S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, and K. Miki Structure, 20, 2124-2137 (2012). pubmed PDBID:3VYR, 3VYS, 3VYT, 3VYU Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway. R. Aono, T. Sato, A. Yano, S. Yoshida, Y. Nishitani, K. Miki, T. Imanaka, and H. Atomi J. Bacteriol., 194, 6847-6855 (2012). pubmed Crystal sample pins and a storage cassette system compatible with the protein crystallography beamlines at both the Photon Factory and SPring-8. M. Fujihashi, M. Hiraki, G. Ueno, S. Baba, H. Murakami, M. Suzuki, N. Watanabe, I. Tanaka, A. Nakagawa, S. Wakatsuki, M. Yamamoto, and K. Miki J. Appl. Crystallogr., 45, 1156-1161 (2012). A detailed biochemical characterization of phosphopantothenate synthetase, a novel enzyme involved in coenzyme A biosynthesis in the Archaea. T. Ishibashi, H. Tomita, Y. Yokooji, T. Morikita, B. Watanabe, J. Hiratake, A. Kishimoto, A. Kita, K. Miki, T. Imanaka, and H. Atomi Extremophiles, 16, 819-828 (2012). pubmed Structural basis of [NiFe] hydrogenase maturation by Hyp proteins. S. Watanabe, D. Sasaki, T. Tominaga, and K. Miki Biol. Chem., 393, 1089-1100 (2012). pubmed Structure of the [NiFe]-hydrogenase maturation protein HypF from Thermococcus kodakarensis KOD1. T. Tominaga, S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka and K. Miki Acta Crystallogr., F68, 1153-1157 (2012). pubmed PDBID:4G9I