Publications

2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1997 1996 1995 1994 

2012 ^†

Dynamic, ligand-dependent conformational change triggers the reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1.
A. Nakamura, M. Fujihashi, R. Aono, T. Sato, Y. Nishiba, S. Yoshida, A. Yano, H. Atomi, T. Imanaka, and K. Miki
J. Biol. Chem., in press pubmed PDBID:3A11, 3A9C, 3VM6

Characterization and in vitro interaction study of a [NiFe] hydrogenase large subunit from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1.
D. Sasaki, S. Watanabe, T. Kanai, H. Atomi, T. Imanaka, and K. Miki
Biochem. Biophys. Res. Commun., 417, 192-196 (2012). pubmed

2011 ^†

Structure and mutation analysis of archaeal geranylgeranyl reductase.
D. Sasaki, M. Fujihashi, Y. Iwata, M. Murakami, T. Yoshimura, H. Hemmi, and K. Miki
J. Mol. Biol., 409, 543-557 (2011). pubmed PDBID:3OZ2

Dimer structure and conformational variability in the N-terminal region of an archaeal small heat shock protein, StHsp14.0.
K. Takeda, T. Hayashi, T. Abe, Y. Hirano, Y. Hanazono, M. Yohda, and K. Miki
J. Struct. Biol., 174, 92-99 (2011). pubmed PDBID: 3AAB, 3AAC

Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation.
D. Sasaki, M. Fujihashi, N. Okuyama, Y. Kobayashi, M. Noike, T. Koyama, and K. Miki
J. Biol. Chem., 286, 3729-3740 (2011). pubmed PDBID:3AQB, 3AQC

2010 ^†

Crystal structure of 3-hexulose-6-phosphate synthase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily.
I. Orita, A. Kita, H. Yurimoto, N. Kato, Y. Sakai, and K. Miki
Proteins: Struct., Funct., Bioinfo., 78, 3488-3492 (2010). pubmed PDBID:3AJX

Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile.
Y. Nishitani, S. Yoshida, M. Fujihashi, K. Kitagawa, T. Doi, H. Atomi, T. Imanaka, and K. Miki
J. Biol. Chem., 285, 39339-39346 (2010). pubmed PDBID:3A12, 3KDN, 3KDO

Monomer-Dimer Transition of the Conserved N-terminal Domain of the Mammalian Peroxisomal Matrix Protein Import Receptor, Pex14p.
J.-R. Su, K. Takeda, S. Tamura, Y. Fujiki, and K. Miki
Biochem. Biophys. Res. Commun., 394, 217-221 (2010). pubmed

Crystal Structure of the Electron Carrier Domain of the Reaction Center Cytochrome c_z Subunit from Green Photosynthetic Bacterium Chlorobium tepidum.
Y. Hirano, M. Higuchi, C. Azai, H. Oh-oka, K. Miki, and ZY Wang
J. Mol. Biol., 397, 1175-1187 (2010). pubmed PDBID: 3A9F

Crystal Structure of a Thermophilic GrpE Protein: Insight into Thermosensing Function for the DnaK Chaperone System.
A. Nakamura, K. Takumi, and K. Miki
J. Mol. Biol., 396, 1000-1011 (2010). pubmed PDBID: 3A6M

Detailed Assessment of X-ray Induced Structural Perturbation in a Crystalline State Protein.
K. Takeda, K. Kusumoto, Y. Hirano, and K. Miki
J. Struct. Biol., 169, 135-144 (2010). pubmed PDBID: 3A38, 3A39

2009 ^†

Crystal Structure of HypA, a Nickel-binding Metallochaperone for [NiFe] Hydrogenase Maturation.
S. Watanabe, T. Arai, R. Matsumi, H. Atomi, T. Imanaka, and K. Miki
J. Mol. Biol., 394, 448-459 (2009). pubmed PDBID: 3A43, 3A44

Inter-subunit Interaction and Quaternary Rearrangement Defined by the Central Stalk of Prokaryotic V1-ATPase.
N. Numoto, Y. Hasegawa, K. Takeda, and K. Miki
EMBO Rep., 10, 1228-1234 (2009). pubmed PDBID: 3A5C, 3A5D

Crystallization and Heavy-atom Derivatization of StHsp14.0, a Small Heat-shock Protein from Sulfolobus tokodaii.
T. Hayashi, T. Abe, K. Takeda, N. Akiyama, M. Yohda, and K. Miki
Acta Crystallogr., F65, 1007-1010 (2009). pubmed

Overexpression, Characterization, and Crystallization of the Functional Domain of Cytochrome c(z) from Chlorobium tepidum.
M. Higuchi, Y. Hirano, Y. Kimura, H. Oh-oka, K. Miki, and ZY Wang
Photosynth Res., 102, 77-84 (2009). pubmed

Crystal Structure of a Periplasmic Substrate-binding Protein in Complex with Calcium Lactate.
N. Akiyama, K. Takeda, and K. Miki
J. Mol. Biol., 392, 559-565 (2009). pubmed PDBID: 2ZZV, 2ZZW, 2ZZX

Crystal Structure of the Conserved N-terminal Domain of the Peroxisomal Matrix Protein Import Receptor, Pex14p.
J.-R. Su, K. Takeda, S. Tamura, Y. Fujiki, and K. Miki
Proc. Natl. Acad. Sci. USA, 106, 417-421 (2009). pubmed PDBID: 3FF5

Crystal Structure of PH1733, an Aspartate Racemase Homologue, from Pyrococcus horikoshii OT3
A. Kita, S. Tasaki, M. Yohda, and K. Miki
Proteins: Struct., Funct., Bioinfo., 74, 240-244 (2009). pubmed PDBID: 2ZSK

2008 ^†

Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin
N. Numoto, T. Nakagawa, A. Kita, Y. Sasayama, Y. Fukumori, and K. Miki
Biochemistry, 47, 11231-11238 (2008). pubmed PDBID: 2ZS0, 2ZS1

Structural and Molecular Characterization of the Prefoldin Beta Subunit from Thermococcus strain KS-1
H. Kida, Y. Sugano, R. Iizuka, M. Fujihashi, M. Yohda, and K. Miki
J. Mol. Biol., 383, 465-474 (2008). pubmed PDBID: 2ZQM

Structure of the Partially Unliganded met State of 400 kDa Hemoglobin: Insights into Ligand-induced Structural Changes of Giant Hemoglobins
N. Numoto, T. Nakagawa, A. Kita, Y. Sasayama, Y. Fukumori, and K. Miki
Proteins: Struct., Funct., Bioinfo., 73, 113-125 (2008). pubmed PDBID: 2ZFO

Introduction of a Lethal Redox Switch That Controls the Opening and Closing of the Hydrophobic Cavity in LolA
S. Watanabe, Y. Oguchi, K. Takeda, K. Miki, and H. Tokuda
J. Biol. Chem., 283, 25421-25427 (2008). pubmed

Opening and Closing of the Hydrophobic Cavity of LolA Coupled to the Lipoprotein Binding and Release
Y. Oguchi, K. Takeda, S. Watanabe, N. Yokota, K. Miki, and H. Tokuda
J. Biol. Chem., 283, 25414-25420 (2008). pubmed PDBID: 2ZPC, 2ZPD

Crystal Structure of N-Acylamino Acid Racemase from Thermus thermophilus HB8
M. Hayashida, S.-H. Kim, K. Takeda, T. Hisano, and K. Miki
Proteins: Struct., Funct., Bioinfo., 71, 519-523 (2008). pubmed PDBID: 2ZC8

Crystal Structure of the [2Fe-2S] Oxidative-Stress Sensor SoxR bound to DNA
S. Watanabe, A. Kita, K. Kobayashi, and K. Miki
Proc. Natl. Acad. Sci. USA, 105, 4121-4126 (2008). pubmed PDBID: 2ZHH, 2ZHG

Crystal Structure of Human Cyclophilin D in Complex with Its Inhibitor, Cyclosporin A at 0.96 A Resolution
K. Kajitani, M. Fujihashi, Y. Kobayashi, S. Shimizu, Y. Tsujimoto, and K. Miki
Proteins: Struct., Funct., Bioinfo., 70, 1635-1639 (2008). pubmed PDBID: 2Z6W

Structure and Molecular Dynamics Simulation of Archaeal Prefoldin: The Molecular Mechanism for Binding and Recognition of Nonnative Substrate Proteins
A. Ohtaki, H. Kida, Y. Miyata, N. Ide, A. Yonezawa, T. Arakawa, R. Iizuka, K. Noguchi, A. Kita, M. Odaka, K. Miki, and M. Yohda
J. Mol. Biol., 376, 1130-1141 (2008). pubmed PDBID: 2ZDI

Crystal Structures of the Flavin Reductase Component (HpaC) of 4-Hydroxyphenylacetate 3-Monooxygenase from Thermus thermophilus HB8: Strcutural Basis for the Flavin Affinity
S.-H. Kim, T. Hisano, W. Iwasaki, A. Ebihara, and K. Miki
Proteins: Struct., Funct., Bioinfo., 70, 718-730 (2008). pubmed PDBID: 2ECR, 2ECU, 2ED4

2007 ^†

Structural Basis for Regulation of Bifunctional Roles in Replication Initiator Protein
A. Nakamura, C. Wada, and K. Miki
Proc. Natl. Acad. Sci. USA, 104, 18484-18489 (2007). pubmed PDBID: 2Z9O

Crystal Structure of the Oxygenase Component (HpaB) of the 4-Hydroxyphenylacetate 3-Monooxygenase from Thermus thermophilus HB8
S.-H. Kim, T. Hisano, K. Takeda, W. Iwasaki, A. Ebihara, and K. Miki
J. Biol. Chem., 282, 33107-33117 (2007). pubmed PDBID: 2YYG, 2YYI, 2YYJ

Crystallization and Preliminary X-ray Crystallographic Study of [NiFe] Hydrogenase Maturation Factor HypE from Thermococcus kodakaraensis KOD1
T. Arai, S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, and K. Miki
Acta Crystallogr., F63, 765-767 (2007). pubmed

Structural Studies of the Cpx Pathway Activator NlpE on the Outer Membrane of Escherichia coli
Y. Hirano, Md. M. Hossain, K. Takeda, H. Tokuda, and K. Miki
Structure, 15, 963-976 (2007). pubmed PDBID: 2Z4H, 2Z4I

Purification, Characterization and Crystallization of the Core Complex from Thermophilic Purple Sulfur Bacterium Thermochromatium tepidum
H. Suzuki, Y. Hirano, Y. Kimura, S. Takaichi, M. Kobayashi, K. Miki, and Z.-Y. Wang
Biochim. Biophys. Acta, 1767, 1057-1063 (2007). pubmed

Crystal Structure of the Stationary Phase Survival Protein SurE with Metal Ion and AMP
W. Iwasaki and K. Miki
J. Mol. Biol., 371, 123-136 (2007). pubmed PDBID: 2E69, 2E6B, 2E6C, 2E6E, 2E6G, 2E6H

Crystal Structures of [NiFe] Hydrogenase Maturation Proteins, HypC, HypD and HypE: Insights into Cyanation Reaction by Thiol Redox Signaling
S. Watanabe, R. Matsumi, T. Arai, H. Atomi, T. Imanaka, and K. Miki
Mol. Cell, 27, 29-40 (2007). pubmed PDBID: 2Z1C, 2Z1D, 2Z1E, 2Z1F

Crystallization and Preliminary X-ray Analysis of the Oxygenase Component (HpaB) of 4-Hydroxyphenylacetate 3-Monooxygenase from Thermus thermophilus HB8
S.-H. Kim, H. Miyatake, T. Hisano, W. Iwasaki, A. Ebihara, and K. Miki
Acta Crystallogr., F63, 556-559 (2007). pubmed

Crystal Structures of Uridine-diphospho-N-acetylglucosamine Pyrophosphorylase from Candida albicans and Catalytic Reaction Mechanism
D. Maruyama, Y. Nishitani, T. Nonaka, A. Kita, T. A. Fukami, T. Mio, H. Yamada-Okabe, T. Yamada-Okabe, and K. Miki
J. Biol. Chem., 282, 17221-17230 (2007). pubmed PDBID: 2YQC, 2YQH, 2YQJ, 2YQS

Crystallization and Preliminary X-ray Crystallographic Studies of [NiFe] Hydrogenase Maturation Proteins, HypC and HypD
S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, and K. Miki
Acta Crystallogr., F63, 538-541 (2007). pubmed

Expression and Purification of F Plasmid RepE and Preliminary X-ray Crystallographic Study of Its Complex with Operator DNA
A. Nakamura, C. Wada, and K. Miki
Acta Crystallogr., F63, 346-349 (2007). pubmed

Crystal Structure of TTHA1657 (AT-rich DNA-binding protein; p25) from Thermus thermophilus HB8 at 2.16 A Resolution
A. Nakamura, A. Sosa, H. Komori, A. Kita, and K. Miki
Proteins: Struct., Funct., Bioinfo., 66, 755-759 (2007). pubmed PDBID: 2DT5

Crystal Structure of Archaeal Photolyase from Sulfolobus tokodaii with Two FAD Molecules: Implication of a Novel Light-harvesting Cofactor
M. Fujihashi, N. Numoto, Y. Kobayashi, A. Mizushima, M. Tsujimura, A. Nakamura, Y. Kawarabayasi, and K. Miki
J. Mol. Biol., 365, 903-910 (2007). pubmed PDBID: 2E0I

2006 ^†

Crystallization and Preliminary X-ray Crystallographic Studies of Oxidative Stress Sensor SoxR and Its Complex with DNA
S. Watanabe, A. Kita, K. Kobayashi, Y. Takahashi, and K. Miki
Acta Crystallogr., F62, 1275-1277 (2006). pubmed

Purification, Crystallization and Preliminary X-ray Crystallographic Analysis of the Outer Membrane Lipoprotein NlpE from Escherichia coli
Y. Hirano, Md. M. Hossain, K. Takeda, H. Tokuda, and K. Miki
Acta Crystallogr., F62, 1227-1230 (2006). pubmed

Purification, Crystallization and Preliminary X-ray Diffraction Studies of UDP-N-acetylglucosamine pyrophosphorylase from Candida albicans
D. Maruyama, Y. Nishitani, T. Nonaka, A. Kita, T. A. Fukami, T. Mio, H. Yamada-Okabe, T. Yamada-Okabe, and K. Miki
Acta Crystallogr., F62, 1206-1208 (2006). pubmed

Fate Determination of the Flavin Photoreceptions in the Cyanobacterial Blue Light Receptor TePixD (Tll0078)
K. Okajima, Y. Fukushima, H. Suzuki, A. Kita, Y. Ochiai, M. Katayama, Y. Shibata, K. Miki, S. Itoh, and M. Ikeuchi
J. Mol. Biol., 363, 10-18 (2006). pubmed

Roles of Conserved Basic Amino Acid Residues and Activation Mechanism of the Hyperthermophilic Aspartate Racemase at High Temperature
T. Yoshida, T. Seko, O. Okada, K. Iwata, L. Liu, K. Miki, and M. Yohda
Proteins: Struct., Funct., Bioinfo., 64, 502-512 (2006). pubmed

Crystal Structures of N-acetylglucosamine-phosphate Mutase, a Member of the α-D-Phosphohexomutase Superfamily, and Its Substrate and Product Complexes
Y. Nishitani, D. Maruyama, T. Nonaka, A. Kita, T. A. Fukami, T. Mio, H. Yamada-Okabe, T. Yamada-Okabe, and K. Miki
J. Biol. Chem., 281, 19740-19747 (2006). pubmed PDBID: 2DKA, 2DKC, 2DKD

Differential Analysis of D-β-Asp-Containing Proteins Found in Normal and Infrared Irradiated Rabbit Lens
T. Takata, T. Shimo-Oka, M. Kojima, K. Miki, and N. Fujii
Biochem. Biophys. Res. Commun., 344, 263-271 (2006). pubmed

Purification, Crystallization, and Preliminary X-ray Diffraction Studies of N-acetylglucosamine-phosphate Mutase from Candida albicans
Y. Nishitani, D. Maruyama, T. Nonaka, A. Kita, T. A. Fukami, T. Mio, H. Yamada-Okabe, T. Yamada-Okabe, and K. Miki
Acta Crystallogr., F62, 419-421 (2006). pubmed

The Crystal Structure of Polyhydroxybutyrate Depolymerase from Penicillium Funiculosum Provide insights into Recognition and Degradation of Biopolyesters
T. Hisano, K. Kasuya, Y. Tezuka, N. Ishii, E. Oroudjev, H. Hansma, T. Kobayashi, M. Shiraki, T. Iwata, Y. Doi, T. Saito, and K. Miki
J. Mol. Biol., 356, 993-1004 (2006). pubmed PDBID: 2D80, 2D81

Crystal Structure of the C2 Domain of Class II Phosphatidylinositide 3-Kinase C2α
L. Liu, X. Song, D. He, C. Komma, A. Kita, J. V. Virbasius, G. Huang, H. D. Bellamy, K. Miki, M. P. Czech, and G. W. Zhou
J. Biol. Chem., 281, 4254-4260 (2006). pubmed PDBID: 2B3R

2005 ^†

Improved expression, purification, and crystallization of a putative N-acetyl-γ-glutamyl- phosphate reductase from rice (Oryza sativa)
J. Miura-Ohnuma, T. Nonaka, S. Katoh, K. Murata, A. Kita, K. Miki, and E. Katoh
Acta Crystallogr., F61, 1058-1061 (2005). pubmed

Crystal Structure of Putative N-acetyl-γ-glutamyl-phosphate Reductase (AK071544) from Rice (Oryza sativa)
T. Nonaka, A. Kita, J. Miura-Ohnuma, E. Katoh, N. Inagaki, T. Yamazaki, and K. Miki
Proteins: Struct., Funct., Bioinfo., 61, 1137-1140 (2005). pubmed PDBID: 2CVO

Crystal Structure of the Small Form of Glucose-Inhibited Division Protein A from Thermus thermophilus HB8
W. Iwasaki, H. Miyatake, and K. Miki
Proteins: Struct., Funct., Bioinfo., 61, 1121-1126 (2005). pubmed PDBID: 2CUL

Crystal Structure of Atypical Cytoplasmic ABC-ATPase SufC from Thermus thermophilus HB8
S. Watanabe, A. Kita, and K. Miki
J. Mol. Biol., 353, 1043-1054 (2005). pubmed PDBID: 2D2E, 2D2F

Bacillus circulans MH-K1 Chitosanase: Amino Acid Residues Responsible for Substrate Binding
T. Fukamizo, S. Amano, K. Yamaguchi, T. Yoshikawa, T. Katsumi, J. Saito, M. Suzuki, K. Miki, Y. Nagata, and A. Ando
J. Biochem., 138, 563-569 (2005). pubmed PDBID: 2D05

Structure of an Extracellular Giant Haemoglobin of the Gutless Beard Worm Oligobrachia mashikoi
N. Numoto, T. Nakagawa, A. Kita, Y. Sasayama, Y. Fukumori, and K. Miki
Proc. Natl. Acad. Sci. USA, 102, 14521-14526 (2005). pubmed PDBID: 2D2M, 2D2N

Characterization of New D-β-Aspartate-containing Proteins in a Lens-derived Cell Line
T. Takata, T. Shimo-Oka, K. Miki, and N. Fujii
Biochem. Biophys. Res. Commun., 334, 1022-1031 (2005). pubmed

Crystal Structure of Stilbene Synthase from Arachis hypogaea
Y. Shomura, I. Torayama, D.-Y. Suh, T. Xiang, A. Kita, U. Sankawa, and K. Miki
Proteins: Struct., Funct., Bioinfo., 60, 803-806 (2005). pubmed PDBID: 1Z1E, 1Z1F

Structural and Functional Studies on the Tetraheme Cytochrome Subunit and Its Electron Donor Proteins: the Possible Docking Mechanisms during the Electron Transfer Reaction
T. Nogi, Y. Hirano, and K. Miki
Photosynthesis Res., 85, 87-99 (2005). pubmed

Crystallization and preliminary X-ray crystallographic analysis of extracellular giant hemoglobin from pogonophoran Oligobrachia mashikoi
N. Numoto, T. Nakagawa, A. Kita, Y. Sasayama, Y. Fukumori, and K. Miki
Biochim. Biophys. Acta, 1750, 103-117 (2005). pubmed

Electric Charge-Separation of Protein Samples for X-ray Crystallography Using Free-flow Isoelectric Focusing
S.-H. Kim, H. Miyatake, T. Ueno, T. Nagao, and K. Miki
Acta Crystallogr., D61, 799-802 (2005). pubmed

Development of a Fully-Automated Macromolecular Crystallization / Observation Robotic System, HTS-80
H. Miyatake, S.-H. Kim, I. Motegi, H. Matsuzaki, H. Kitahara, A. Higuchi, and K. Miki
Acta Crystallogr., D61, 658-663 (2005). pubmed

Structure of a Cynobacterial BLUF Protein, Tll0078, Containing a Novel FAD-binding Blue Light Sensor Domain
A. Kita, K. Okajima, Y. Morimoto. M. Ikeuchi, and K. Miki
J. Mol. Biol., 349, 1-9 (2005). pubmed PDBID: 1X0P

Crystal Structure of Decameric Peroxiredoxin (AhpC) from Amphibacillus xylanus
K. Kitano, A. Kita, T. Hakoshima, Y. Niimura, and K. Miki
Proteins: Struct., Funct., Bioinfo., 59, 644-647 (2005). pubmed PDBID: 1WE0

An Engineered Chaperonin Caging a Guest Protein: Structural Insights and Potential As a Protein Expression Tool
M. Furutani, J. Hata, Y. Shomura, K. Itami, T. Yoshida, Y. Izumoto, A. Togi, A Ideno, T. Yasunaga, K. Miki, and T. Maruyama
Prot. Sci., 14, 341-350 (2005). pubmed

Crystal Structure of the Co-chaperonin Cpn10 from Thermus thermophilus HB8
N. Numoto, A. Kita, and K. Miki
Proteins: Struct., Funct., Bioinfo., 58, 498-500 (2005). pubmed PDBID: 1WNR

2004 ^†

Multi-wavelength anomalous diffraction method for I and Xe atoms using ultra-high-energy X-rays from SPring-8
K. Takeda, H. Miyatake, S.-Y. Park, M. Kawamoto, N. Kamiya, and K. Miki
J. Appl. Crystallogr., 37, 925-933 (2004).

The crystal structure of an oxidatively-stable subtilisin-like alkaline serine protease, KP-43, with a C-terminal beta-barrel domain
T. Nonaka, M. Fujihashi, A. Kita, K. Saeki, S. Ito, K. Horikoshi, and K. Miki
J. Biol. Chem., 279, 47344-47351 (2004). pubmed PDBID: 1WMD, 1WME, 1WMF

DNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF reconstitution and X-ray induced FAD-reduction
R. Kort H. Komori, S. Adachi, K. Miki, and A. P. M. Eker
Acta Crystallogr., D60, 1205-1213 (2004). pubmed PDBID: 1OWM, 1OWN, 1OWO, 1OWP, 1OWL

Structure of the C subunit of V-type ATPase from Thermus thermophilus at 1.85 A resolution
N. Numoto, A. Kita, and K. Miki
Acta Crystallogr., D60, 810-815 (2004). pubmed PDBID: 1V9M

Involvement of Tyrosines at Fucose-Binding Sites of Aleuria aurantia Lectin: Non-Equal Response to Site-Directed Mutagenesis among Five Sites
K. Amano, M. Fujihashi, A. Ando, K. Miki, and Y. Nagata
Biosci. Biotechnol. Biochem., 68, 841-847 (2004). pubmed

Crystallization and Preliminary X-ray Crystallographic Studies on the Small Form of Glucose-inhibited Division Protein A from Thermus thermophilus HB8
W. Iwasaki, H. Miyatake, A. Ebihara, and K. Miki
Acta Crystallogr., D60, 515-517 (2004). pubmed

The N-terminal Domain of the Replication Initiator Protein RepE Is a Dimerization Domain Forming a Stable Dimer
A. Nakamura, H. Komori, G. Kobayashi, A. Kita, C. Wada, and K. Miki
Biochem. Biophys. Res. Commun., 315, 10-15 (2004). pubmed

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
Y. Shomura, T. Yoshida, R. Iizuka, T. Maruyama, M. Yohda, and K. Miki
J. Mol. Biol., 335, 1265-1278 (2004). pubmed PDBID: 1Q2V, 1Q3Q, 1Q3R, 1Q3S

Crystal Structure of Human Pirin: An Iron-Bonding Nuclear Protein and Transcription Cofactors
H. Pang, M. Bartlam, Q. Zeng, H. Miyatake, T. Hisano, K. Miki, L.-L. Wong, G. F. Gao, and Z. Rao
J. Biol. Chem., 279, 1491-1498 (2004). pubmed PDBID: 1J1L

2003 ^†

Significance of Highly Conserved Aromatic Residues in Micrococcus luteus B-P 26 Undecaprenyl Diphosphate Synthase
Y. Kharel, Y.-W. Zhang, M. Fujihashi, K. Miki, and T. Koyama
J. Biochem., 134, 819-826 (2003). pubmed

Crystallization and Preliminary X-ray Analysis of a Small Component of 4-Hydroxyphenyl-acetate 3-monooxygenase (HpaC) and Its Cofactor Complex from Thermus thermophilus HB8
S.-H. Kim, H. Miyatake, T. Hisano, N. Ohtani, and K. Miki
Acta Crystallogr., D59, 2275-2278 (2003). pubmed

ATP Binding Is Critical for the Conformational Change from an Open to Closed State in Archaeal Group II Chaperonin
R. Iizuka, T. Yoshida, Y. Shomura, K. Miki, T. Maruyama, M. Odaka, and M. Yohda
J. Biol. Chem., 278, 44959-44965 (2003). pubmed

Crystal Structure of Fucose Specific Lectin from Aleuria aurantia Binding Ligands at Three of Its Five Sugar Recognition Sites
M. Fujihashi, D. H. Peapus, N. Kamiya, Y. Nagata, and K. Miki
Biochemistry, 42, 11093-11099 (2003). pubmed PDBID: 1IUC, 1IUB

Crystal Structure of Dissimilatory Sulfite Reductase D (DsrD) Protein --- Possible Interaction with B- and Z-DNA by Its Winged-Helix Motif
N. Mizuno, G. Voordouw, K. Miki, A. Sarai, and Y. Higuchi
Structure, 11, 1133-1140 (2003). pubmed PDBID: 1UCR

A Practical Phasing Procedure Using the MAD Method without the Aid of XAFS Measurements: Successful Solution in the Structure Determination of the Outer-Membrane Lipoprotein Carrier LolA
K. Takeda, H. Miyatake, N. Yokota, S. Matsuyama, H. Tokuda, and K. Miki
Acta Crystallogr., D59, 1440-1446 (2003). pubmed

Crystal Structure of Calcium-free alpha-Amylase from Bacillus sp. Strain KSM-K38 (AmyK38) and Its Sodium Ion Binding Sites
T. Nonaka, M. Fujihashi, A. Kita, H. Hagihara, K. Ozaki, S. Ito, and K. Miki
J. Biol. Chem., 278, 24818-24824 (2003). pubmed PDBID: 1UD2, 1UD3, 1UD4, 1UD5, 1UD6, 1UD8

Crystal Structures of Bacterial Lipoprotein Localization Factors, LolA and LolB
K. Takeda, H. Miyatake, N. Yokota, S. Matsuyama, H. Tokuda, and K. Miki
EMBO J., 22, 3199-3209 (2003). pubmed PDBID: 1IWL, 1UA8, 1IWM, 1IWN

Crystallization and Preliminary Crystallographic Study of the Outer-Membrane Lipoprotein Receptor LolB, a Member of the Lipoprotein Localization Factors
K. Takeda, H. Miyatake, N. Yokota, S. Matsuyama, H. Tokuda, and K. Miki
Acta Crystallogr., D59, 1224-1226 (2003). pubmed

Mutational Analysis of Allylic Substrate Binding Site of Micrococcus luteus B-P 26 Undecaprenyl Diphosphate Synthase
K. Fujikura, Y.-W. Zhang, M. Fujihashi, K. Miki, and T. Koyama
Biochemistry, 42, 4035-4041 (2003). pubmed

X-ray Crystallographic Characterization and Phasing of a Fucose Specific Lectin from Aleuria Aurantia
M. Fujihashi, D. H. Peapus, E. Nakajima, T. Yamada, J. Saito, A. Kita, Y. Higuchi, Y. Sugawara, A. Ando, N. Kamiya, Y. Nagata, and K. Miki
Acta Crystallogr., D59, 378-380 (2003). pubmed

Crystal Structure of the (R)-Specific Enoyl-CoA Hydratase from Aeromonas caviae Involved in Polyhydroxyalkanoate Synthesis
T. Hisano, T. Tsuge, T. Fukui, T. Iwata, K. Miki, and Y. Doi
J. Biol. Chem., 278, 617-624 (2003). pubmed PDBID: 1IQ6

2002 ^†

Structural Studies of the Carbon Monoxide Complex of [NiFe] Hydrogenase from Desulfovibrio vulgaris Miyazaki F: Suggestion for the Initial Activation Site for Dihydrogen
H. Ogata, Y. Mizoguchi, N. Mizuno, K. Miki, S. Adachi, N. Yasuoka, T. Yagi, O. Yamauchi, S. Hirota, and Y. Higuchi
J. Am. Chem. Soc., 124, 11628-11635 (2002). pubmed PDBID: 1UBH, 1UBJ, 1UBK, 1UBL, 1UBO, 1UBR, 1UBM, 1UBT, 1UBU

Structure and Reaction Mechanism of Catechol 2,3-Dioxygenase (Metapyrocatechase)
T. Ishida, A. Kita, K. Miki, M. Nozaki, and K. Horiike
"Oxygen and Life, Oxygenase, Oxidases and Lipid Mediators", International Congress Series No. 1233, Y. Ishimura, M. Nozaki, S. Yamamoto, T. Shimizu, S. Narumiya, and F. Mitani, eds., Elsevier, Amsterdam, 213-220 (2002).

Structural Insight into Gene Duplication, Gene Fusion and Domain Swapping in the Evolution of PLP-independent Amino Acid Racemases
L. Liu, K. Iwata, M. Yohda, and K. Miki
FEBS Lett., 528, 114-118 (2002). pubmed PDBID: 1IU9

Crystallization and Preliminary X-ray Characterization of Archaeal Group II Chaperonin alpha Subunit from Thermococcus strain KS-1
Y. Shomura, T. Yoshida, T. Maruyama, M. Yohda, and K. Miki
Acta Crystallogr., D58, 1830-1832 (2002). pubmed

Ultrahigh-Resolution Structure of High-Potential Iron-Sulfur Protein from Thermochromatium tepidum
L. Liu, T. Nogi, M. Kobayashi, T. Nozawa, and K. Miki
Acta Crystallogr., D58, 1085-1091 (2002). pubmed PDBID: 1IUA

Crystal Structure of Aspartate Racemase from Pyrococcus horikoshii OT3 and Its Implication for Molecular Mechanism of PLP-independent Racemization
L. Liu, K. Iwata, A. Kita, Y. Kawarabayasi, M. Yohda, and K. Miki
J. Mol. Biol., 319, 479-489 (2002). pubmed PDBID: 1JFL

Crystal Structure of the Complex between Calyculin A and the Catalytic Subunit of Protein Phosphatase 1
A. Kita, S. Matsunaga, A. Takai, H. Kataiwa, T. Wakimoto, N. Fusetani, M. Isobe, and K. Miki
Structure, 10, 715-724 (2002). pubmed PDBID: 1IT6

2001 ^†

Glycine at the 65th Position Plays an Essential Role in ATP Dependent Protein Folding by Archaeal Group II Chaperonin
R. Iizuka, T. Yoshida, T. Maruyama, Y. Shomura, K. Miki, and M. Yohda
Biochem. Biophys. Res. Commun., 289, 1118-1124 (2001). pubmed

Crystal Structure of Thermostable DNA Photolyase: Pyrimidine-Dimer Recognition Mechanism
H. Komori, R. Masui, S. Kuramitsu, S. Yokoyama, T. Shibata, Y. Inoue, and K. Miki
Proc. Natl. Acad. Sci. USA, 98, 13560-13565 (2001). pubmed PDBID: 1IQR, 1IQU

Crystallzation and Preliminary X-ray Studies of a Thermostable DNA Photolyase from Thermus thermophilus
H. Komori, H. Tsujiuchi, R. Masui, S. Kuramitsu, S. Yokoyama, T. Shibata, Y. Inoue, and K. Miki
Protein Peptide Lett., 8, 495-498 (2001).

Crystallization and Preliminary X-ray Analysis of Aspartate Racemase from Pyrococcus horikoshii OT3
L. Liu, K. Iwata, Y. Kawarabayasi, H. Kikuchi, A. Kita, M. Yohda, and K. Miki
Acta Crystallogr., D57, 1674-1676 (2001). pubmed

Crystal Structure of Chaperonin-60 from Paracoccus denitrificans
T. A. Fukami, M. Yohda, H. Taguchi, M. Yoshida, and K. Miki
J. Mol. Biol., 312, 501-509 (2001). pubmed PDBID: 1IOK

Identification of Significant Residues for Homoallylic Substrate Binding of Micrococcus luteus B-P 26 Undecaprenyl Diphosphate Synthase
Y. Kharel, Y.-W. Zhang, M. Fujihashi, K. Miki, and T. Koyama
J. Biol. Chem., 276, 28459-28464 (2001). pubmed

Different Mechanisms of the Binding of Soluble Electron Donors to the Photosynthetic Reaction Center of Rubrivivax gelatinosus and Blastochloris viridis
A. Osyczka, K. V. P. Nagashima, S. Sogabe, K. Miki, K. Shimada, and K. Matsuura
J. Biol. Chem., 276, 24108-24112 (2001). pubmed

Crystal Structure of a Novel-Type Archaeal Rubisco with Pentagonal Symmetry
K. Kitano, N. Maeda, T. Fukui, H. Atomi, T. Imanaka, and K. Miki
Structure, 9, 473-481 (2001). pubmed PDBID: 1GEH

Cytochrome c₂
K. Miki and S. Sogabe
"Handbook of Metalloproteins", A. Messerschmidt, R. Huber, T. L. Poulos and K. Wieghardt eds., John Wiley, Chichester, 55-68 (2001).

Crystal Structure of a Mutant Human Lysozyme with a Substituted Disulfide Bond
K. Inaka, E. Kanaya, M. Kikuchi, and K. Miki
Proteins: Struct., Funct., Genet., 43, 413-419 (2001). pubmed PDBID: 1QSW

Structure of the H Subunit of the Photosynthetic Reaction Center from the Thermophilic Purple Sulfur Bacterium, Thermochromatium tepidum:
Implications for the Specific Binding of the Lipid Molecule to the Membrane Protein Complex
I. Fathir, T. Mori, T. Nogi, M. Kobayashi, K. Miki and T. Nozawa
Eur. J. Biochem., 268, 2652-2657 (2001). pubmed PDBID: 1EYS

Crystallization and Preliminary X-ray Diffraction Studies of a Novel Alkaline Serine Protease (KP-43) from Alkaliphilic Bacillus sp. Strain KSM-KP43
T. Nonaka, M. Fujihashi, A. Kita, K. Saeki, S. Ito and K. Miki
Acta Crystallogr., D57, 717-718 (2001). pubmed

Structural Basis of Bacterial Photosynthetic Reaction Centers
T. Nogi and K. Miki
J. Biochem., 130, 319-329 (2001). pubmed

Crystal Structure of cis-Prenyl Chain Elongating Enzyme, Undecaprenyl Diphosphate Synthase
M. Fujihashi, Y.-W. Zhang, Y. Higuchi, X.-Y. Li, T. Koyama, and K. Miki
Proc. Natl. Acad. Sci. USA, 98, 4337-4342 (2001). pubmed PDBID: 1F75

Crystal Structure of the Oxidized Cytochrome c₂ from Blastochloris viridis
S. Sogabe and K. Miki
FEBS Lett., 491, 174-179 (2001). pubmed PDBID: 1IO3

2000 ^†

Crystal Structures of Photosynthetic Reaction Center and High-Potential Iron-Sulfur Protein from Thermochromatium tepidum; Thermostability and Electron Transfer
T. Nogi, I. Fathir, M. Kobayashi, T. Nozawa, and K. Miki
Proc. Natl. Acad. Sci. USA, 97, 13561-13566 (2000). pubmed PDBID: 1EYS, 1EYT

Structural Genomics Projects in Japan
S. Yokoyama, H. Hirota, T. Kigawa, T. Yabuki, M. Shirouzu, T. Terada, Y. Ito, Y. Nishimura, Y. Kyogoku, K. Miki, R. Masui, and S. Kuramitsu
Nature Struct. Biol., 7, 943-945 (2000). pubmed

Preliminary X-ray Crystallographic Studies of DsrD Protein from the Sulfate-reducing Bacterium Desulfovibrio vulgaris
N. Mizuno, D. S. Hittel, K. Miki, G. Voordouw, and Y. Higuchi
Acta Crystallogr., D56, 754-755 (2000). pubmed

Crystallization and Preliminary Crystallographic Analysis of the High-Potential Iron-Sulfur Protein from Thermochromatium tepidum
T. Nogi, M. Kobayashi, T. Nozawa, and K. Miki
Acta Crystallogr., D56, 656-658 (2000). pubmed

The Iteron Regions Necessary for the RepE-Iteron Interaction In vivo in Mini-F Plasmids of Escherichia coli
H. Uga, H. Komori, K. Miki, and C. Wada
J. Biochem., 127, 537-541 (2000). pubmed

Effect of an Alternative Disulfide Bond on the Structure, Stability and Folding of Human Lysozyme
M. Arai, P. Hamel, E. Kanaya, K. Inaka, K. Miki, M. Kikuchi, and K. Kuwajima
Biochemistry, 39, 3472-3479 (2000). pubmed

Utilization of Microgravity to Improve the Crystal Quality of Biologically Important Proteins: Chaperonin-60, GrpE, B-subunit of V-type ATPase, and MIF
K. Kitano, R. Sasaki, T. Nogi, T. A. Fukami, A. Nakagawa, K. Miki, and I. Tanaka
J. Cryst. Growth, 210, 819-823 (2000).

1999 ^†

Comparison of the Binding Sites for High-Potential Iron-Sulfur Protein and Cytochrome c on the Tetraheme Cytochrome Subunit Bound to the Bacterial Photosynthetic Reaction Center
A. Osyczka, K. V. P. Nagashima, S. Sogabe, K. Miki, K. Shimada, and K. Matsuura
Biochemistry, 38, 15779-15790 (1999). pubmed

Crystal Structure of Chitosanase from Bacillus circulans MH-K1 at 1.6 A Resolution and Its Substrate Recognition Mechanism
J. Saito, A. Kita, Y. Higuchi, Y. Nagata, A. Ando, and K. Miki
J. Biol. Chem., 274, 30818-30825 (1999). pubmed PDBID: 1QGI

Ribulose Bisphosphate Carboxylase/oxygenase from Hyperthermophilic Archaeon Pyrococcus kodakaraensis KOD1 is Composed Solely of Large Subunits and Forms a Pentagonal Structure
N. Maeda, K. Kitano, T. Fukui, S. Ezaki, H. Atomi, K. Miki, and T. Imanaka
J. Mol. Biol., 293, 57-66 (1999). pubmed

Crystallization and Preliminary X-ray Diffraction Studies of Undecaprenyl Diphosphate Synthase from Micrococcus luteus B-P 26
M. Fujihashi, N. Shimizu, Y.-W. Zhang, T. Koyama, and K. Miki
Acta Crystallogr., D55, 1606-1607 (1999). pubmed

Crystal Structure of a Prokaryotic Replication Initiator Protein Bound to DNA at 2.6 A Resolution
H. Komori, F. Matsunaga, Y. Higuchi, M. Ishiai, C. Wada and K. Miki
EMBO J., 18, 4597-4607 (1999). pubmed PDBID: 1REP

Stimulation of Peroxidase Activity by Decamerization Related with Ionic Strength: AhpC Protein from Amphibacillus Xylanus
K. Kitano, Y. Niimura, Y. Nishiyama, and K. Miki
J. Biochem., 126, 313-319 (1999). pubmed

Purification, Crystallization and Preliminary X-ray Crystallographic Analysis of Thermus thermophilus V₁-ATPase B Subunit
T. Nogi, T. A. Fukami, M. Ishida, M. Yoshida, and K. Miki
J. Struct. Biol., 127, 79-82 (1999). pubmed

An Archetypical Extradiol-Cleaving Catecholic Dioxygenase: The Crystal Structure of Catechol 2,3-Dioxygenase (Metapyrocatechase)
A. Kita, S. Kita, I. Fujisawa, K. Inaka, T. Ishida, K. Horiike, M. Nozaki, and K. Miki
Structure, 7, 25-34 (1999). pubmed PDBID: 1MPY

Crystallization and Preliminary X-ray Diffraction Studies of a Replication Initiator Protein(RepE54) of the Mini-F Plasmid Complexed with Iteron DNA
H. Komori, N. Sasai, F. Matsunaga, C. Wada and K. Miki
J. Biochem., 125, 24-26 (1999). pubmed

1998 ^†

Crystallization and Preliminary X-ray Diffraction Study of Lactonohydrolase from Fusarium oxysporum
M. Kataoka, K. Yamamoto, S. Shimizu, M. Ohta, A. Kita, Y. Higuchi, and K. Miki
Acta Crystallogr., D54, 1432-1434 (1998). pubmed

Interaction Site for Soluble Cytochromes on the Tetraheme Cytochrome Subunit Bound to the Bacterial Photosynthetic Reaction Center Mapped by Site-Directed Mutagenesis
A. Osyczka, K. V. P. Nagashima, S. Sogabe, K. Miki, M. Yoshida, K. Shimada, and K. Matsuura
Biochemistry, 37, 11732-11744 (1998). pubmed

A Novel Approach to Crystallizing Proteins with Temperature Induction Method: GrpE Protein from Thermus thermophilus
K. Kitano, K. Motohashi, M. Yoshida, and K. Miki
J. Cryst. Growth, 186, 456-460 (1998).

1997 ^†

Crystal Structure of DNA Photolyase from Anacystis nidulans
T. Tamada, K. Kitadokoro, Y. Higuchi, K. Inaka, A. Yasui, P. E. de Ruiter, A. P. M. Eker, and K. Miki
Nature Struct. Biol., 4, 887-891 (1997). pubmed PDBID: 1QNF

Crystallization and Preliminary X-Ray Diffraction Studies of Expressed Pseudomonas putida Catechol 2,3-Dioxygenase
A. Kita, S. Kita, K. Inaka, T. Ishida, K. Horiike, M. Nozaki, and K. Miki
J. Biochem., 122, 201-204 (1997). pubmed

1996 ^†

Crystallization and Preliminary X-ray Characterization of Chaperonin 60 from Paracoccus denitrificans
T. A. Fukami, Y. Takasuga, M. Sumi, M. Yohda, M. Yoshida, and K. Miki
J. Cryst. Growth, 168, 297-300 (1996).

Crystallization and preliminary X-ray diffraction studies of θ-toxin (perfringolysin O), a pore-forming cytolysin of Clostridium perfringens
M. Sugahara, N. Sekine-Suzuki, Y. Ohno-Iwashita, and K. Miki
J. Cryst. Growth, 168, 288-291 (1996).

Electrostatic Properties Deduced from Refined Structures of NADH-Cytochrome b₅ Reductase and the Other Flavin-Dependent Reductases: Pyridine Nucleotide-Binding and Interaction with an Electron-Transfer Partner
H. Nishida and K. Miki
Proteins: Struct., Funct., Genet., 26, 32-41 (1996). pubmed

Crystallization and Preliminary X-ray Diffraction Study of Aldehyde Reductase from a Red Yeast, Sporobolomyces salmonicolor
M. Kataoka, K. Yamamoto, S. Shimizu, K. Kita, T. Hashimoto, H. Yamane, A. Kita, and K. Miki
Acta Crystallogr., D52, 405-406 (1996). pubmed

Structure of Flavoprotein FP₃₉₀ from a Luminescent Bacterium, Photobacterium phosphoreum at 2.7 A Resolution
A. Kita, S. Kasai, M. Miyata, and K. Miki
Acta Crystallogr., D52, 77-86 (1996). pubmed PDBID: 1FVP

1995 ^†

Preliminary X-ray Diffraction Studies of a New Crystal Form of C-1027-AG, the Apoprotein of the Macromolecular Antitumor Antibiotic C-1027 from Streptomyces globisporus
F. Motojima, K. Inaka, Y. Minami, T. Otani, and K. Miki
Acta Crystallogr., D51, 1084-1085 (1995). pubmed

Refined Crystal Structure of Ferrocytochrome c₂ from Rhodopseudomonas viridis at 1.6 A Resolution
S. Sogabe and K. Miki
J. Mol. Biol., 252, 235-247 (1995). pubmed PDBID: 1CO6

Crystallization and Preliminary X-ray Crystallographic Analysis of Chitosanase from Bacillus circulans MH-K1
J. Saito, Y. Nagata, A. Ando, A. Kita, and K. Miki
Acta Crystallogr., D51, 856-857 (1995). pubmed

Structure of a Glutathionylated Human Lysozyme: a Folding Intermediate Mimic in the Formation of a Disulfide Bond
K. Inaka, M. Kikuchi, K. Miki, Y. Taniyama, and M. Matsushima
Acta Crystallogr., D51, 619-625 (1995). pubmed PDBID: 1HNL

A New Crystal Form of Photolyase (Photoreactivating Enzyme) from the Cyanobacterium Anacystis nidulans
T. Tamada, H. Nishida, K. Inaka, A. Yasui, P. E. de Ruiter, A. P. M. Eker, and K. Miki
J. Struct. Biol., 115, 37-40 (1995).

Specific Arrangement of Three Amino Acid Residues for Flavin-binding Barrel Structures in NADH-Cytochrome b₅ Reductase and the Other Flavin-dependent Reductases
H. Nishida, K. Inaka, and K. Miki
FEBS Lett., 361, 97-100 (1995). pubmed

Crystal Structure of NADH-Cytochrome b₅ Reductase from Pig Liver at 2.4 A Resolution
H. Nishida, K. Inaka, M. Yamanaka, S. Kaida, K. Kobayashi, and K. Miki
Biochemistry, 34, 2763-2767 (1995). pubmed PDBID: 1NDH

Crystal Structure Determination of a Flavoprotein FP₃₉₀ from a Luminescent Bacterium, Photobacterium phosphoreum
A. Kita, S. Kasai, and K. Miki
J. Biochem., 117, 575-578 (1995). pubmed PDBID: 1FVP

Fundamental Design of the High Energy Undulator Pilot Beamline for Macromolecular Crystallography at SPring-8
N. Kamiya, T. Uraga, H. Kimura, H. Yamaoka, M. Yamamoto, Y. Kawano, T. Ishikawa, H. Kitamura, T. Ueki, Y. Kashihara, N. Tanaka, H. Moriyama, K. Hamada, K. Miki, and I. Tanaka
Rev. Sci. Instrum., 66, 1703-1705 (1995).

1994 ^†

Crystallization of Mutant β Subunit of F₁-ATPase from Thermophilic Bacillus PS3
K. Saika, K. Inaka, T. Matsui, M. Yoshida, and K. Miki
J. Mol. Biol., 242, 709-711 (1994). pubmed

Preliminary X-ray Crystallographic Studies of Photosynthetic Reaction Center from a Thermophilic Sulfur Bacterium, Chromatium tepidum
N. Katayama, M. Kobayashi, F. Motojima, K. Inaka, T. Nozawa, and K. Miki
FEBS Lett., 348, 158-160 (1994). pubmed

Structural Similarity of Cytochrome c₂ from Rhodopseudomonas viridis to Mitochondrial Cytochromes c Revealed by Its Crystal Structure at 2.7 A Resolution
S. Sogabe, T. Ezoe, N. Kasai, M. Saeda, A. Uno, M. Miki, and K. Miki
FEBS Lett., 345, 5-8 (1994). pubmed

Application of Automatic Molecular Replacement Procedure to Crystal Structure Analysis of Cytochrome c₂ from Rhodopseudomonas viridis
K. Miki, S. Sogabe, A. Uno, T. Ezoe, N. Kasai, M. Saeda, Y. Matsuura, and M. Miki
Acta Crystallogr., D50, 271-275 (1994). pubmed PDBID: 1CRY