Original Papers (only) <Year 2004>

Takahashi H., Inagaki E., Fujimoto Y., Kuroishi C., Nodake Y., Nakamura Y., Arisaka F., Yutani K., Kuramitsu S., Yokoyama S., Yamamoto M., Miyano M., and Tahirov T. H.: “Structure and implications for the thermal stability of phosphopantetheine adenylyltransferase from Thermus thermophilusActa Cryst.D60, 97-104 (2004)BL26B1

Nishio K., Nodake Y., Hamada K., Suto K., Nakagawa N., Kuramitsu S. and Miura K.: “Expression, purification, crystallization and preliminary X-ray studies of geranylgeranyl diphosphate synthase from Thermus thermophilus HB8” Acta Cryst.D60,178-180 (2004)BL40B2

Sengoku T., Nureki O., Dohmae N., Nakamura A., and Yokoyama S.: “Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue” Acta Cryst.D60, 320-322 (2004)

Rehsh P. H., Nodake Y., Kuroishi C., and Tahirov T. H.: “Expression, purification, crystallization and preliminary crystallographic analysis of osmotically inducible protein C” Acta Cryst.D60, 357-358 (2004)BL26B1

Iwasaki W., Miyatake H., Ebihara A., and Miki K.: “Crystallization and preliminary X-ray crystallographic studies on the small form of glucose-inhibited division protein A from Thermus thermophilus HB8” Acta Cryst. D60, 515-517 (2004)BL44B2/BL45XU

Omi R., Goto M., Nakagawa N., MiyaharaI., and Hirotsu K.: “Expression, purification and preliminary X-ray characterization of histidinol phosphate phosphatase” Acta Cryst.D60, 574-576 (2004)BL44B2

Inagaki E., Ukita Y., Kumei M., Kajihara Y., and Tahirov T. H.: “Crystallization and preliminary crystallographic analysis of 2-keto-3-deoxygluconate kinase from Thermus thermophilusActa Cryst.D60, 761-763 (2004)BL44B2/BL26B1

Numoto N., Kita A. and Miki K.: “Structure of the C subunit of V-type ATPase from Thermus thermophilus at 1.85 Å resolution” Acta Cryst. D60, 810-815 (2004)

Kort R., Komori H., Adachi S., Miki K. and Eker A.: “DNA apophotolyase from Anacystis nidulans: 1.8 Å structure, 8-HDF reconstitution and X-ray induced FAD-reduction” Acta Cryst. D60, 1205-1213 (2004)

Kamo M., Kudo N., Lee W. C., Motoshima H., and Tanokura M.: “Crystallization and preliminary X-ray crystallofraphic analysis of peptide deformylase from Thermus thermophilus HB8” Acta Cryst.D60, 1299-1300 (2004)BL41XU

Nagata K., Tsutsui S., LeeW. C., Ito K., Kamo M., Inoue Y., and Tanokura M.: “Crystallization and preliminary X-ray analysis of carboxypeptidase 1 from Thermus thermophilusActa Cryst. D60, 1445-1446 (2004)

Lokanath N. K., Kuroishi C., Okazaki N., and Kunishima N.: “Purification, crystallization and preliminary crystallographic analysis of the glycine-cleavage system component T-protein from Pyrococcus horikoshii OT3” Acta Crys. D60, 1450-1452 (2004)

Vassylyeva M. N., Perederina A. A., Svetlov V., Yokoyama S., Artsimovitch I., and Vassylyev D. G.: “Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription factor DksA from Escherichia coli” Acta Cryst. D60, 1611-1613 (2004)

Takahashi H., Inagaki E., Kuroishi C., and Tahir T. H.: “Crystal Structure of the Thermus thermophilus Putative Periplasmic Glutamate/Glutamine-binding Protein” Acta Cryst. D60, 1846-1854 (2004)

Fukunaga R., and Yokoyama S.: “Crystallization and preliminary X-ray crystallographic study of the editing domain of Thermus thermophilus isoleucyl-tRNA synthetase complexed with pre- and post-transfer editing-substrate analogues” Acta Cryst.D60, 1900-1902 (2004) BL26B1/BL38B1

Fukunaga R., and Yokoyama S.: “Crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshiiActa Cryst. D60, 1916-1918 (2004)BL26B1

Imagawa T., Nakayama H., Katunuma N., Sakuraba H., Ohshima T., Itoh T., Sako Y., Nomura N., and Tsuge H.: “Crystallization and preliminary X-ray diffraction analysis of homing endonuclease I-Tsp061I”, Acta Cryst.D60, 2006-2008 (2004)BL44B2

Adachi S, Inoue K, Oka T, Yagi N, Tanaka Y, Ishikawa T, Shiro Y, “Subnanosecond-resolved X-ray diffraction at the SPring-8 high flux beamline BL40XU” AIP Conference Proceedings 705, 1383-1386 (2004)

Yokota H, Okamura T, Takahashi M, Horiuchi T, Kikuchi J, Yokoyama S, Maeda H, “4.5 K cooling system for a cryogenically cooled probe for a 920 MHz NMR” AIP Conference Proceedings 710, 1826-1833 (2004)

Nakamura A., Komori H., Kobayashi G., Kita A., Wada C., and Miki K.: “The N-terminal domain of the replication initiator protein RepE is a dimerization domain forming a stable dimer” Biochem. Biophys. Res. Commun. 315, 10-15 (2004) BL38B1/BL41XU/BL44B2

Suruga K., Murakami K., Taniyama Y., Hama T., Chida H., Satoh T., Yamada S., Hakamata W., Kawachi R., Isogai Y., Nishio T. and Oku T.: “A novel microperoxidase activity: Methyl viologen-linked nitrite reducing activity of microperoxidase” Biochem. Biophys. Res. Commun.315, 815-822 (2004)

Tamura T., and Iwamoto H.: “Thymol: a classical small-molecule compound that has a dual effect (potentiating and inhibitory) on myosin” Biochem. Biophys. Res. Commu. 318, 786-791 (2004)

Hirao I., Harada Y., Nojima T., Osawa Y., Masaki H., and Yokoyama S.: “In vitro selection of RNA aptamers that bind to colicin E3 and structurally resemble the decoding site of 16S ribosomal RNA” Biochemistry43, 3214-3221 (2004)

Taguchi Y., Sugishima M., and Fukuyama K.: “Crystal structure of a novel zinc-binding ATP sulfurylase from Thermus thermophilus HB8” Biochemistry 43, 4111-4118 (2004)BL44B2

Mizutani K., Machida Y., Unzai S., Unzai S., Park S.-Y., and Park S.-Y.: “Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coliBiochemistry43, 4454-4463 (2004)

Ishida M., Dohmae N., Shiro Y., Oku T., Iizuka T. and Isogai Y.: “Design and Synthesis of de Novo Cytochrome cBiochemistry43, 9823-9833 (2004)

Iimura S., Yagi H., Ogasahara K., Akutsu H., Noda Y., Segawa S., and Yutani K.: “Unusually Slow Denaturation and Refolding Process of Pyrrolidone Carboxyl Peptidase from a Hyperthermophile Are Highly Cooperative: Real-Time NMR Studies” Biochemistry43, 11906-11915 (2004)

Nakasako M., Iwata T., Matsuoka D., and Tokutomi S.: “Light-induced structural changes of lov domain-containing polypeptides from arabidopsis phototropin 1 and 2 studied by small-angle x-ray scattering” Biochemistry43, 14881-14890 (2004) BL40B2

Ogiso H., Kagi N., Matsumoto E., Nishimoto M., Arai R., Shirouzu M., Mimura J., Fujii-Kuriyama Y., and Yokoyama S.: “Phosphorylation analysis of 90kDa heat shock protein within the cytosolic arylhydrocardon receptor complex” Biochemistry 43, 15510-15519 (2004)

Chikayama E., Kurotani A., Kuroda Y., and Yokoyama S.: “ProteoMix: An integrated and flexible system for interactively analyzing large numbers of protein sequences” Bioinformatics20, 2836-2838 (2004)

Endo M., Mitsui T., Okuni T., Kimoto M., HiraoI., and Yokoyama S.: “Unnatural base pairs mediate the site-specific incorporation of an unnatural hydrophobic component into RNA transcripts” Bioorg. Med. Chem. Lett.14, 2593-2596 (2004)

HiraoI., Fujiwara T., Kimoto M., and Yokoyama S.: “Unnatural base pairs between 2- and 6-substituted purines and 2-oxo(1H)pyridine for expansion of the genetic alphabet” Bioorg. Med. Chem. Lett. 14, 4887-4890 (2004)

Wakayama J., Tamura T., Yagi N. and Iwamoto H.: “Structural transients of contractile proteins upon sudden ATP liberation in skeletal muscle fibers” Biophysical J.87, 430-441 (2004)

Amano K., Fujihashi M., Ando A., Miki K., and Nagata Y.: “Involvement of tyrosines at fucose-binding sites of Aleuria aurantia lectin: Non-equal response to site-directed mutagenesis among five sites” Biosci. Biotechnol. Biochem. 68, 841-847 (2004)

Kimoto M., Yokoyama S., and HiraoI.: “A quantitative, non-radioactive single-nucleotide insertion assay for analysis of DNA replication fidelity by using an automated DNA sequencer” Biotechnol. Lett.26, 999-1005 (2004)

Temiakov D., Patlan V., Anikin M., McAllister W. T., Yokoyama S., and Vassylyev D. G.: “Structural Basis for Substrate Selection by T7 RNA Polymerase” Cell116, 381-391 (2004)

Artsimovitch I., Patlan V., Sekine S., Vassylyeva M. N., Hosaka T., Ochi K., Yokoyama S., and Vassylyev D. G.: “Structural Basis for Transcription Regulation by Alarmone ppGpp” Cell117, 299-310 (2004)BL45XU

Perederina A., Svetlov V., Vassylyeva M. N., Wakatsuki S., Artsimovitch I., Yokoyama S., and Vassylyev D. G.: “Regulation through the secondary channel?structural framework for ppGpp-DksA synergism during transcription” Cell118, 297-309 (2004)

Kimoto M, Endo M, Mitsui T, Okuni T, Hirao I, Yokoyama S, “Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs” Chem. Biol.11 47-55 (2004)

MatsunagaI., and Shiro Y.: “Peroxide utilizing biocatalysts: structural and functional diversity of heme-containing enzymes” Current Opinion Chem. Biol.8, 127-132 (2004)

Matsubara M., Nakatsu T., Kato H., and Taniguchi H.: “Crystal structure of a myristoylated CAP-23/NAP-22 N-terminal domain complexed with Ca2+/calmodulin” EMBO J. 23, 712-718 (2004)

Ifuku K., Nakatsu T., Kato H., and Sato F.:“Crystalstructure of the PsbP protein of photosystem II from Nicotiana tabacum” EMBO Rep.5, 4 362-367 (2004)

Chumpolkulwong N., Hori-Takemoto C., Hosaka T., Inaoka T., Kigawa T., Shirouzu M., Ochi K., and Yokoyama S.: “Effects of Escherichia coil ribosomal protein S12 Mutations on Cell-Free Protein Synthesis” Eur. J. Biochem. 271, 1127-1134 (2004)

Umemura M., Su F., Takaya N., Shiro Y. and Shoun H.: “D88A mutant of cytochrome P450nor provides kinetic evidence for direct complex formation with electron donor NADH” Eur. J. Biochem. 271, 2887-2894 (2004)

Vasil'ev S., Shen J., Kamiya N. and Bruce D.: “The orientations of core antenna chlorophylls in photosystem II are optimized to maximize the quantum yield of photosynthesis” FEBS Letter561, 111-116 (2004)

Takizawa Y, Kinebuchi T, Kagawa W, Yokoyama S, Shibata T, Kurumizaka H, “Mutational analyses of the human Rad51-Tyr315 residue, a sitr for phosphorylation in leukaemia cells” Genes to Cells9 781-790 (2004)

HiraoI., Harada Y., Kimoto M., Mitsui T., Fujiwara T., and Yokoyama S.: “A two-unnatural-base-pair system toward the expansion of the genetic code” J. Am. Chem. Soc. 126, 13298-13305 (2004)

Ueno G., Hirose R., Ida K., Kumasaka T. and Yamamoto M.: “Sample management system for a vast amount of frozen crystals at SPring-8” J. Appl. Cryst.37, 867-873 (2004)BL26B1/BL26B2

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

Sakamoto K., Ishimaru S., Kobayashi T., Nagata T., Walker J. R., and Yokoyama S.: “The Escherichia coli argU10(Ts) phenotype is caused by a reduction in the cellular level of the argU tRNA for the rare codons AGA and AGG” J. Bacteriol. 186, 5899-5905 (2004)

Takeuchi F., Hori H., Obayashi E., Shiro Y., and Tsubaki M.: “Properties of two distinct heme centers of Cytochrome b561 from bovine chromaffin vesicles studied by EPR, resonance raman, and ascorbate reduction assay” J. Biochem.135, 53-64 (2004)

Fukui K., Masui R., and Kuramitsu S.: “Thermus thermophilus MutS2, a MutS paralogue, possesses an endonuclease activity promoted by MutL” J. Biochem.135, 375-384 (2004)

Suzuki H., Nojiri M., Kamiya N. and Noguchi T.: “Thermal equilibrium of two conformations of photosensitive nitrile hydratase probed by a nitric oxide vibration” J. Biochem. 136, 115-121 (2004)

Kondo N., Kuramitus S., and Masui R.: “Biochemical characterization of TT1383 ftom Thermus thermophilus identifies a novel dNTP triphosphohydrolase activity stimulated by dATP and dTTP” J. Biochem.136, 221-231 (2004)

Arai R., Ito K., Wakiyama M., Matsumoto E., Sakamoto A., Etou Y., Otsuki M., Inoue M., Hayashizaki Y., Miyagishi M., Taira K., Shirouzu M., and Yokoyama S.: “Establishment of Stable hFis1 Knockdown Cells with an siRNA Expression Vector” J. Biochem. 136, 421-425 (2004)

Kobayashi S., Masui R., Yokoyama S., Kuramitsu S. and Takagi H.: “A Novel Metal-Activated l-Serine O-Acetyltransferase from Thermus thermophilus HB8” J. Biochem.136, 629-634 (2004)

Kikuchi M., Hatano N., Yokota S., Shimozawa N., Imanaka T., and Taniguchi H.: “Proteomic Analysis of Rat Liver Peroxisome: Presence of peroxisome-specific isozyme of lon protease” J. Biol. Chem.279, 421-428 (2004)

Pang H., Bartlam M., Zeng Q., Miyatake H., Hisano T., Miki K., Wong L.-L., Gao G. F., and Rao Z.: “Crystal structure of human pirin: An iron-bonding nuclear protein and transcription cofactors” J. Biol. Chem. 279, 1491-1498 (2004)


Takemoto A., Kimura K., Yokoyama S., and Hanaoka F.: “Cell cycle-dependent phosphorylation, nuclear localization, and activation of human condensin” J. Biol. Chem. 279, 4551-4559 (2004)

Hiromasa Y., Fujisawa T., Aso Y., and Roche T.: “Organization of the cores of the mammalian pyruvate dehydrogenase complex formed by E2 and E2 plus the E3-binding protein and their capacities to bind the E1 and E3 components.” J. Biol. Chem.279, 6921-6933 (2004)

Fukunaga R., Fukai S., Ishitani R., Nureki O., and Yokoyama S.: “Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine” J. Biol. Chem. 279, 8396-8402 (2004)


Hirotsu S., Chu G. C., Unno M., Lee D.-S., Yoshida T., Park S.-Y., Shiro Y., and Ikeda-Saito M.: “The Crystal Structures of the Ferric and Ferrous Forms of the Heme Complex of Hmu O, a Heme Oxygenase of Corynebacterium diphtheriaeJ. Biol. Chem.279, 11937-11947 (2004)BL45XU

Maeda T., Inoue M., Koshiba S., Yabuki T., Aoki M., Nunokawa E., Seki E., Matsuda T., Motoda Y., Kobayashi A., Hiroyasu F., Shirouzu M., Terada T., Hayami N., Ishizuka Y., Shinya N., Tatsuguchi A., Yoshida M., Hirota H., Matsuo Y., Tani K., Arakawa T., Carninci P., Kawai J., Hayashizaki Y., Kigawa T., and Yokoyama S.: “Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16)” J. Biol. Chem. 279, 13174-13182 (2004)

Goto M., Omi R., Miyahara I., Hosono A., Mizuguchi H., Hayashi H., Kagamiyama H., and Hirotsu K.: “Crystal structures of glutamine: phenylpyruvate aminotransferase from Thermus thermophilus HB8” J. Biol. Chem.279, 16518-16525 (2004)BL45XU

Iwai T., Kuramitsu S., and Masui R.: “The Nudix hydrolase Ndx1 from Thermus thermophilus HB8 is a diadenosine hexaphosphate hydrolase with a novel activity” J. Biol. Chem.279, 21732-21739 (2004)

Hori T., Yokomizo T., Ago H., Sugahara M., Ueno G., Yamamoto M., Kumasaka T., Shimizu T., and Miyano M.: “Structural basis of leukotriene B4 12-Hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop” J. Biol. Chem. 279, 22615-22623 (2004) BL26B2/BL45XU/PX

Okubo S., Hara F., Tsuchida Y., Shimotakahara S., Suzuki S., Hatanaka H., Yokoyama S., Tanaka H., Yasuda H., and Shindo H.: “NMR Structure of the N-terminal Domain of SUMO Ligase PIAS1 and its Interaction with Tumor Suppressor p53 and A/T-rich DNA Oligomers” J. Biol. Chem., 279, 31455-31461 (2004)

Hisanaga Y., Ago H., Nakagawa N., Hamada K., Ida K., Yamamoto M., Hori T., Arii Y., Sugahara M., Kuramitsu S., Yokoyama S., and Miyano M.: “Structural basis of the substrate specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer” J. Biol. Chem. 279, 31717-31726 (2004)BL26B1/BL41XU/BL45XU

Randau L., Schauer S., Ambrogelly A., Salazar J. C., Moser J., Sekine S., Yokoyama S., Soll D., and Jahn D.: “tRNA recognition by glutamyl-tRNA reductase” J. Biol. Chem. 279, 34931-34937 (2004)

Enomoto R., Kinebuchi T., Sato M., Yagi H., Shibata T., Kurumizaka H., and Yokoyama S.: “Positive role of the mammalian TBPIP/Hop2 protein in Dmc1-mediated homologous pairing” J. Biol. Chem.279, 35263-35272 (2004)

Yoshiba S., Ooga T., Nakagawa N., Shibata T., Inoue Y., Yokoyama S., Kuramitsu S., and Masui R.: “Structural insights into the thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal” J. Biol. Chem. 279, 37163-37174 (2004)BL44B2/BL26B2

Svetlov V., Vassylyev D. G., and ArtsimovitchI.: “Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase” J. Biol. Chem. 279, 38087-38090 (2004)

Nonaka T., Fujihashi M., Kita A., Saeki K., Itoh S., Horikoshi K. and Miki K.: “The crystal structure of an oxidatively stable subtilisin-like Alkaline Serine Protease, KP-43, with a C-terminal β-barrel domain” J. Biol. Chem.279, 47344-47351 (2004)

Uchida T., Mogi T., Nakamura H. and Kitagawa T.: “Role of Tyr-288 at the dioxygen reduction site of cytochrome bo studied by stable isotope labeling and resonance raman spectroscopy” J. Biol. Chem. 279, 53613-53620 (2004)

Kumita H., Matsuura K., Hino T., Takahashi S., Hori H., Fukumori Y., Morishima I. and Shiro Y.: “NO reduction by nitric-oxide reductase from denitrifying bacterium pseudomonas aeruginosa” J. Biol. Chem.279, 55247-55254 (2004)

Lopez-Mendez B., Pantoja-Uceda D., Tomizawa T., Koshiba S., Kigawa T., Shirouzu M., Terada T., Inoue M., Yabuki T., Aoki M., Seki E., Matsuda T., Hirota H., Yoshida M., Tanaka A., Osanai T., Seki M., Shinozaki K., Yokoyama S. and Guntert P.: “NMR assignment of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thalianaJ. Biomol. NMR29 205-206 (2004)

Pantoja-Uceda D., Lopez-Mendez B., Koshiba S., Kigawa T., Shirouzu M., Terada T., Inoue M., Yabuki T., Aoki M., Seki E., Matsuda T., Hirota H., Yoshida M., Tanaka A., Osanai T., Seki M., Shinozaki K., Yokoyama S. and Guntert P.: “NMR assignment of the hypothetical rhodanese domain At4g01050 from Arabidopsis thalianaJ. Biomol. NMR29, 207-208 (2004)

Scott A., Pantoja-Uceda D., Koshiba S., Inoue M., Kigawa T., Terada T., Shirouzu M., Tanaka A., Sugano S., Yokoyama S., and Guentert P.: “NMR Assignment of the SH2 Domain from the Human Feline Sarcoma Oncogene FES” J. Biomol. NMR 30, 463-464 (2004)

Kim K., Yamashita A., Wear M. A., Maeda Y. and Cooper John A.: “Capping Protein Binding to Actin in Yeast:Biochemical Mechanizm and Physiological Relevance” J. Cell Biology164, 567-580 (2004)

Shomura Y., Yoshida T., Iizuka R., Maruyama T., Yohda M., and Miki K.: “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” J. Mol. Biol. 335, 1265-1278 (2004)BL41XU/BL44B2/BL44XU/BL45XU

Sato C., Hamada K., Ogura T., Miyazawa A., Iwasaki K., Hiroaki Y., Tani K., Terauchi A., Fujiyoshi Y. and Mikoshiba K.: “Inositol 1,4,5-trisphosphate receptor contains multiple cavities and L-shaped ligand-binding domains” J. Mol. Biol. 336, 155-164 (2004)

Yamasaki K., Kigawa T., Inoue M., Tateno M., Yamasaki T., Yabuki T., Aoki M., Seki E., Matsuda T., Nunokawa E., Ishizuka Y., Terada T., Shirouzu M., Osanai T., Tanaka A., Seki M., Shinozaki K., and Yokoyama S.: “A Novel Zinc-binding Motif Revealed by Solution Structures of DNA-binding Domains of Arabidopsis SBP-family Transcription Factors” J. Mol. Biol. 337, 49-63 (2004)

Kukimoto-Niino M., Murayama K., Inoue M., Terada T., Tame J. R. H., Kuramitsu S., Shirouzu M., and Yokoyama S.: “Crystal Structure of the GTP-binding Protein Obg from Thermus thermophilus HB8” J. Mol. Biol. 337, 761-770 (2004)

Nakai T., Nakagawa N., Maoka N., Masui R., Kuramitsu S., and Kamiya N.: “Ligand-induced Conformational Changes and a Reaction Intermediate in Branched-chain 2-Oxo Acid Dehydrogenase (E1) from Thermus thermophilus HB8, as Revealed by X-ray Crystallography” J. Mol. Biol.337, 1011-1033 (2004)BL44B2/BL45XU

Tahirov T. H., Inagaki E., Ohshima N., Kitao T., Kuroishi C., Ukita Y., Takio K., Kobayashi M., Kuramitsu S., Yokoyama S., and Miyano M.: “Crystal Structure of Purine Nucleoside Phosphorylase from Thermus thermophilusJ. Mol. Biol. 337, 1149-1160 (2004)

Rehse P.H., Ohshima N., Nodake Y., and Tahirov T. H.: “Crystallographic structure and biochemical analysis of the Thermus Thermophilus osmotically inducible protein C” J. Mol. Biol. 338, 959-968 (2004)BL26B1

Sugimoto H., Makino M., Sawai H., Kawada N., Yoshizato K. and Shiro Y.: “Structural basis of human cytoglobin for ligand binding” J. Mol. Biol.339, 873-885 (2004)BL44B2

Ohshima N., Inagaki E., Yasuike k., Takio K., and Tahirov T. H.: “Structure of Thermus thermophilus 2-keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate” J. Mol .Biol.340, 477-489 (2004)


Takeda K., Matsui Y., Kamiya N., Adachi S., Okumura H., and Kouyama T.: “Crystal structure of the M Intermediate of Bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix” J. Mol Biol341, 1023-1037 (2004)

Matsumoto F., Makino K., Maeda K., Maeda Y. and Fujiwara S.: “Conformational changes of troponin C within the thin filaments detected by neutron scattering” J. Mol. Biol. 342 1209-1221 (2004)

Nishimura M., Yoshida T., Shirouzu M., Terada T., Kuramitsu S., Yokoyama S., Ohkubo T., and Kobayashi Y.: “Solution Structure of Ribosomal Protein L16 from Thermus thermophilus HB8” J. Mol. Biol. 344, 1369-1383 (2004)

Tamura T., Wakayama J., Fujisawa T., Yagi N. and Iwamoto H.: “Intensity of X-ray reflections from skeletal muscle thin filaments partially occupied with myosin heads: Effect of cooperative binding” J. Muscle Res. Cell Motil25, 329-335 (2004) BL45XU

Kigawa T., Yabuki T., Matsuda N., Matsuda T., Nakajima R., Tanaka A., and Yokoyama S.: “Preparation of Escherichia coli cell extract for highly productive cell-free protein expression” J. Struct. Funct. Genomics5, 63-68 (2004)

Hirata K., Yamashita E., Aoyama H., Muramoto K., Yoshikawa S. and Tsukihara T.: “Scaling of one-shot oscillation images with a reference data set” J. Synchrotron Radiat11, 60-63 (2004)BL44XU

Yagi N., Yamamoto M., Uesugi K. and Inoue K.: “A large-area CMOS imager as an X-ray detector for synchrotron radiation experiments” J. Synchrotron Radiat. 11, 347-352 (2004)BL20XU/BL38B1/BL40XU

Kuwamoto S., Akiyama S. and Fujisawa T.: “Radiation damage to a protein solution,detected by synchrotron X-ray small-angle scattering: dose-related considerations and suppression by cryoprotectants” J. Synchrotron Radiat11, 462-468 (2004)BL45XU

Miyano M. and Sugahara M.: “Full automated crystallization and observation robot system” Med. Sci. Dig. / Medical Science Digest30, 11-12 (2004)

Tanaka Y., Tawaramoto-Sasanuma M., Kawaguchi S., Ohta T., Yoda K., Kurumizaka H., and Yokoyama S.: “Expression and purification of recombinant human histones” Methods33, 3-11 (2004)

Kamatari Y. O., Kitahara R., Yamada H., Yokoyama S., and Akasaka K.: “High-pressure NMR spectroscopy for characterizing folding intermediates and denatured states of proteins” Methods34, 133-143 (2004)

Kinebuchi T., Kagawa W., Enomoto R., Tanaka K., Miyagawa K., Shibata T., Kurumizaka H., and Yokoyama S.: “Structural basis for octameric ring formation and DNA Interaction of the human homologous-pairing protein Dmc1” Mol. Cell14, 363-374 (2004)

Jiang M., Ma N., Vassylyev D. G., and McAllister W. T.: “RNA displacement and resolution of the transcription bubble during transcription by T7 RNA polymerase” Mol. Cell15, 777-788 (2004)BL45XU

Hosaka T., Tamehiro N., Chumpolkulwong N., Hori-Takemoto C., Shirouzu M., Yokoyama S., and Ochi K.: “The novel mutation K87E in ribosomal protein S12 enhances protein synthesis activity during the late growth phase in Escherichia coliMol. Genet. Genomics271, 317-324 (2004)

Tomita K., Fukai S., Ishitani R., Ueda T., Takeuchi N., Vassylyev D. G., and Nureki O.: “Structural basis for template-independent RNA polymerization” Nature430, 700-704 (2004) BL44XU

ShinboI., Nakajima R., Yokoyama S., and Sumikura K.: “Patent protection for protein structure analysis” Nature Biotechnology22, 109-112 (2004)

Kise Y., Lee SW., Park SG., Fukai S., Sengoku T., Ishii R., Yokoyama S., Kim S., and Nureki O.: “A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase” Nat. Struct. Mol. Biol.11, 149-156 (2004)

Uzumaki T., Fujita M., Nakatsu T., Hayashi F., Shibata H., Ito N., Kato H., and Ishiura M.: “Crystal structure of the C-terminal clock-oscillator domain of the cyanobacterial KaiA protein” Nat. Struct. Mol. Biol.11, 623-631 (2004)

Fujikawa N., Kurumizaka H., Nureki O., Tanaka Y., Yamazoe M., Hiraga S., and Yokoyama S.: “Structural and biochemical analyses of hemimethylated-DNA binding by the SeqA protein” Nucleic Acids Res.32, 82-92 (2004)

Yokoyama H., Sarai N., Kagawa W., Enomoto R., Shibata T., Kurumizaka H., and Yokoyama S.: “Preferential binding to branched DNA strands and strand-annealing activity of the human Rad51B, Rad51C, Rad51D and Xrcc2 protein complex” Nucleic Acids Res. 32, 2556-2565 (2004)

Yamasaki K., Kigawa T., Inoue M., Tateno M., Yamasaki T., Yabuki T., Aoki M., Seki E., Matsuda T., Tomo Y., Hayami N., Terada T., Shirouzu M., Osanai T., Tanaka A., Seki M., Shinozaki K., and Yokoyama S.: “Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1” The Plant Cell16, 3448-3459 (2004)

Nakasako M.: “Water-protein interactions from high-resolution protein crystallography” Phil. Trans. R. Soc. Lond. B359, 1191-1206 (2004) BL41XU

Uzawa T., Akiyama S., Kimura T., Takahashi S., Ishimori K., Morishima I., and Fujisawa T.: “Collapse and search dynamics of apomyoglobin folding revealed by submillisecond observations of Alfa-helical contents and compactness” Proc. Natl. Acad. Sci USA101, 1171-1176 (2004)

Nakamura H., Kumita H., Imai K., Iizuka T., and Shiro Y.:“ADP Reduces the Oxygen Binding Affinity of A Sensory Histidine Kinase, FixL: Possibility of the Enhanced Reciprocating Kinase Reaction” Proc. Natl. Acad. Sci. USA101, 2742-2746 (2004)

Hanawa-Suetsugu K., Sekine S., Sakai H., Hori-Takemoto C., Terada T., Unzai S., Tame J. R. H., Kuramitsu S., Shirouzu M., and Yokoyama S.: “Crystal structure of elongation factor P from Thermus thermophilus HB8” Proc. Natl. Acad. Sci. USA101, 9595-9600 (2004)

Kasai T., Inoue M., Koshiba S., Yabuki T., Aoki M., Nunokawa E., Seki E., Matsuda T., Matsuda N., Tomo Y., Shirouzu M., Terada T., Obayashi N., Hamana H., Shinya N., Tatsuguchi A., Yasuda S., Yoshida M., Hirota H., Matsuo Y., Tani K., Suzuki H., Arakawa T., Carninci P., Kawai J., Hayashizaki Y., Kigawa T., and Yokoyama S.: “Solution structure of a BolA-like protein from Mus musculusProtein Sci. 13, 545-548 (2004)

Nameki N., Yoneyama M., Koshiba S., Tochio N., Inoue M., Seki E., Matsuda T., Tomo Y., Saito K., Kobayashi N., Yabuki T., Aoki M., Nunokawa E., Matsuda N., Sakagami N., Terada T., Shirouzu M., Yoshida M., Hirota H., Osanai T., Tanaka A., Arakawa T., Carninci P., Kawai J., Hayashizaki Y., Kinoshita K., Guntert P., Kigawa T., and Yokoyama S.: “Solution structure of the RWD domain of the mouse GCN2 protein” Protein sci. 13, 2089-2100 (2004)

Wang H., Hori-Takemoto C., Murayama K., Sakai H., Tatsuguchi A., Terada T., Shirouzu M., Kuramitsu S., and Yokoyama S.: “Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8” Protein Sci.13, 2806-2810 (2004) BL44B2/BL26B1

Kukimoto-Niino M., Murayama K., Kato-Murayama M., Idaka M., Bessho Y., Tatsuguchi A., Ushikoshi-Nakayama R., Terada T., Kuramitsu S., Shirouzu M., and Yokoyama S.: “Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8” Protein Sci.13, 3038-3042 (2004)BL26B1

Katsura Y., Shirouzu M., Yamaguchi H., Ishitani R., Nureki O., Kuramitsu S., Hayashi H., and Yokoyama S.: “Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV” Proteins55, 487-492 (2004)BL41XU

Wada T., Shirouzu M., Terada T., Kamewari Y., Park S-Y., Tame J. R. H., Kuramitsu S., and Yokoyama S.: “Crystal structure of the conserved hypothetical protein TT1380 from Thermus thermophilus HB8” Proteins55, 778-780 (2004)BL44B2

Reay P., Yamasaki K., Terada T., Kuramitsu S., Shirouzu M., and Yokoyama S.: “Structural and sequence comparisons arising from the solution structure of the transcription elongation factor NusG from Thermus thermophilusProteins56, 40-51 (2004)

Arai R., Wriggers W., Nishikawa Y., Nagamune T. and Fujisawa T.: “Conformations of variably linked chimeric proteins evaluated by synchrotron X-ray small-angle scattering” Proteins: Structure, Function, and Bioinformatics57, 829-838 (2004)BL45XU

Kishishita S., Tatsuguchi A., Ushikoshi-Nakayama R., Terada T., Kuramitsu S., Park SY., Tame J. R., Shirouzu M., and Yokoyama S.: “Crystal structure of a conserved hypothetical protein TT1751 from Thermus thermophilus HB8” Proteins57, 883-887 (2004)

Seto A., Murayama K., Toyama M., Ebihara A., Nakagawa N., Kuramitsu S., Shirouzu M., and Yokoyama S.: “ATP-induced structural change of dephosphocoenzyme A kinase from Thermus thermophilus HB8” Proteins58, 235-242 (2004)

Numoto N., Kita A. and Miki K.: “Crystal structure of the co-chaperonin Cpn10 from Thermus thermophilus HB8” Proteins58, 498-500 (2004)

Takeda S.: “Structure of the Core Domain of Human Cardiac Troponin in the Ca2+-Saturated Form” SPring-8 Research Frontiers, 12-13 (2004)

Yamashita A. and Maeda Y.: “Actin Filament Capping Protein(CapZ):The Story After Crystal Structure Elucidation” SPring-8 Research Frontiers, 14-15 (2004)

Nureki O., Watanabe K., Fukai S., Ishii R., Endo Y., Hori H., and Yokoyama S.: “Deep Knot Structure for Construction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme” Structure12, 593-602 (2004)BL41XU

Saito K., Kigawa T., Koshiba S., Sato K., Matsuo Y., Sakamoto A., Takagi T., Shirouzu M., Yabuki T., Nunokawa E., Seki E., Matsuda T., Aoki M., Miyata Y., Hirakawa N., Inoue M., Terada T., Nagase T., Kikuno R., Nakayama M., Ohara O., Tanaka A., and Yokoyama S.: “The CAP-Gly domain of CYLD associates with the proline-rich sequence in NEMO/IKKg” Structure 12, 1719-1728 (2004)

Goto M., Omi R., Nakagawa N., MiyaharaI., and Hirotsu K.: “Crystal Structures of CTP Synthetase Reveal ATP, UTP, and Glutamine Binding Sites” Structure12, 1413-1423 (2004)BL44B2

Nakamura M., Mamino M., Masaki M., Maki S., Matsui R., Kojima S., Hirano T., Ohmiya Y., and Niwa H.: “Bioluminescence activity of Latia luciferin analogues: replacement of the 2,6,6-trimethylcyclohexene ring onto the methyl-substituted phenyl groups” Tetrahedron Letters46, 53-56 (2004)