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 thermophilus” Acta
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 andpreliminary 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., Miyahara I., and Hirotsu K.: “Expression, purification and preliminary
X-ray characterization of histidinol phosphate phosphatase” Acta Cryst. D60, 574-576 (2004)
BL44B2Inagaki E., Ukita Y., Kumei M., Kajihara Y., and Tahirov T. H.: “Crystallization and preliminary
crystallographic analysis of 2-keto-3-deoxygluconate kinase from Thermus thermophilus” Acta 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: 1.8Å 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., Lee W. C., Ito K., Kamo M., Inoue Y., and Tanokura M.:“Crystallization andpreliminary X-ray analysis of carboxypeptidase 1 from Thermus thermophilus”Acta Cryst. D60,
1445-1446 (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)
Fukunaga R., and Yokoyama S.: “Crystallization and preliminary X-ray crystallographic study of theediting domain of Thermus thermophilus isoleucyl-tRNA synthetase complexed with pre- andpost-transfer
editing-substrateanalogues”
Acta
Cryst.
D60,
1900-1902(2004)
BL26B1/BL38B1
Fukunaga R., and Yokoyama S.: “Crystallization and preliminary X-ray crystallographic study ofleucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii” Acta Cryst. D60, 1916-1918 (2004)
BL26B1
Nakamura A., Komori H., Kobayashi G., Kita A., Wada C., and Miki K.:“The N-terminal domain of thereplication 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”
Biochemistry 43, 3214-3221 (2004)
Taguchi Y., Sugishima M., and Fukuyama K.: “Crystal structure of a novel zinc-binding ATP sulfurylasefrom Thermus thermophilus HB8” Biochemistry 43, 4111-4118 (2004)
BL44B2Ishida M., Dohmae N., Shiro Y., Oku T., Iizuka T. and Isogai Y.: “Design and Synthesis of de Novo
Cytochrome c” Biochemistry 43, 9823-9833 (2004)
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” Bioinformatics, 20, 2836-2838 (2004)
Endo M., Mitsui T., Okuni T., Kimoto M., Hirao I., and Yokoyama S.: “Unnatural base pairs mediate thesite-specific incorporation of an unnatural hydrophobic component into RNA transcripts” Bioorg. Med.
Chem. Lett. 14, 2593-2596 (2004)
Hirao I., 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 uponsudden 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-bindingsites 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 Hirao I.: “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” Cell 116, 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” Cell 117, 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” Cell 118, 297-309 (2004)
Matsunaga I., and Shiro Y.:“Peroxide utilizing biocatalysts: structural and functional diversity ofheme-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.: “Crystal structure of the PsbP protein of photosystem II from
Nicotiana tabacum”EMBO Rep.5, 4 362-367 (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)
Chumpolkulwong N., Hori-Takemoto C., Hosaka T., Inaoka T., Kigawa T., Shirouzu M., Ochi K., andYokoyama S.: “Effects of Escherichia coil ribosomal protein S12 Mutations on Cell-Free Protein
Synthesis” Eur. J. Biochem. 271, 1127-1134 (2004)
Vasil'ev S., Shen J., Kamiya N. and Bruce D.:“The orientations of core antenna chlorophylls inphotosystem II are optimized to maximize the quantum yield of photosynthesis”FEBS Letter 561,
111-116 (2004)

Hirao I., Harada Y., Kimoto M., Mitsui T., Fujiwara T., and Yokoyama S.: “A two-unnatural-base-pairsystem 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 rarecodons 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 ofCytochrome 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 anendonuclease activity promoted by MutL” J. Biochem. 135, 375-384 (2004)
Suzuki H., Nojiri M., Kamiya N. and Noguchi T.:“Thermal equilibrium of two conformations ofphotosensitive 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. Biochemistry 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)
BL44B2
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 theE1 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 domainfrom Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine” J. Biol. Chem.
279, 8396-8402 (2004)
BL41XU/BL44XU
Hirotsu S., Chu G. C., Unno M., Lee D.-S., Yoshida T., Park S.-Y., Shiro Y., and Ikeda-Saito M.: “TheCrystal Structures of the Ferric and Ferrous Forms of the Heme Complex of Hmu O, a Heme Oxygenase
of Corynebacterium diphtheriae” J. 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 adiadenosine 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., andMiyano 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., Söll 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 roleof 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 Artsimovitch I.: “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 anoxidatively 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 ofcytochrome 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.:“NOreduction by nitric-oxide reductase from denitrifying bacterium pseudomonas aeruginosa” J. Biol. Chem.
279, 55247-55254 (2004)
López-Méndez 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 Güntert P.: “NMR assignment of the hypothetical ENTH-VHS domain
At3g16270 from Arabidopsis thaliana” J. Biomol. NMR 29 205-206 (2004)
Pantoja-Uceda D., López-Méndez B., Koshiba S., Kigawa T., Shirouzu M., Terada T., Inoue M., YabukiT., Aoki M., Seki E., Matsuda T., Hirota H., Yoshida M., Tanaka A., Osanai T., Seki M., Shinozaki K.,
Yokoyama S. and Güntert P.: “NMR assignment of the hypothetical rhodanese domain At4g01050 from
Arabidopsis thaliana” J. Biomol. NMR 29, 207-208 (2004)
Scott A., Pantoja-Uceda D., Koshiba S., Inoue M., Kigawa T., Terada T., Shirouzu M., Tanaka A., SuganoS., 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., Maéda Y. and Cooper John A.:“Capping Protein Binding to Actin in
Yeast:Biochemical Mechanizm and Physiological Relevance”J. Cell Biology 164, 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, andinter-subunit rearrangement between two crystal forms” J. Mol. Biol. 335, 1265-1278 (2004)
BL41XU/BL44B2/BL44XU/BL45XUSato 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., andYokoyama S.: “A Novel Zinc-binding Motif Revealed by Solution Structures of DNA-binding Domainsof 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., andYokoyama 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 thermophilus” J. 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)
BL44B2/BL26B1
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., andKobayashi 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 fromskeletal muscle thin filaments partially occupied with myosin heads: Effect of cooperative binding”J.
Muscle Res. Cell Motil 25, 329-335 (2004)
BL45XU
Kigawa T., Yabuki T., Matsuda N., Matsuda T., Nakajima R., Tanaka A., and Yokoyama S.: “Preparationof Escherichia coli cell extract for highly productive cell-free protein expression” J. Struct. Funct.
Genomics 5, 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 Radiat 11, 60-63 (2004)

BL44XU

Yagi N., Yamamoto M., Uesugi K. and Inoue K.:“A large-area CMOS imager as an X-ray detector forsynchrotron 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 bysynchrotron X-ray small-angle scattering: dose-related considerations and suppression bycryoprotectants”J. Synchrotron Radiat 11, 462-468 (2004)
BL45XU
Miyano M. and Sugahara M.:“Full automated crystallization and observation robot system”Med. Sci. Dig.
/ Medical Science Digest 30, 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” Methods 33, 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” Methods 34,
133-143 (2004)
Kinebuchi T., Kagawa W., Enomoto R., Tanaka K., Miyagawa K., Shibata T., Kurumizaka H., andYokoyama S.: “Structural basis for octameric ring formation and DNA Interaction of the humanhomologous-pairing protein Dmc1” Mol. Cell 14, 363-374 (2004)
Jiang M., Ma N., Vassylyev D. G., and McAllister W. T.: “RNA displacement and resolution of thetranscription bubble during transcription by T7 RNA polymerase” Mol. Cell 15, 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 thelate growth phase in Escherichia coli” Mol. Genet. Genomics 271, 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” Nature 430, 700-704 (2004)
BL44XU
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, 1-12 (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)
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-helicalcontents and compactness” Proc. Natl. Acad. Sci USA 101, 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. USA 101, 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. USA 101, 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., YoshidaM., 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 musculus” Protein 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., Güntert P., Kigawa T., and Yokoyama S.: “Solution structure of the RWD domain of themouse 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 ofpossible 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” Proteins 55,
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”
Proteins 55, 778-780 (2004)
BL44B2

Reay P., Yamasaki K., Terada T., Kuramitsu S., Shirouzu M., and Yokoyama S.: “Structural and sequencecomparisons arising from the solution structure of the transcription elongation factor NusG from Thermus
thermophilus” Proteins 56, 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 Bioinformatics 57, 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” Proteins 57, 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”
Proteins 58, 235-242 (2004)
Numoto N., Kita A. and Miki K.:“Crystal structure of the co-chaperonin Cpn10 from Thermus
thermophilus HB8”Proteins 58, 498-500 (2004)
Nureki O., Watanabe K., Fukai S., Ishii R., Endo Y., Hori H., and Yokoyama S.: “Deep Knot Structure forConstruction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme” Structure 12,593-602 (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., Miyahara I., and Hirotsu K.: “Crystal Structures of CTP Synthetase
Reveal ATP, UTP, and Glutamine Binding Sites” Structure 12, 1413-1423 (2004)
BL44B2
Nakanishi T., Nakatsu T., Matsuoka M., Sakata K. and Kato H.: “Crystal structures of Pyruvate Phophate
Dikinase from Maise Revealed an Alternative Confrontation in the Swiveling-Domain Motion ”
Biochemistry 44, 1136-1144 (2005)
Oinuma K., Kumita H., Ohta T., Konishi K., Hashimoto Y., Higashibata H., Kitagawa T., Shiro Y., andKobayashi M.: “ Stopped-flow spectrophotometric and resonance Raman analyses of aldoxime
dehydratase involved in carbon-nitrogen triple bond synthesis”FEBS Letters 579, 1394-1398 (2005)
Kimura T., Uzawa T., Ishimori K., Morishima I., Takahashi S., Konno T., Akiyama S. and Fujisawa T.:“Specific collapse followed by slow hydrogen bond formation of sheet in the folding of single chainmonellin” Proc. Natl. Acad. Sci. USA 102, 2748-2753 (2005)
BL45XU
Ebihara A., Okamoto A., Kousumi Y., Yamamoto H., Masui R., Ueyama N., Yokoyama S. and Kuramitsu
S.: “ Structure-based functional identification of a novel heme-binding protein from Thermus

thermophilus HB8” J. Struct. Funct. Genomic 31, 1-12 (2005)