Original Papers (only)＜ Year 2002 >Shimizu H., Park S.-Y., Shiro Y., and Adachi S.: “X-ray structure of nitric oxide reductase (cytochromeP450nor) at atomic resolution”, Acta Cryst. D58, 81-89 (2002).
BL44B2
Nakano H., Uchiyama S., Yoshida T., Ohkubo T., Kato H., Yamagata Y., and Kobayashi Y.:“Crystallization and preliminary X-ray crystallographic studies of a mutant of ribosome recycling factor
from Escherichia coli, Arg132Gly”, Acta Cryst. D58, 124-126 (2002).
Hibi T., Hisada H., Nakatsu T., Kato H., and Oda J.: “Escherichia coli β γ -glutamylcysteine synthetase:modification, purification, crystallization and preliminary crystallographic analysis”, Acta Cryst. D58,316-318 (2002).
Lee D.-S., Yamada A., Matsunaga I., Ichihara K., Adachi S., Park S.-Y., and Shiro Y.: “Crystallization andpreliminary X-ray diffraction analysis of fatty-acid hydroxylase cytochrome P450BSβ from Bacillus
subtilis”, Acta Cryst. D58, 687-689 (2002).
Liu L., Nogi T., Kobayashi M., Nozawa T., and Miki K.: “Ultrahigh-resolution structure of high-potentialiron-sulfur protein from Thermochromatium tepidum”, Acta Cryst., D58, 1085-1091 (2002).
BL44B2
Nureki O., Shirouzu M., Hashimoto K., Ishitani R., Terada T., Tamakoshi M., Oshima T., Chijimatsu M.,
Takio K., Vassylyev D., Shibata T., Inoue Y., Kuramitsu S., and Yokoyama S.: “An enzyme with a deep
trefoil knot for the active-site architecture” Acta Cryst. D58, 1129-1137 (2002).
Shimomura K., Sumiguchi-Agari K., Masui R., Kuramitsu S., and Fukuyama K.: “Overproduction,
crystallization, and preliminary X-ray diffraction analysis of a quinone oxidoreductase from Thermus
thermophilus HB8”, Acta Cryst. D58, 1365-1367 (2002).
BL44B2
Vassylyeva M., Jookyung L., Sekine S., Oleg L., Kuramitsu S., Shibata T., Inoue Y., Sergei B., Vassylyev
D., and Yokoyama S.: “Purification, crystallization and initial crystallographic analysis of RNApolymerase holoenzyme from Thermus thermophilus” Acta Cryst. D58, 1497-1500 (2002).
Shomura Y., Yoshida T., Maruyama T., Yohda M., and Miki K.: “Crystallization and preliminary X-ray
characterization of archaeal group II chaperonin subunit from Thermococcus strain KS-1”, Acta Cryst.,
D58, 1830-1832 (2002).
BL41XU/BL45PXYamamoto H., Yamauchi E., Taniguchi H., Ono T., and Miyamoto E.: “Phosphorylation of
microtubule-associated protein tau by Ca2+/Calmodulin-activated protein kinase II in its tubulin bindingsites.” Arch. Biochem. Biophys. 408, 255-262 (2002).
Kimura M., Furuichi M., Yamamoto M., Kumasaka T., Mizuno H., Miyano M., and Yamaguchi I.: “Theflexible C-terminal region of Aspergillus terreus blasticidin S deaminase: Identification of its functionalroles with deletion enzymes”, Biochem. Biophys. Res. Commun. 290, 421-426 (2002).
Matsunaga I., Yamada A., Lee D.-S., Obayashi E., Fujiwara N., Kobayashi K., Ogura H., and Shiro Y.:

“Enzymatic reaction of hydrogen peroxide-dependent peroxygenase cytochrome P450s: Kinetic
deuterium isotope effects and analyses by resonance Raman spectroscopy”, Biochemistry 41, 1886-1892(2002).
Noguchi T., and Sugiura M.: “Flash-induced FTIR difference spectra of the water oxidizing complex inmoderately hydrated photosystem II core films: Effect of hydration extent on S-state transitions”,
Biochemistry 41, 2322-2330 (2002).
Shimizu T., Nakatsu T., Miyairi K., Okuno T., and Kato H.: “Active-site architecture ofendopolygalacturonase I from Stereum purpureum revealed by crystal structures in native andligand-bound forms at atomic resolution”, Biochemistry 41, 6651-6659 (2002).
Tanaka M., Machida Y., Nishikawa Y., Akagi T., Morishima I., Hashikawa T., Fujisawa T., and Nukina
N.: “The effects of aggregation-inducing motifs on amyloid formation of model proteins related toneurodegenerative diseases”, Biochemistry 41, 10277-10286 (2002).
BL45SAXSFujisawa T., Kato M., Taguchi Y., Stanley H. E., and Ludwig H.: “The small angle X-ray scattering fromproteins under pressure”, Biological Systems Under Extreme Conditions: Structure and Function,
121-138 (2002).
Iwamoto H., Nishikawa Y., Wakayama J., and Fujisawa T.: “Direct X-ray observation of a single
hexagonal myofilament lattice in native myofibrils of striated muscle”, Biophys. J. 83, 1074-1081 (2002).
BL45SAXS
Krieger I., Kostyukova A., Yamashita A., Nitanai Y., and Maéda Y.: “Crystal structure of the C-terminal
half of tropomodulin and structural basis of actin filament pointed-end capping”, Biophys. J. 83,2716-2725 (2002).
BL44B2
Tahirov T. H., Sato K., Ichikawa E., Sasaki M., Bungo T., Shiina M., Kimura K., Takata S., Fujikawa A.,
Morii H., Kumasaka T., Yamamoto M., Ishii S., and Ogata K.: “Mechanism of c-Myb-C/EBP β
cooperation from separated sites on a promoter”, Cell 108, 57-70 (2002).
BL45XU
Ogiso H., Ishitani R., Nureki O., Fukai S., Yamanaka., Kim J-H., Saito K., Sakamoto A., Inoue M.,
Shirouzu M., and Yokoyama S.: “Crystal structure of the complex of human epidermal growth factor andreceptor extracellular domains” Cell 110, 775-787 (2002).
Nureki O., Fukai S., Sekine S., Shimada A., Terada T., Nakama T., Shirouzu M., Vassylyev D.G., andYokoyama S.: “Structural basis for amino acid and tRNA recognition by Class I aminoacyl-tRNAsynthetases” Cold Spring Harbor Laboratory Symposia on Quantitative Biology LXVI, 167-173 (2002).
Kimoto M., Shirouzu M., Mizutani S., Koide H., Kaziro Y., Hirao I., and Yokoyama S.: “Anti-(Raf-1)
RNA aptamers that inhibit Ras-induced Raf-1 activation”, Eur. J. Biochem. 269, 697-704 (2002).
Liu L., Iwata K., Yohda M., and Miki K.: “Structural insight into gene duplication, gene fusion anddomain swapping in the evolution of PLP-independent amino acid racemases”, FEBS Lett., 528, 114-118(2002).
BL44B2

Satoh T., Itoga A., Isogai Y., Kurihara M., Yamada S., Natori M., Suzuki N., Suruga K., Kawachi R.,
Arahira M., Nishio T., Fukazawa C., and Oku T.: “Increasing the conformational stability by replacementof heme axial ligand in c-type cytochrome” FEBS Lett. 531, 543-547 (2002).
Sano K., Maeda K., Oki M., and Maéda Y.: “Enhancement of protein expression in insect cells by alobster tropomyosin cDNA leader sequence” FEBS Lett. 532, 143-146 (2002).
Nameki N., Someya T., Hosoi H., Suzuki S., Hatanaka H., Fujii M., Terada T., Shirouzu M., Inoue Y.,
Shibata T., Kuramitsu S., Yokoyama S., and Kawai G.: “Solution structure of a tmRNA-binding protein,
SmpB, from Thermus thermophilus” FEBS Lett. 535, 94-100 (2002).
Hori H., Suzuki T., Sugawara K., Inoue Y., Shibata T., Kuramitsu S., Yokoyama S., Oshima T., andWatanabe K.: “Identification and characterization of tRNA (Gm18) methyltransferase from Thermus
thermophilus HB8: domain structure and conserved amino acid sequence motifs” Genes Cells 7, 259-272(2002).
Ogata H., Mizoguchi Y., Mizuno N., Miki K., Adachi S., Yasuoka N., Yagi T., Yamauchi O., Hirota S.,
and Higuchi Y.: “Structural studies of the carbon monoxide complex of [NiFe] hydrogenase from
Desulfovibrio vulgaris Miyazaki F: Suggestion for the initial activation site for dihydrogen”, J. Am. Chem.
Soc., 39, 11628-11635 (2002).
BL44B2
Sakai K., Matsui Y., Kohyama T., Shiro Y., and Adachi S.: “Optical monitoring of freeze-trapped reaction
intermediates in protein crystals: a microspectro-photometer for cryogenic protein crystallography”, J.
Appl. Crystallogr. 35, 270-273 (2002).
Hai H., Sano K., Maeda K., Maéda Y., and Miki M.: “Ca2+- and S1-induced conformational changes ofreconstituted skeletal muscle thin filaments observed by fluorescence energy transfer spectroscopy:
Structural evidence for three states of thin filament”, J. Biochem. 131, 407-418 (2002).
Kuwahara H., Yamasaki T., Hatakeyama T., Aoyagi H., and Fujisawa T.: “Oligomerization process of thehemolytic lectin CEL-III purified from a sea cucumber, Cucumaria echinata”, J. Biochem. 131, 751-756(2002).
BL45SAXS
Kimura C., Maeda K., Maéda Y., and Miki M.: “Ca2+- and S1-induced movement of troponin T on
reconstituted skeletal muscle thin filaments observed by fluorescence energy transfer spectroscopy1”, J.
Biochem. 132, 93-102 (2002).
Kimura C., Maeda K., Hai H., and Miki M.: “Ca2+ -and S1-induced movement of troponin T on mutant
thin filaments reconstituted with functionally deficient mutant tropomyosin”, J. Biochem. 132, 345-352(2002).
Omi R., Mizuguchi H., Goto M., Miyahara I., Hayashi H., Kagamiyama H., and Hirotsu K.: “Structure ofImidazole Glycerol Phosphate Synthase from Thermus thermophilus HB8: Open-Closed Conformational
Change and Ammonia Tunneling1” J. Biochem. 132, 759-765 (2002).

Kurumizaka H., Ikawa S., Nakada M., Enomoto R., Kagawa W., Kinebuchi T., Yamazoe M., YokoyamaS., and Shibata T.: “Homologous pairing and ring and filament structure formation activities of the humanXrcc2·Rad51D complex”, J. Biol. Chem. 277, 14315-14320 (2002).
Goto M., Nakajima Y., and Hirotsu K.: “Crystal structure of argininosuccinate synthetase from Thermus
thermophilus HB8: Structural basis for the catalytic action”, J. Biol. Chem. 277, 15890-15896 (2002).
BL41XU/BL44B2/BL45XU.
Kikuchi J., Iwahara J., Kigawa T., Murakami Y., Okazaki T., and Yokoyama S.: “Solution structure of thetwo DNA-binding domains in Shizosaccharomyces pombe Abp1 protein by a combination of dipolar
coupling and diffusion anisotropy restraints” J. Biomol. NMR 22, 333-347 (2002).
Hayashi T., Matsuo T., Hitomi Y., Okawa K., Shiro Y., Iizuka T., Hisaeda Y., and Ogoshi H.:“Contribution of heme-propionate side chains to structure and function of myoglobin: Chemical approachby artificially created prosthetic groups” J. Inorg. Biochem. 91, 94-100 (2002).
Park S.-Y., Yamane K., Adachi S., Shiro Y., Weiss K. E., Maves S. A., and Sligar S. G.: “Thermophiliccytochrome P450 (CYP119) from Sulfolobus solfataricus: High resolution structural origin of its
thermostability and functional properties” J. Inorg. Biochem. 91, 491-501 (2002).
BL44B2
Iwamoto H., Oiwa K., Suzuki T., and Fujisawa T.: “States of thin filament regulatory proteins as revealedby combined cross-linking/X-ray diffraction techniques”, J. Mol. Biol. 317, 707-720 (2002). BL45SAXS
Ishitani R., Nureki O., Fukai S., Kijimoto T., Nameki N., Watanabe M., Kondo H., Sekine M., Okada N.,
Nishimura S., and Yokoyama S.: “Crystal structure of Archaeosine tRNA-guanine Transglycosylase” J.
Mol. Biol. 318, 665-677 (2002).
Furukawa Y., Imada K., Vonderviszt F., Matsunami H., Sano K., Kutukake K., and Namba K.:“Interaction between bacterial flagellar axial proteins in their monomeric state in solution” J. Mol. Biol.
318, 889-900 (2002).
Irie K., Nakatsu T., Mitsuoka K., Miyazawa A., Sobue K., Hiroaki Y., Doi T., Fujiyoshi Y., and Kato H.:“Crystal structure of the homer 1 family conserved region reveals the interaction between the EVH1
domain and own proline-rich motif”, J. Mol. Biol. 318, 1117-1126 (2002).
Liu L., Iwata K., Kita A., Kawarabayasi Y., Yohda M., and Miki K.: “Crystal structure of aspartate
racemase from Pyrococcus horikoshii OT3 and its implication for molecular mechanism of
PLP-independent racemization”, J. Mol. Biol., 319, 479-489 (2002).
BL44B2
Unwin N., Miyazawa A., Li J., and Fujiyoshi Y.: “Activation of the nicotinic acetylcholine receptor
involves a switch in conformation of the α subunits”, J. Mol. Biol. 319, 1165-1176 (2002).
Fukushima K., Kikuchi J., Koshiba S., Kuroda Y., and Yokoyama S.: “Solution structure of the C-terminal
domain of DEF45/ICAD. A structural basis for the regulation of apoptotic DNA fragmentation” J. Mol.
Biol. 321, 317-327 (2002).

Ohyama A., Hosaka K., Komiya Y., Akagawa K., Yamauchi E., Taniguchi H., Sasagawa N., Kumakura K.,
Mochida S., Yamauchi T., and Igarashi M.: “Regulation of exocytosis through Ca2+/ATP-dependent
binding of autophosphorylated Ca2+/Calmodulin-activated protein kinase II to syntaxin 1A ” J. Neurosci.
22, 3342-3351 (2002).
Hasegawa K., Ono T., and Noguchi T.: “Ab initio density functional theory calculations and vibrational
analysis of zinc-bound 4-methylimidazole as a model of a histidine ligand in metalloenzymes”, J. Phys.
Chem. A 106, 3377-3390 (2002).
Hendrickson T. L., Nomanbhoy T. K., DeCrecy-Lagard V., Fukai S., Nureki O., Yokoyama S., andSchimmel P.: “Mutational separation of two pathways for editing by a class I tRNA synthetase” Mol. Cell
9, 353-362 (2002).
Kagawa W., Kurumizaka H., Ishitani R., Fukai S., Nureki O., Shibata T., and Yokoyama S.: “Crystal
structure of the homologous-pairing domain from the human Rad52 recombinase in the undecamericform” Mol. Cell 10, 359-371 (2002).
Vassylyev D., Sekine S, Oleg L., Jookyung L., Vassylyeva M., Sergei B., and Yokoyama S.: “Crystal
structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution” Nature 417, 712-719 (2002).
Tahir T. H., Temiakov D., Anikin M., Patlan V., McAllister W. T., Vassylyev D., and Yokoyama S.:“Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution” Nature 420, 43-50 (2002).
Kita A., Matsunaga S., Takai A., Kataiwa H., Wakimoto T., Fusetani N., Isobe M., and Miki K.: “Crystalstructure of the complex between calyculin A and the catalytic subunit of protein phosphatase 1”
Structure 10, 715-724 (2002).
Hirao I., Ohtsuki T., Fujiwara T., Mitsui T., Yokogawa T., Okuni T., Nakayama H., Takio K., Yabuki T.,
and Kigawa T.: “An unnatural base pair for incorporating amino acid analogs into proteins”, Nature
Biotechnol. 20, 177-182 (2002).
Terada T., Nureki O., Ishitani R., Ambrogelly A., Ibba M., Soll D., and Yokoyama S.: “Functionalconvergence of two lysyl-tRNA synthetases with unrelated topologies” Nat. Struct. Biol. 9, 257-262(2002).
Hardingham G., Fukunaga Y., and Bading H.: “Extrasynaptic NMDARs oppose synaptic NMDARs bytriggering CREB shut-off and cell death pathways”, Nature Neuroscience 5, 405-414 (2002).
Sakamoto K., Hayashi A., Sakamoto A., Kiga D., Nakayama H., Soma A., Kobayashi T., Kitabatake M.,
Takio K., Saito K., Shirouzu M., Hirao I., and Yokoyama S.: “Site-specific incorporation of an unnaturalamino acid into proteins in mammalian cells” Nucleic Acids Res. 30, 4692-4699 (2002).
Yamamoto A., and Yamaguchi I.: “Profilometry of sloped plane surfaces by wavelength scanninginterferometry”, Opt. Rev. 9, 112-121 (2002).
Tohri A., Suzuki T., Okuyama S., Kamino K., Motoki A., Hirano M., Ohta H., Shen J.R., Yamamoto Y.,and Enami I.: “Comparison of the structure of the extrinsic 33 kDA protein from different organisms”
Plant Cell Physiol. 43, 429-439 (2002).
Akiyama S., Takahashi S., Kimura T., Ishimori K., Morishima I., Nishikawa Y., and Fujisawa T.:“Conformational landscape of cytochrome c folding studied by microsecond-resolved small-angle x-rayscattering”, Proc. Natl. Acad. Sci. USA 99, 1329-1334 (2002).
BL45SAXS
Yamagata A., Masui R., Kakuta Y., Fukuyama K.: “The crystal structure of exonuclease RecJ bound to
Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity”, Proc. Natl. Acad.
Sci. USA 99, 5908-5912 (2002).
BL41XU
Isogai Y., Ota M., Ishii A., Ishida M., and Nishikawa K.: “Identification of amino acids involved inprotein structural uniqueness: implication for de novo protein design” Protein Eng. 15, 555-560 (2002).
Kita A., Matsunaga S., Takai A., Kataiwa H., Wakimoto T., Fusetani N., Isobe M., and Miki K.: “Crystalstructure of the complex between calyculin A and the catalytic subunit of protein phosphatase 1”,
Structure, 10, 715-724 (2002).
BL44B2
Fujisawa T., Nisikawa Y., Inoko Y., and Hayashi R.: “The use of a small-angle X-ray scattering techniquewith a third generation synchrotron X-ray source in high-pressure biochemistry”, Trends in High Pressure
Bioscience and Biotechnology , 615-620 (2002).
BL45SAXS