1999 Fiscal Year Annual Research Report

シンクロトロン放射光による生物マシーナリーの構造生物学

Research Project

Project/Area Number	10188101
Research Institution	The University of Tokyo
Principal Investigator	田之倉優東京大学, 大学院・農学生命科学研究科, 教授 (60136786)
Co-Investigator(Kenkyū-buntansha)	三木邦夫京都大学, 大学院・理学研究科, 教授 (10116105) 田中勲北海道大学, 大学院・理学研究科, 教授 (70093052) 月原冨武大阪大学, 蛋白質研究所, 教授 (00032277) 千田俊哉長岡技術科学大学, 工学部, 助手 (30272868) 豊島近東京大学, 分子細胞生物学研究所, 教授 (70172210)
Keywords	シンクロトロン放射光 / 生物マシーナリー / 構造生物学 / X線結晶学 / 蛋白結晶学 / 超分子複合体 / 膜蛋白質
Research Abstract	1 第2回ワークショップの開催平成11年8月19日(金)、20日(土)の2日間にわたって、長岡技術科学大学(新潟県、長岡市)において、第2回のワークショップを行った。参加者は計画班研究者、公募班研究者及び「班友」併せて総計名に及んだ。ワークショップでは、口頭発表の他、ポスター発表も行われた。 2 ニュースレターの発行今年度は、ニュースレター「生物マシーナリー」のNo.1及びNo.2を発行した。No.1は、研究者間の連携を強めるための、研究組織及び研究者名簿号で第2回ワークショップにおいて配付した。また、No.2には、数名の研究者による研究成果発表及び解説記事を掲載し、第一回公開シンポジウムにおいて配付した。 3 第一回公開シンポジウムの開催平成12年1月10日(月)、11日(火)の2日間にわたって、千里ライフサイエンスセンター(大阪府吹田市)において第一回公開シンポジウム「生体超分子複合体の結晶構造解析の最前線構造構築の秩序性と構造による精巧な機能制御」を行った。本領域以外からも多くの参加者があった。発表は全て招待講演で構成され、本領域の研究者らの最新の研究成果が報告された。 4 第2回総括班会議の開催上記の公開シンポジウム中に、第2回総括班会議を行った。これまでの活動報告及び、平成12年度、13年度の活動予定(ワークショップ及び公開シンポジウムの開催計画等)が話しあわれた。 5 ホームページの維持、管理本領域のメンバーに対するアナウンス等の目的で回折しているホームページの維持、管理を行った。 6 e-mail連絡網の整備領域内の連絡を迅速に行うため、事務局においてe-mail連絡網の整備を行った。

Research Products

(34 results)

All Other

All Publications (34 results)

[Publications] Kobashi, N: "Kinetic and mutation analyses of aspartate kinase from Thermus thermophilus"J. Biosci. Bioeng.. 87. 739-745 (1999)
[Publications] Iwasaki, W.: "Crystallization and preliminary X-ray diffraction studies of a 40kDa calcium binding protein specifically expressed in plasmodia of Physarum polycephlum"J. Biochem. 126. 7-9 (1999)
[Publications] Tohyama, T.: "Gene structure and amino acid sequence of Latimeria Chalumnae (Coelacanth) myelin DM20: Phylogenetic relation of the fish"Neurochem. Res. 24. 867-873 (1999)
[Publications] Kobori, T.: "Crystallization and preliminary crystallographic analysis of major nitroreductase from Escherichia coli"Acta Crystallogr.. D55. 1901-1902 (1999)
[Publications] Watanabe, S.: "Molecular cloning of the Lon protease gene from Thermus thermophilus HB8 and characterization of its gene product"Eur. J. Biochem. 266 (in press). (1999)
[Publications] Kojima, M.: "pH-dependent unfolding of Aspergillus niger acid proteinase A studied by small-angle X-ray scattering."Biochemistry. (in press). (1999)
[Publications] Mitsuhashi, S.: "X-ray structure of beta-carbonic anhydrase from the red alga, porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration"J. Biol. Chem.. 275. 5521-5526 (1999)
[Publications] Mitsuhashi, S.: "Crystallization and preliminary X-ray diffraction studies of a beta-carbonic anhydrase from the red alga porphyridium purpureum"Acta Crystallogr.. D56. 210-211 (1999)
[Publications] Mochizuki, M.: "Quantitative reevaluation of the redox active sites of crystalline bovine heart cytochrome oxidase"J. Biol. Chem.. 274. 33403-33411 (1999)
[Publications] Tomizaki, T.: "Structure analysis of bovine heart cytochrome c oxidase at 2.8 A resolution"Acta Crystallogr. D55. 31-45 (1999)
[Publications] Naitow, H.: "A low-resolution structure of rice dwarf virus determined by ab initio phasing"Acta Crystallogr. D55. 77-84 (1999)
[Publications] Sugimoto, H.: "Crystal structure of human D-dopachrome tautomerase, a homologue of macrophage migration inhibitory factor at 1.54【encircled a】 resolution"Biochemistry. 38. 3268-3279 (1999)
[Publications] Tominaga, T.: "High-Resolution Crystals of the HU Mutant K38N from Bacillus Stearothermophilus"J. Struct. Biol.. 125. 86-89 (1999)
[Publications] Nakagawa, A.: "The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome"The EMBO J.. 18. 1459-1467 (1999)
[Publications] White, S.W.: "The high-resolution structure of DNA-binding protein HU from Bacillus Stearothermophilus"Acta Crystallogr. D55. 801-809 (1999)
[Publications] Nakagawa, A.: "Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75A resolution"Biochem. Biophys. Acta. 1433. 253-260 (1999)
[Publications] Miyamoto, A.: "Role of the N-terminal region of ribosomal protein S7 in its interaction with 16S rRNA which binds to the concavity formed by the β-ribbon arm and the α-helix"Eur. J. Biochem,. 266. 591-598 (1999)
[Publications] Saitoh, F.: "Arginine-55 in the β-Arm is Essential for the Activity of DNA-Binding Protein HU from Bacillus Stearothermophilus"Biosci. Biotech. Biochem.. 63. 2232-2235 (1999)
[Publications] Saito, J.: "Crystal structure of chitosanase from Bacillus circuland MH-K1 at 1.6A resolution and its substrate recognition mechanism"J. Biol. Chem.. 293. 57-66 (1999)
[Publications] Maeda, N: "Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a pentagonal structure."J. Mol. Biol.. 293. 57-66 (1999)
[Publications] Fujihashi, M.: "Crystallization and preliminary X-ray diffraction studies of undecaprenyl diphosphate synthase from Micrococcus luteus B-P 26"Acta Crystallogr.. 55. 1606-1607 (1999)
[Publications] Komori, H.: "Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6A resolution"The EMBO J.. 18. 4597-4607 (1999)
[Publications] Higuchi, Y.: "Removal of the bridging ligand atom at the Ni-Fe active Site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4A resolution"Structure Fold Des.. 7. 548-556 (1999)
[Publications] Kita, A: "An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Pseudomonas putida nt02"Structure Folds Des.. 7. 25-34 (1999)
[Publications] Sugimoto, K.: "Purification and crystallization of a protocatechuate 4,5-dioxygenase LigAB from sphingomonas pausimobilis SYK-6"Protein and Peptide Lett.. 6. 55-58 (1999)
[Publications] Sugimoto, K.: "Crystal structure of an aromatic-ring-opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, in aerobic condition"Structure Fold Dex.. 7. 953-965 (1999)
[Publications] Sugimoto, K.: "Purification and Crystallization of a Catechol 2,3-Dioxygenase PheB from Bacillus stearothermophilus BR219"Protein and Peptide Lett.. 6. 403-406 (1999)
[Publications] Ohtsubo, Y.: "PcpA, which is involved in the degradation of pentachlorophenol in Sphingomonas chlorophenolica ATCC39723, is a novel type of ring-cleavage dioxygenase"FEBS Letters. 459. 395-398 (1999)
[Publications] Toyoshima, C: "Structure determination of tubular crystals pf membrane proteins. I. Indexing of diffraction patterns"Ultramicroscopy. (in press). (2000)
[Publications] Yonekura, K.: "Structure determination of tubular crystals of membrane proteins. II. Averaging of tubular crystals of different helical classes"Ultramicroscopy. (in press). (2000)
[Publications] 田之倉優: "タンパク質工学"丸善. 15 (1999)
[Publications] 田之倉優: "魚介類筋肉タンパク質その構造と機能"恒星社厚生閣. 8 (1999)
[Publications] 豊島近: "蛋白質核酸酵素構造生物学のフロンティア"共立出版(株). 9 (1999)
[Publications] 千田俊哉: "蛋白質核酸酵素構造生物学のフロンティア"共立出版(株). 7 (1999)

1999 Fiscal Year Annual Research Report

シンクロトロン放射光による生物マシーナリーの構造生物学

Principal Investigator

田之倉 優 東京大学, 大学院・農学生命科学研究科, 教授 (60136786)

Research Products

[Publications] Kobashi, N: "Kinetic and mutation analyses of aspartate kinase from Thermus thermophilus"J. Biosci. Bioeng.. 87. 739-745 (1999)

[Publications] Iwasaki, W.: "Crystallization and preliminary X-ray diffraction studies of a 40kDa calcium binding protein specifically expressed in plasmodia of Physarum polycephlum"J. Biochem. 126. 7-9 (1999)

[Publications] Tohyama, T.: "Gene structure and amino acid sequence of Latimeria Chalumnae (Coelacanth) myelin DM20: Phylogenetic relation of the fish"Neurochem. Res. 24. 867-873 (1999)

[Publications] Kobori, T.: "Crystallization and preliminary crystallographic analysis of major nitroreductase from Escherichia coli"Acta Crystallogr.. D55. 1901-1902 (1999)

[Publications] Watanabe, S.: "Molecular cloning of the Lon protease gene from Thermus thermophilus HB8 and characterization of its gene product"Eur. J. Biochem. 266 (in press). (1999)

[Publications] Kojima, M.: "pH-dependent unfolding of Aspergillus niger acid proteinase A studied by small-angle X-ray scattering."Biochemistry. (in press). (1999)

[Publications] Mitsuhashi, S.: "X-ray structure of beta-carbonic anhydrase from the red alga, porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration"J. Biol. Chem.. 275. 5521-5526 (1999)

[Publications] Mitsuhashi, S.: "Crystallization and preliminary X-ray diffraction studies of a beta-carbonic anhydrase from the red alga porphyridium purpureum"Acta Crystallogr.. D56. 210-211 (1999)

[Publications] Mochizuki, M.: "Quantitative reevaluation of the redox active sites of crystalline bovine heart cytochrome oxidase"J. Biol. Chem.. 274. 33403-33411 (1999)

[Publications] Tomizaki, T.: "Structure analysis of bovine heart cytochrome c oxidase at 2.8 A resolution"Acta Crystallogr. D55. 31-45 (1999)

[Publications] Naitow, H.: "A low-resolution structure of rice dwarf virus determined by ab initio phasing"Acta Crystallogr. D55. 77-84 (1999)

[Publications] Sugimoto, H.: "Crystal structure of human D-dopachrome tautomerase, a homologue of macrophage migration inhibitory factor at 1.54【encircled a】 resolution"Biochemistry. 38. 3268-3279 (1999)

[Publications] Tominaga, T.: "High-Resolution Crystals of the HU Mutant K38N from Bacillus Stearothermophilus"J. Struct. Biol.. 125. 86-89 (1999)

[Publications] Nakagawa, A.: "The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome"The EMBO J.. 18. 1459-1467 (1999)

[Publications] White, S.W.: "The high-resolution structure of DNA-binding protein HU from Bacillus Stearothermophilus"Acta Crystallogr. D55. 801-809 (1999)

[Publications] Nakagawa, A.: "Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75A resolution"Biochem. Biophys. Acta. 1433. 253-260 (1999)

[Publications] Miyamoto, A.: "Role of the N-terminal region of ribosomal protein S7 in its interaction with 16S rRNA which binds to the concavity formed by the β-ribbon arm and the α-helix"Eur. J. Biochem,. 266. 591-598 (1999)

[Publications] Saitoh, F.: "Arginine-55 in the β-Arm is Essential for the Activity of DNA-Binding Protein HU from Bacillus Stearothermophilus"Biosci. Biotech. Biochem.. 63. 2232-2235 (1999)

[Publications] Saito, J.: "Crystal structure of chitosanase from Bacillus circuland MH-K1 at 1.6A resolution and its substrate recognition mechanism"J. Biol. Chem.. 293. 57-66 (1999)

[Publications] Maeda, N: "Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a pentagonal structure."J. Mol. Biol.. 293. 57-66 (1999)

[Publications] Fujihashi, M.: "Crystallization and preliminary X-ray diffraction studies of undecaprenyl diphosphate synthase from Micrococcus luteus B-P 26"Acta Crystallogr.. 55. 1606-1607 (1999)

[Publications] Komori, H.: "Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6A resolution"The EMBO J.. 18. 4597-4607 (1999)

[Publications] Higuchi, Y.: "Removal of the bridging ligand atom at the Ni-Fe active Site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4A resolution"Structure Fold Des.. 7. 548-556 (1999)

[Publications] Kita, A: "An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Pseudomonas putida nt02"Structure Folds Des.. 7. 25-34 (1999)

[Publications] Sugimoto, K.: "Purification and crystallization of a protocatechuate 4,5-dioxygenase LigAB from sphingomonas pausimobilis SYK-6"Protein and Peptide Lett.. 6. 55-58 (1999)

[Publications] Sugimoto, K.: "Crystal structure of an aromatic-ring-opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, in aerobic condition"Structure Fold Dex.. 7. 953-965 (1999)

[Publications] Sugimoto, K.: "Purification and Crystallization of a Catechol 2,3-Dioxygenase PheB from Bacillus stearothermophilus BR219"Protein and Peptide Lett.. 6. 403-406 (1999)

[Publications] Ohtsubo, Y.: "PcpA, which is involved in the degradation of pentachlorophenol in Sphingomonas chlorophenolica ATCC39723, is a novel type of ring-cleavage dioxygenase"FEBS Letters. 459. 395-398 (1999)

[Publications] Toyoshima, C: "Structure determination of tubular crystals pf membrane proteins. I. Indexing of diffraction patterns"Ultramicroscopy. (in press). (2000)

[Publications] Yonekura, K.: "Structure determination of tubular crystals of membrane proteins. II. Averaging of tubular crystals of different helical classes"Ultramicroscopy. (in press). (2000)

[Publications] 田之倉優: "タンパク質工学"丸善. 15 (1999)

[Publications] 田之倉優: "魚介類筋肉タンパク質 その構造と機能"恒星社厚生閣. 8 (1999)

[Publications] 豊島近: "蛋白質核酸酵素 構造生物学のフロンティア"共立出版(株). 9 (1999)

[Publications] 千田俊哉: "蛋白質核酸酵素 構造生物学のフロンティア"共立出版(株). 7 (1999)

田之倉優東京大学, 大学院・農学生命科学研究科, 教授 (60136786)

[Publications] 田之倉優: "魚介類筋肉タンパク質その構造と機能"恒星社厚生閣. 8 (1999)

[Publications] 豊島近: "蛋白質核酸酵素構造生物学のフロンティア"共立出版(株). 9 (1999)

[Publications] 千田俊哉: "蛋白質核酸酵素構造生物学のフロンティア"共立出版(株). 7 (1999)