Study on the mechanism of the ribonucleoprotein complex

• Project/Area Number: 19380060
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Applied biochemistry
• Research Institution: Kyushu University
• Principal Investigator: KIMURA Makoto Kyushu University, 大学院・農学研究院, 教授 (10204992)
• Co-Investigator(Kenkyū-buntansha): KAKUTA Yoshimitsu 九州大学, 大学院・農学研究院, 准教授 (00314360)
• Project Period (FY): 2007 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥20,020,000 (Direct Cost: ¥15,400,000、Indirect Cost: ¥4,620,000); Fiscal Year 2009: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2008: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2007: ¥10,400,000 (Direct Cost: ¥8,000,000、Indirect Cost: ¥2,400,000)
• Keywords: リボヌクレアーゼP / tRNA / RNAプロセシング / リボザイム / 結晶構造 / リボ核タンパク質 / 前駆体tRNA / タンパク質結晶構造 / 超好熱古細菌 / 酵素利用学 / RNAシャペロン / リボ核ダンパク質

Research Abstract

Ribonuclease P (RNase P) is composed of a catalytic RNA (PhopRNA) and five proteins (PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, PhoRpp38). In this study, we determined the crystal structure of the protein complex composed of PhoRpp21 and PhoRpp29. Furthermore, we examined the protein binding sites on PhopRNA by biochemical methods and analyzed the activated structure of RNase P RNA (PhopRNA) in Pyrococcus horikoshii OT3 was characterized by circular dichroism (CD) and ultraviolet (UV) absorbance spectra.

Research Products

• [Journal Article] Archaeal homologs of human RNase P protein pairs Pop5 with Rpp30 and Rpp21 with Rpp29 word on distinct functional domains of the RNA subunit. (2010)
  • Author(s): T. Honda, T. Hara, J. Nan, X. Zhang, M. Kimura
  • Journal Title: Biosci. Biotechnol. Biochem. 74 Pages: 266-273
  • Peer Reviewed
• [Journal Article] Structural changes in ribonuclease P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 induced on interaction with proteins. (2010)
  • Author(s): S. Kosaka, K. Hada, T. Nakashima, M. Kimura
  • Journal Title: Biosci. Biotechnol. Biochem. 74 Pages: 394-396
  • Peer Reviewed
• [Journal Article] Archaeal homologs of human RNase P protein pairs Pop5 with Rpp30 and Rpp21 with Rpp29 word on distinct functional domains of the RNA subunit. (2010)
  • Author(s): T.Honda, T.Hara, J.Nan, X.Zhang, M.Kimura
  • Journal Title: Biosci. Biotechnol. Biochem. 74 Pages: 266-273
  • Peer Reviewed
• [Journal Article] Structural changes in ribonuclease P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 induced on interaction with proteins. (2010)
  • Author(s): S.Kosaka, K.Hada, T.Nakashima, M.Kimura
  • Journal Title: Biosci. Biotechnol. Biochem. 74 Pages: 394-396
  • Peer Reviewed
• [Journal Article] Steady-state and time-resolved fluorescence spectroscopic studies on interaction of the N-terminal region with the hairpin loop of the phytocystatin Scb. (2009)
  • Author(s): K. Doi-Kawano, E. Nishimoto, Y. Kouzuma, D. Takahashi, S. Yamashita, M. Kimura
  • Journal Title: J. Fluoresc. 19 Pages: 631-639
  • Peer Reviewed
• [Journal Article] Crystal structure of chondroitin polymerase from Escherichia coli K4. (2009)
  • Author(s): T. Osawa, N. Sugiura, H. Shimada, R. Hirooka, A. Tsuji, T. Shirakawa, K. Fukuyama, M. Kimura, K. Kimata, Y. Kakuta
  • Journal Title: Biochem. Biophys. Res. Commun. 378 Pages: 10-14
  • Peer Reviewed
• [Journal Article] Structural basis for the broad range substrate specificity of a novel mouse cytosolic sulfotransferase-mSULT1D1. (2009)
  • Author(s): T. Teramoto, Y. Sakakibara, M-C. Liu, M. Suiko, M. Kimura, Y. Kakuta
  • Journal Title: Biochem. Biophys. Res. Commun. 379 Pages: 76-80
  • Peer Reviewed
• [Journal Article] Molecular and biochemical characterization of a zeta-class glutathione S-transferase of the silkmoth. (2009)
  • Author(s): K. Yamamoto, Y. Shigeoka, Y. Aso, Y. Banno, M. Kimura, T. Nakashima
  • Journal Title: Pest. Biochem. Physiol. 94 Pages: 30-35
  • Peer Reviewed
• [Journal Article] Snapshot of a Michaelis complex in a sulfuryl transfer reaction: crystal structure of a mouse sulfotransferase, mSULT1D1, complexed with donor substrate and acceptor substrate. (2009)
  • Author(s): T. Teramoto, Y. Sakakibara, M-C. Liu, M. Suiko, M. Kimura, Y. Kakuta
  • Journal Title: Biochem. Biophys. Res. Commun. 383 Pages: 83-87
  • Peer Reviewed
• [Journal Article] The action of rice branching enzyme I (BEI) on starch. Biosci. (2009)
  • Author(s): T. Akasaka, N.T. Vu, K. Chaen, A. Nishi, H. Satoh, H. Ida, T. Omori, M. Kimura
  • Journal Title: Biotechnol. Biochem. 73 Pages: 2516-2518
  • Peer Reviewed
• [Journal Article] The C-terminal portion of an archaeal toxin aRelE plays a crucial role in protein synthesis inhibition. (2009)
  • Author(s): C. Kikutake, M. Shinohara, H. Takagi, T. Nakashima, M. Kimura
  • Journal Title: Biosci. Biotechnol. Biochem. 73 Pages: 2766-2768
  • NAID: 10027549487
  • Peer Reviewed
• [Journal Article] Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3. (2008)
  • Author(s): X. Zhang, T. Nakashima, Y. Kakuta, M. Yao, I. Tanaka, M. Kimura
  • Journal Title: Protein Sci. 17 Pages: 136-45
  • Peer Reviewed
• [Journal Article] Crystal structure and functional analysis of an archaeal chromatin Alba from hyperthermophilic archaeon Pyrococcus horikoshii OT3. (2008)
  • Author(s): K. Hada, T. Nakashima, T. Osawa, H. Shimada, Y. Kakuta, M. Kimura
  • Journal Title: Biosci. Biotechnol. Biochem. 72 Pages: 749-758
  • Peer Reviewed
• [Journal Article] Crystal structure of the covalent intermediate of human cytosolic β-glucosidase. (2008)
  • Author(s): J. Noguchi, Y. Hayashi, Y. Baba, N. Okino, M. Kimura, M. Ito, Y. Kakuta
  • Journal Title: Biochem. Biophys. Res. Commun. 374 Pages: 549-552
  • Peer Reviewed
• [Journal Article] Biochemical and crystallographic characterization of the starch branching enzyme I (BEI) from Oryza sativa L. (2008)
  • Author(s): N.T. Vu, H. Shimada, Y. Kakuta, T. Nakashima, H. Ida, T. Omori, A. Nishi, H. Satoh, M. Kimura
  • Journal Title: Biosci. Biotechnol. Biochem. 72 Pages: 2858-2866
  • NAID: 10027533795
  • Peer Reviewed
• [Journal Article] Structure of an archaeal homolog of the human protein complex Rpp21-Rpp29 that is a key core component for the assembly of active ribonuclease P. (2008)
  • Author(s): T. Honda, Y. Kakuta, K. Kimura, J. Saho, M. Kimura
  • Journal Title: J. Mol. Biol. 384 Pages: 652-662
  • Peer Reviewed
• [Journal Article] Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshiiOT3 (2008)
  • Author(s): X. Zhang, T. Nakashima, Y. Kakuta, M. Yao, I. Tanaka, M. Kimura
  • Journal Title: Protein Sci. 17 Pages: 136-145
  • Peer Reviewed
• [Journal Article] Crystal structure and functional analysis of an archaeal chromatin Alba from hyperthermophilic archaeon Pyrococcus horikoshii 0T3 (2008)
  • Author(s): K. Hada, T. Nakashima. T. Osawa, H. Shimada, Y. Kakuta, M. Kimura
  • Journal Title: Biosci. Biotechnol. Biochem. 72 Pages: 749-758
  • Peer Reviewed
• [Journal Article] Structure of an archaeal homolog of the human protein complex Rpp21-Rpp29 that is a key core component for the assembly of active ribonuclease p. (2008)
  • Author(s): T. Honda, Y. Kakuta, K. Kimura, J. Saho, M. Kimura
  • Journal Title: J. Mol. Biol. 384 Pages: 652-662
  • Peer Reviewed
• [Journal Article] Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3. (2008)
  • Author(s): Zhang, et. al.
  • Journal Title: Protein Sci. 17 Pages: 136-145
  • Peer Reviewed
• [Journal Article] Crystal structure and functional analysis of an archaeal chromatin Alb a from hvnerthermonhilic archaeon Pvrococcus horikoshii OT3. (2008)
  • Author(s): Hada, et. al.
  • Journal Title: Biosci.Biotechnol.Biochem. 72 Pages: 749-758
  • Peer Reviewed
• [Journal Article] Identification of nucleotide residues essential for RNase P activity from the hyperthermophilic archaeon Pyrococcus horikoshii OT3. (2007)
  • Author(s): A. Terada, T. Honda, M. Kimura
  • Journal Title: Biosci. Biotechnol. Biochem. 71 Pages: 1940-1945
  • NAID: 10027517644
  • Peer Reviewed
• [Journal Article] Characterization of superoxide dismutase from the fall webworm, Hyphantria cunea: comparison of its properties to superoxide dismutase from the silkworm Bombyx mori. (2007)
  • Author(s): K. Yamamoto, M. Kimura, Y. Aso, Y. Banno, K. Koga.
  • Journal Title: Appl. Entomol. Zool. 42 Pages: 465-472
  • NAID: 110006379849
  • Peer Reviewed
• [Journal Article] Identification of nucIeotide residues essential for RNase'P activity from the hvnerthermoohilic archaeon Pvrococcus horikoshii OT3. (2007)
  • Author(s): Terada, et. al.
  • Journal Title: Biosci.Biotechnol.Biochem. 71 Pages: 1940-1945
  • Peer Reviewed
• [Presentation] タンパク質合成抑制因子・RelEのC末端塩基性アミノ酸の役割 (2010)
  • Author(s): 篠原雅明、郭巾旭、森美佐子、中島崇、西本悦子、山下昭二、木村誠
  • Organizer: 日本農芸化学会
  • Place of Presentation: 東京大学
  • Year and Date: 2010-03-29
• [Presentation] RNase Pタンパク質はRNAシャペロンとして機能する (2010)
  • Author(s): 小坂俊介、波田一誠、中島崇、木村誠
  • Organizer: 日本農芸化学会
  • Place of Presentation: 東京大学
  • Year and Date: 2010-03-29
• [Presentation] RNase Pタンパク質複合体Pop5-Rpp30とRpp21-Rpp29はそれぞれRNase P RNAの触媒(C)ドメインと特異性(S)ドメインを活性化する (2009)
  • Author(s): 原唯史、本田貴史、中尾祐士、木村誠
  • Organizer: 日本農芸化学会西日本、中四国、関西支部合同大会
  • Place of Presentation: 琉球大学
  • Year and Date: 2009-10-31
• [Presentation] タンパク質合成抑制因子・RelEのC末端領域の重要性 (2009)
  • Author(s): 篠原雅明、菊竹智恵、今村悠佑、森美佐子、中島崇、木村誠
  • Organizer: 日本農芸化学会西日本、中四国、関西支部合同大会
  • Place of Presentation: 琉球大学
  • Year and Date: 2009-10-31
• [Presentation] RNase Pタンパク質はRNase P RNAを解くことにより活性化する (2009)
  • Author(s): 小坂俊介、波田一誠、木村誠
  • Organizer: 日本農芸化学会西日本、中四国、関西支部合同大会
  • Place of Presentation: 琉球大学
  • Year and Date: 2009-10-31
• [Presentation] 大腸菌トキシン-アンチトキシン・DinJ-YafQの生化学的性質と結晶化 (2009)
  • Author(s): 松尾尚紀、角田佳充、木村誠
  • Organizer: 日本農芸化学会西日本、中四国、関西支部合同大会
  • Place of Presentation: 琉球大学
  • Year and Date: 2009-10-31
• [Presentation] イネ澱粉枝作り酵素I(BEI)の澱粉に対する作用 (2009)
  • Author(s): 赤坂泰輝、茶円喜美子、西愛子、佐藤光、井田寛子、大森俊郎、木村誠
  • Organizer: 日本農芸化学会西日本、中四国、関西支部合同大会
  • Place of Presentation: 琉球大学
  • Year and Date: 2009-10-31
• [Presentation] 大腸菌トキシン・アンチトキシン(RelE-RelB)複合体の調製とその性質 (2009)
  • Author(s): 今村悠佑、郭巾旭、木村誠
  • Organizer: 日本農芸化学会
  • Place of Presentation: 福岡国際会議場
  • Year and Date: 2009-03-27
• [Presentation] 超高熱古細菌Pyrococcus horikoshii Ski2p様タンパク質の酵素活性について (2009)
  • Author(s): 閻思遠、原田実季、張小冬、木村誠
  • Organizer: 日本農芸化学会
  • Place of Presentation: 福岡国際会議場
  • Year and Date: 2009-03-27
• [Presentation] リボヌクレアーゼpタンパク質Rpp21とRpp29の複合体形成が触媒活性に重要である (2008)
  • Author(s): 本田貴史、角田佳充、木村誠
  • Organizer: 日本生物物理学会
  • Place of Presentation: 福岡国際会議場
  • Year and Date: 2008-12-04
• [Presentation] 前駆体tRNAプロセシング酵素・リボヌクレアーゼPの構造生物学的研究 (2007)
  • Author(s): 木村 誠
  • Organizer: 日本生物物理学会第45回年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2007-12-21
• [Remarks]
  • URL: http://www.agr.kyushu-u.ac.jp/biosci-biotech/seibutu/