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Yoshimitsu Kakuta Last modified date:2024.03.08



Graduate School
Undergraduate School


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Homepage
https://kyushu-u.elsevierpure.com/en/persons/yoshimitsu-kakuta
 Reseacher Profiling Tool Kyushu University Pure
Academic Degree
PhD.
Country of degree conferring institution (Overseas)
No
Field of Specialization
Structural Biology
Outline Activities
My main research is structural biology about sulfotransferase and glycosyltransferase.
Research
Research Interests
  • Structural biology about sulfotransferase and glycosyltransferase
    keyword : Structural biology, Crystallograpy, Sulfotransferase, Glycosyltransferase
    1995.04.
Academic Activities
Reports
1. Ayami Matsushima, Takamasa Teramoto, Yoshimitsu Kakuta, Crystal structure of endocrine-disrupting chemical bisphenol A and estrogen-related receptor γ, The Journal of Biochemistry, https://doi.org/10.1093/jb/mvab145, 171,1,2022,23-25, 2022.01.
Papers
1. Katsuhisa Kurogi, Yoichi Sakakibara, Takuyu Hashiguchi, Yoshimitsu Kakuta, Miho Kanekiyo, Takamasa Teramoto, Tsuyoshi Fukushima, Takeshi Bamba, Jin Matsumoto, Eiichiro Fukusaki, Hiroaki Kataoka, Masahito Suiko, A new type of sulfation reaction: C-sulfonation for α, β-unsaturated carbonyl groups by a novel sulfotransferase, PNAS Nexus, https://doi.org/10.1093/pnasnexus/pgae097, 2024.02.
2. Takahiro Okada, Takamasa Teramoto, Hideyuki Ihara, Yoshitaka Ikeda, Yoshimitsu Kakuta, Crystal structure of mango α1,3/α1,4-fucosyltransferase elucidates unique elements that regulate Lewis a-dominant oligosaccharide assembly, Glycobiology, https://doi.org/10.1093/glycob/cwae015, 2024.02.
3. Misa Yoshimura, Takamasa Teramoto, Hirai Asano, Yuka Iwamoto, Mariko Kondo, Etsuko Nishimoto, Yoshimitsu Kakuta, Crystal structure of tick tyrosylprotein sulfotransferase reveals the activation mechanism of the tick anticoagulant protein madanin, J Biol Chem., https://doi.org/10.1016/j.jbc.2024.105748, 2024.02.
4. Takuo Minato, Takamasa Teramoto, Naruhiko Adachi, Nguyen Khac Hung, Kaho Yamada, Masato Kawasaki, Masato Akutsu, Toshio Moriya, Toshiya Senda, Seiji Ogo, Yoshimitsu Kakuta, Ki-Seok Yoon, Non-conventional octameric structure of C-phycocyanin, Communications biology, 10.1038/s42003-021-02767-x, 4, Article number: 1238, 2021.10.
5. Takamasa Teramoto, Takeshi Koyasu, Naruhiko Adachi, Masato Kawasaki, Toshio Moriya, Tomoyuki Numata, Toshiya Senda, Yoshimitsu Kakuta, Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis, The Journal of Biological Chemistry, 10.1016/j.jbc.2021.101028., 297, 3, 2021.09, Ribonuclease P (RNase P) is an endoribonuclease that catalyzes the processing of the 5' leader sequence of precursor tRNA (pre-tRNA). Ribonucleoprotein RNase P and protein-only RNase P (PRORP) in eukaryotes have been extensively studied, but the mechanism by which a prokaryotic nuclease recognizes and cleaves pre-tRNA is unclear. To gain insights into this mechanism, we studied homologs of Aquifex RNase P (HARPs), thought to be enzymes of approximately 23 kDa comprising only this nuclease domain. We determined the cryo-EM structure of Aq880, the first identified HARP enzyme. The structure unexpectedly revealed that Aq880 consists of both the nuclease and protruding helical (PrH) domains. Aq880 monomers assemble into a dimer via the PrH domain. Six dimers form a dodecamer with a left-handed one-turn superhelical structure. The structure also revealed that the active site of Aq880 is analogous to that of eukaryotic PRORPs. The pre-tRNA docking model demonstrated that 5' processing of pre-tRNAs is achieved by two adjacent dimers within the dodecamer. One dimer is responsible for catalysis, and the PrH domains of the other dimer are responsible for pre-tRNA elbow recognition. Our study suggests that HARPs measure an invariant distance from the pre-tRNA elbow to cleave the 5' leader sequence, which is analogous to the mechanism of eukaryotic PRORPs and the ribonucleoprotein RNase P. Collectively, these findings shed light on how different types of RNase P enzymes utilize the same pre-tRNA processing..
6. Zakaria Omahdi, Yuto Horikawa, Masamichi Nagae, Kenji Toyonaga, Akihiro Imamura, Koichi Takato, Takamasa Teramoto, Hideharu Ishida, Yoshimitsu Kakuta, Sho Yamasaki, Structural Insight Into the Recognition of Pathogen-Derived Phosphoglycolipids by C-type Lectin Receptor DCAR, The Journal of Biological Chemistry, 10.1074/jbc.RA120.012491, 2020.03.
7. Tanaka S, Nishiyori T, Kojo H, Otsubo R, Tsuruta M, Kurogi K, Liu MC, Suiko M, Sakakibara Y, Kakuta Y, Structural basis for the broad substrate specificity of the human tyrosylprotein sulfotransferase-1., Scientific Reports, 10.1038/s41598-017-07141-8., 2017.08.
8. Yujiro Higuchi, Yoshinaga S, Tateno H, Hirabaysshi J, Nakakita S, Kenakiyo M, Kakuta Y, Takegawa K, A rationally engineered yeast pyruvyltransferase Pvg1p introduces sialylation-like properties in neo-human-type complex oligosaccharide., Scientific Reports, 10.1038/srep26349., 6, Article number: 26349, 2016.05.
9. Kawaguchi Y, Sugiura N, Kimata K, Kimura M, Kakuta Y, The crystal structure of novel chondroitin lyase ODV-E66, a baculovirus envelope protein, FEBS Letters, 587,24,3947-3948, 2013.12.
10. Teramoto T, Fujikawa Y, Kawaguchi Y, Kurogi K, Soejima M, Adachi R, Nakanishi Y, Mishiro-Sato E, Liu MC, Sakakibara Y, Suiko M, Kimura M, Kakuta Y, Crystal structure of human tyrosylprotein sulfotransferase-2 reveals the mechanism of protein tyrosine sulfation reaction, Nature Communications, 10.1038, 4:1572, 2013.03, ヒトタンパク質チロシン硫酸転移酵素が、ターゲットとなるタンパク質を硫酸化修飾するメカニズムを明らかにするために、この酵素とターゲットタンパク質が結合している状態の立体構造を、X線結晶構造解析により原子レベルで決定しました。
 その結果、この酵素は二量体を形成し、その二量体の間につくられる奥深い溝の部分でターゲットとなるタンパク質のチロシン残基部分を結合して、その部分で特異的に硫酸基をつけていることがわかりました。また、硫酸化修飾を受ける部分は、特徴的なL字型に90度折れ曲がっていました。この構造が決定されたことにより、これまで謎であったターゲットとなるタンパク質の選別方法が明らかになりました。
 その選別方法とは、「ターゲットとなるタンパク質の柔軟性の違い」と、「電荷による相互作用」の2つによるものでした。柔らかい構造をしたターゲットタンパク質は、タンパク質チロシン硫酸転移酵素の深い溝の奥に入り込み、さらに90度折れ曲がることで活性部位の適切な位置に結合して、硫酸化修飾をうけることができます。しかし、硬い構造をしたタンパク質は、この溝に入ることができず、硫酸化修飾をうけることができません。また、タンパク質チロシン硫酸転移酵素が持つ深い溝表面には、プラスの電荷が多数準備されていて、ターゲットとなるタンパク質のマイナスの電荷を持った部分を特異的に認識します。
このように、タンパク質チロシン硫酸転移酵素は、様々なタンパク質の柔軟性の違いと電荷による相互作用の両方を用いて、硫酸基をつけるターゲットタンパク質を選別していることが明らかになりました。
 タンパク質チロシン硫酸転移酵素の立体構造が明らかになり、そのターゲットとなるタンパク質の認識方法がわかったことで、この酵素に対する阻害剤の開発が可能になりました。硫酸基がつくことによるタンパク質の機能変化は、様々な生命現象に関わっています。したがって、特異的な阻害剤が開発できれば、ウイルス感染に対する薬としての利用だけでなく、生体防御反応の制御など、新しいタイプの医薬品としての応用が期待できます。.
11. Sugiura N, Baba Y, Kawaguchi Y, Iwatani T, Suzuki K, Kusakabe T, Yamagishi K, Kimata K, Kakuta Y, Watanabe H., Glucuronyltransferase activity of KfiC from Escherichia coli strain K5 requires association of KfiA: KfiC and KfiA are essential enzymes for production of K5 polysaccharide, N-acetylheparosan., The Journal of Biological Chemistry, 285, 3, 1597-1606, 285(3):1597-1606. , 2010.01.
12. Teramoto T, Adachi R, Sakakibara Y, Liu MC, Suiko M, Kimura M, Kakuta Y., On the similar spatial arrangement of active site residues in PAPS-dependent and phenolic sulfate-utilizing sulfotransferases., FEBS Lett., 583(18):3091-3094., 2009.09.
13. Teramoto T, Sakakibara Y, Liu MC, Suiko M, Kimura M, Kakuta Y., Snapshot of a Michaelis complex in a sulfuryl transfer reaction: Crystal structure of a mouse sulfotransferase, mSULT1D1, complexed with donor substrate and accepter substrate., Biochem Biophys Res Commun., 383(1):83-87., 2009.05.
14. Teramoto T, Sakakibara Y, Liu MC, Suiko M, Kimura M, Kakuta Y., Structural basis for the broad range substrate specificity of a novel mouse cytosolic sulfotransferase--mSULT1D1., Biochem Biophys Res Commun., 379(1):76-80., 2009.01.
15. Osawa T, Sugiura N, Shimada H, Hirooka R, Tsuji A, Shirakawa T, Fukuyama K, Kimura M, Kimata K, Kakuta Y., Crystal structure of chondroitin polymerase from Escherichia coli K4., Biochem Biophys Res Commun., 2009.01.
16. Takagi H, Kakuta Y, Okada T, Yao M, Tanaka I, Kimura M., Crystal structure of archaeal toxin-antitoxin RelE-RelB complex with implications for toxin activity and antitoxin effects., Nature structural & molecular biology, 10.1038/nsmb911, 12, 4, 327-331, 12(4):327-331, 2005.04.
17. Osawa T, Matsubara Y, Muramatsu T, Kimura M, Kakuta Y., Crystal structure of the alginate (poly alpha-l-guluronate) lyase from Corynebacterium sp. at 1.2 A resolution., The Journal of Molecular Biology, 10.1016/j.jmb.2004.10.081, 345, 5, 1111-1118, 345(5):1111-8., 2005.02.
18. Yamagata A., Kakuta Y., Masui R., Fukuyama K., The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity., Proceedings of the National Academy of Sciences of the United States of America., 99(9), 5908-5912, 2002.04.
19. Kakuta, Y., Sueyoshi, T., Negishi, M., and Pedersen, L.C., Crystal structure of sulfotransferase domain of human heparan sulfate N-deacetylase/N-sulfotransferase 1., The Journal of Biological Chemistry, 274(16), 10673-6, 1999.01.
20. Kakuta, Y., Pedersen, L.C., Pedersen, L.G., and Negishi, M., Conserved structural motifs of the sulfotransferase family., Trends in Biochemical Sciences, 23(4), 129-130, 1998.01.
21. Kakuta Y, Pedersen LG, Carter CW, Negishi M, Pedersen LC., Crystal structure of estrogen sulphotransferase., Nature structural biology, 4(11):904-908., 1997.11.