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Yoshimitsu Kakuta Last modified date:2023.08.18

Graduate School
Undergraduate School

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Academic Degree
Country of degree conferring institution (Overseas)
Field of Specialization
Structural Biology
Outline Activities
My main research is structural biology about sulfotransferase and glycosyltransferase.
Research Interests
  • Structural biology about sulfotransferase and glycosyltransferase
    keyword : Structural biology, Crystallograpy, Sulfotransferase, Glycosyltransferase
Academic Activities
1. Ayami Matsushima, Takamasa Teramoto, Yoshimitsu Kakuta, Crystal structure of endocrine-disrupting chemical bisphenol A and estrogen-related receptor γ, The Journal of Biochemistry,, 171,1,2022,23-25, 2022.01.
1. 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.
2. 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..
3. 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.
4. 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.
5. 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.
6. 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.
7. 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。
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. Kakuta Y, Pedersen LG, Carter CW, Negishi M, Pedersen LC., Crystal structure of estrogen sulphotransferase., Nature structural biology, 4(11):904-908., 1997.11.