Kyushu University Academic Staff Educational and Research Activities Database
List of Papers
Yoshimitsu Kakuta Last modified date:2024.01.06

Professor / Molecular Biosciences / Department of Bioscience and Biotechnology / Faculty of Agriculture

1. Yuka Iwamoto, Seira Saito, Takamasa Teramoto, Akiko Maruyama-Nakashita, Yoshimitsu Kakuta, Crystal structure of Arabidopsis thaliana sulfotransferase SOT16 involved in glucosinolate biosynthesis, Biochemical and Biophysical Research Communications,, 677, 149-154, 2023.10.
2. Tomoya Kawakami, Takamasa Teramoto, Yoshimitsu Kakuta, Crystal structure of adenosine 5'-phosphosulfate kinase isolated from Archaeoglobus fulgidus, Biochemical and Biophysical Research Communications, 10.1016/j.bbrc.2022.12.081., 643, 105-110, 2023.02.
3. 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.
4. 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..
5. Takamasa Teramoto, Takeaki Nishio, Katsuhisa Kurogi, Yoichi Sakakibara, Yoshimitsu Kakuta, The crystal structure of mouse SULT2A8 reveals the mechanism of 7α-hydroxyl, bile acid sulfation, Biochemical and Biophysical Research Communications, 10.1016/j.bbrc.2021.04.113, 562, 15-20, 2021.07.
6. Takamasa Teramoto, Kipchumba J Kaitany, Yoshimitsu Kakuta, Makoto Kimura, Carol A Fierke, Traci M Tanaka Hall, Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA
, Nucleic Acids Res, 10.1093/nar/gkaa627, 48, 21, 11815-11826 , 2020.12, シロイヌナズナのProtein-only RNase P 1 (PRORP1)は、PPRドメインを用いて前駆体tRNAを認識するエンドリボヌクレアーゼであり、ヌクレアーゼドメインを用いてpre-tRNAから5′-leader配列を除去する触媒作用を持つ。PRORP1がtRNAを認識するメカニズムを解明するために、我々は、PPRドメインとtRNAPとの複合体の結晶構造を2.85Åの分解能で決定した。PRORP1のPPRドメインは、tRNAの構造的に保存されたエルボー領域に構造特異的に結合していた。PRORP1のPPRドメインによるtRNAの認識様式は、リボヌクレオプロテインRNase PによるtRNAの認識と類似しており、tRNA認識する上で収束進化した結果であると考察される。.
7. Minato, Takuo; Teramoto, Takamasa; Kakuta, Yoshimitsu; Ogo, Seiji; Yoon, Ki-Seok, Biochemical and structural characterization of a thermostable Dps protein with His-type ferroxidase centers and outer metal-binding sites, FEBS Open Bio, 10.1002/2211-5463.12837, 2020.03.
8. 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.
9. Keitaro Suyama, Shuhei Kaneko, Hitoshi Kesamaru, Xiaohui Liu, Ayami Matsushima, Yoshimitsu Kakuta, Takashi Okubo, Kazumi Kasatani, Takeru Nose, Evaluation of the Influence of Halogenation on the Binding of Bisphenol A to the Estrogen-Related Receptor γ, Chemical Research in Toxicology, 10.1021/acs.chemrestox.9b00379, 2020.02.
10. 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.
11. 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.
12. Ueda T, Ishino S, Suematsu K, Nakashima T, Kakuta Y, Kimura M, Mutation of the gene encoding the ribonuclease P RNA in the hyperthermophilic archaeon Thermococcus kodakarensis causes decreased growth rate and impaired process., Biochem Biophys Res Commun., 10.1016/j.bbrc.2015.11.012. , 468, 4, 660-665, 2015.12.
13. Hamasaki M, Hazeyama K, Iwasaki F, Ueda T, Nakashima T, Kakuta Y, Kimura M, Functional implication of archaeal homologues of human RNase P protein pair Pop5 and Rpp30., Journal of Biochemistry, 10.1093/jb/mvv067, 159, 1, 31-40, 2016.01.
14. Miyanoshita M, Nakashima T, Kakuta Y, Kimura M, Archaeal ribonuclease P proteins have potential for biotechnological applications where precise hybridization of nucleic acids is needed., Biosci Biotechnol Biochem., 10.1080/09168451.2015.1058699, 79, 12, 2014-2017, 2015.06.
15. Suematsu K, Ueda T, Nakashima T, Kakuta Y, Kimura M, On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis., Biosci Biotechnol Biochem. , 10.1080/09168451.2014.1003130, Epub ahead of prin, 2015.02.
16. Hino M, Zhang J, Takagi H, Miyoshi T, UchiumiT, Nakashima T, Kakuta Y, Kimura M, Characterization of putative toxin/antitoxin systems in Vibrio parahaemolyticus., J Appl Microbiol., 10.1111, 117(1):185-195., 2014.09.
17. Furutani T, Hazeyama K, Ueda T, Tomita S, Imai T, Gao X, Nakashima T, Kakuta Y, Kimura M, Enhancement of RNA annealing and strand displacement found in archaeal ribonuclease P proteins is conserved in Escherichia coli protein C5 and yeast protein Rpr2, Biosci Biotechnol Biochem. , 10.1080/09168451, 78(10):1700-1702., 2014.10.
18. Imai T, Nakamura T, Maeda T, Nakayama K, Gao X, Nakashima T, Kakuta Y, Kimura M, Pentatricopeptide repeat motifs in the processing enzyme PRORP1 in Arabidopsis thaliana play a crucial role in recognition of nucleotide bases at TψC loop in precursor tRNAs, Biochem Biophys Res Commun, 10.1016, 450(4):1541-1546., 2014.08.
19. Takakura Y, Suzuki J, Oka N, Kakuta Y, Tamavidin 2-HOT, a highly thermostable biotin-binding protein, Journal of Biotechnology, 169, 1–8, 2014.01.
20. Ueda T, Yamaguchi H, Miyanoshita M, Nakashima T, Kakuta Y, Kimura M, Characterization of the peripheral structures of archaeal RNase P RNA from Pyrococcus horikoshii OT3, The Journal of Biochemistry, 10.1093/jb/mvt092, 155(1):25-33., 2014.01.
21. 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.
22. Hazeyama K, Ishihara M, Ueda T, Nishimoto E, Nakashima T, Kakuta Y, Kimura M, Extra-structural elements in the RNA recognition motif in archaeal Pop5 play a crucial role in the activation of RNase P RNA from Pyrococcus horikoshii OT3, Biochemical and Biophysical Research Communications, 440(4):594-598., 2013.11.
23. 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。
24. Mori T, Kodera T, Yoshimine H, Kakuta Y, Sugiura N, Kimata K, Okahata Y, Kinetics of iterative carbohydrate transfer to polysaccharide catalyzed by chondroitin polymerase on a highly sensitive flow-type 27 MHz quartz-crystal microbalance, Chemistry. 2012 ;18(24):7388-93., 2012.06.
25. Sobhany M, Kakuta Y, Sugiura N, Kimata K, Negishi M, The structural basis for a coordinated reaction catalyzed by a bifunctional glycosyltransferase in chondroitin biosynthesis., J Biol Chem. 287(43):36022-8. , 2012.10.
26. Oshima K, Nakashima T, Kakuta Y, Tsumoto K, Kimura M, Thermodynamic analysis of a multifunctional RNA-binding protein, PhoRpp38, in the hyperthermophilic archaeon Pyrococcus horikoshii OT3., Biosci Biotechnol Biochem. 2012;76(6):1252-5. , 2012.06.
27. Mori T, Hirose A, Hagiwara T, Ohtsuka M, Kakuta Y, Kimata K, Okahata Y, Single-molecular enzymatic elongation of hyaluronan polymers visualized by high-speed atomic force microscopy, J Am Chem Soc. 134(50):20254-7., 10.1021, 2012.12.
28. Yamamoto K, Usuda K, Kakuta Y, Kimura M, Higashiura A, Nakagawa A, Aso Y, Suzuki M, Structural basis for catalytic activity of a silkworm Delta-class glutathione transferase, Biochim Biophys Acta. 2012 Oct;1820(10):1469-74. , 2012.10.
29. Kawaguchi Y, Sugiura N, Onishi M, Kimata K, Kimura M, and Kakuta Y., Crystallization and X-ray diffraction analysis of chondroitin lyase from baculovirus: envelope protein ODV-E66., Acta. Crystallogr. Sect F, 68, 190-192, 2012.02.
30. Hossain MM, Moriizumi Y, Tanaka S, Kimura M, Kakuta Y., Crystal structure of sulfotransferase STF9 from Mycobacterium avium., Mol Cell Biochem., 361, 97-104, 2012.02.
31. Zwieb C, Nakao Y, Nakashima H, Takagi H, Goda S, Andersen E.S, Kakuta Y, and Kimura M., Structural modeling of RNase P RNA from the hyperthermophilic archaeon Pyrococcus horikoshii OT3., Biochem Biophys Res Commun., in press, 2011.10.
32. Hossain MM, Moriizumi Y, Tanaka S, Kimura M, Kakuta Y., Molecular cloning, expression, and functional analysis of a predicted sulfotransferase
STF9 from Mycobacterium avium., Mol Cell Biochem., 350, (1-2), 155-162, 2011.10.
33. Hara T, Terada A, Yamaguchi H, Nakashima T, Kakuta Y, Kimura M., The Contribution of Peripheral Stem-Loops to the Catalytic Activity of Archaeal RNase P RNA from Pyrococcus horikoshii OT3., Biosci Biotechnol Biochem. , 75(4), 816-819, 2011.05.
34. Noguchi J, Chaen K, Vu NT, Akasaka T, Shimada H, Nakashima T, Nishi A, Satoh H, Omori T, Kakuta Y, Kimura M., Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding., Glycobiology, 8, 1108-1116, 2011.04.
35. Shinohara M, Guo JX, Mori M, Nakashima T, Takagi H, Nishimoto E, Yamashita S, Tsumoto K, Kakuta Y, Kimura M., The structural mechanism of the inhibition of archaeal RelE toxin by its cognate RelB antitoxin., Biochem Biophys Res Commun., 400, 346-351, 2010.09.
36. Katekaew S, Kuaprasert B, Torikata T, Kakuta Y, Kimura M, Yoneda K, Araki T., Structure of the newly found green turtle egg-white ribonuclease., Acta. Crystallogr. Sect F, 66, 755-759, 2010.06.
37. Liu TA, Bhuiyan S, Liu MY, Sugahara T, Sakakibara Y, Suiko M, Yasuda S, Kakuta Y, Kimura M, Williams FE, Liu MC., Zebrafish as a model for the study of the phase II cytosolic sulfotransferases., Curr. Drug Metab., 6, 538-546, 2010.06.
38. 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.
39. Hossain MM, Kawarabayasi Y, Kimura M, Kakuta Y., Expression and functional analysis of a predicted AtsG arylsulfatase identified from Mycobacterium tuberculosis genomic data., J Biochem., 146, 6, 767-769, 146(6):767-769. , 2009.12.
40. 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.
41. Iwatani T, Okino N, Sakakura M, Kajiwara H, Takakura Y, Kimura M, Ito M, Yamamoto T, Kakuta Y., Crystal structure of alpha/beta-galactoside alpha2,3-sialyltransferase from a luminous marine bacterium, Photobacterium phosphoreum, FEBS Lett., 583(12):2083-2087. , 2009.06.
42. 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.
43. Inoue T, Okino N, Kakuta Y, Hijikata A, Okano H, Goda HM, Tani M, Sueyoshi N, Kambayashi K, Matsumura H, Kai Y, Ito M., Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase., J Biol Chem. , 284(14):9566-9577. , 2009.04.
44. Takakura Y, Tsunashima M, Suzuki J, Usami S, Kakuta Y, Okino N, Ito M, Yamamoto T., Tamavidins--novel avidin-like biotin-binding proteins from the Tamogitake mushroom.
, FEBS J. , 276(5):1383-1397., 2009.03.
45. 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.
46. 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.
47. Honda T, Kakuta Y, Kimura K, Saho J, Kimura M., 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., J Mol Biol., 384(3):652-662. , 2008.12.
48. Satone H, Oshima Y, Shimasaki Y, Tawaratsumida T, Oba Y, Takahashi E, Kitano T, Kawabata S, Kakuta Y, Honjo T., Tributyltin-binding protein type 1 has a distinctive lipocalin-like structure and is involved in the excretion of tributyltin in Japanese flounder, Paralichthys olivaceus., Aquat Toxicol. , 90(4):292-299., 2008.12.
49. Sobhany M, Kakuta Y, Sugiura N, Kimata K, Negishi M., The Chondroitin Polymerase K4CP and the Molecular Mechanism of Selective Bindings of Donor Substrates to Two Active Sites.
, J Biol Chem., 283(47):32328-32333., 2008.11.
50. Teramoto T, Sakakibara Y, Inada K, Kurogi K, Liu MC, Suiko M, Kimura M, Kakuta Y., Crystal structure of mSULT1D1, a mouse catecholamine sulfotransferase., FEBS Lett. , 582(28):3909-3914, 2008.11.
51. Vu NT, Shimada H, Kakuta Y, Nakashima T, Ida H, Omori T, Nishi A, Satoh H, Kimura M., Biochemical and Crystallographic Characterization of the Starch Branching Enzyme I (BEI) from Oryza sativa L., Biosci Biotechnol Biochem., 72(11):2858-2866., 2008.11.
52. Noguchi J, Hayashi Y, Baba Y, Okino N, Kimura M, Ito M, Kakuta Y., Crystal structure of the covalent intermediate of human cytosolic beta-glucosidase, Biochem Biophys Res Commun., 374(3):549-52. , 2008.09.
53. Matsushima A, Teramoto T, Okada H, Liu X, Tokunaga T, Kakuta Y, Shimohigashi Y., ERRgamma tethers strongly bisphenol A and 4-alpha-cumylphenol in an induced-fit manner., Biochem Biophys Res Commun. , 373(3):408-413. , 2008.08.
54. Hada K, Nakashima T, Osawa T, Shimada H, Kakuta Y, Kimura M., Crystal structure and functional analysis of an archaeal chromatin protein Alba from the hyperthermophilic archaeon Pyrococcus horikoshii OT3., Biosci Biotechnol Biochem., 72(3):749-758., 2008.03.
55. Kakuta Y, Okino N, Kajiwara H, Ichikawa M, Takakura Y,Ito M, Yamamoto T , Crystal structure of Vibrionaceae Photobacterium sp. JT-ISH-224 alpha-2,6-sialyltransferase in a ternary complex with donor product CMP and acceptor substrate lactose: catalytic mechanism and substrate recognition., Glycobiology, 18, 66-73, 2008.01.
56. Zhang X, Nakashima T, Kakuta Y, Yao M, Tanaka I, Kimura M., Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3.
, Protein Sci., 17:136-145, 2008.01.
57. Matsushima A, Kakuta Y, Teramoto T, Koshiba T, Liu X, Okada H, Tokunaga T, Kawabata SI, Kimura M, Shimohigashi Y., Structural Evidence for Endocrine Disruptor Bisphenol A Binding to Human Nuclear Receptor ERR{gamma}, J Biochem (Tokyo), 142(4):517-524, 2007.10.
58. Hayashi Y, Okino N, Kakuta Y, Shikanai T, Tani M, Narimatsu H, Ito M., Klotho-related Protein Is a Novel Cytosolic Neutral beta-Glycosylceramidase., J Biol Chem., 282(42):30889-30900, 2007.10.
59. Goto T, Abe Y, Kakuta Y, Takeshita K, Imoto T, Ueda T., Crystal Structure of Tapes japonica Lysozyme with Substrate Analogue: STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND MANIFESTATION OF ITS CHITINASE ACTIVITY ACCOMPANIED BY QUATERNARY STRUCTURAL CHANGE., J Biol Chem. , 282(37):27459-27467. , 2007.09.
60. Okino N, Kakuta Y, Kajiwara H, Ichikawa M, Takakura Y, Ito M, Yamamoto T., Purification, crystallization and preliminary crystallographic characterization of the alpha 2,6-sialyltransferase from Photobacterium sp. JT-ISH-224., Acta Crystallogr Sect F Struct Biol Cryst Commun., 63(Pt 8):662-4. , 2007.08.
61. Kawano S, Kakuta Y, Nakashima T, Kimura M. , Crystal structures of the Nicotiana glutinosa ribonuclease NT in complex with nucleoside monophosphates., J Biochem (Tokyo). , 140(3):375-81., 2006.09.
62. Kawano S, Nakashima T, Kakuta Y, Tanaka I, Kimura M, Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: implication of dimer formation of the holoenzyme, J. Mol Biol. , 357, 583-591. , 2006.03.
63. Fukuhara H, Kifusa M, Watanabe M, Terada A, Honda T, Numata T, Kakuta Y, Kimura M., A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3, J Biochem (Tokyo), 343(3):956-964., 2006.05.
64. Tanaka S, Moriizumi Y, Kimura M, Kakuta Y., Overproduction, purification and preliminary X-ray diffraction analysis of a sulfotransferase from Mycobacterium tuberculosis H37Rv., Acta Crystallograph Sect F Struct Biol Cryst Commun., 10.1107/S1744309104022328, 61, 33-35, 61(Pt 1):33-35., 2005.01.
65. 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.
66. 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.
67. Kakuta Y, Ishimatsu I, Numata T, Kimura K, Yao M, Tanaka I, Kimura M., Crystal Structure of a Ribonuclease P Protein Ph1601p from Pyrococcus horikoshii OT3: An Archaeal Homologue of Human Nuclear Ribonuclease P Protein Rpp21, Biochemistry, 10.1021/bi050738z, 44, 36, 12086-12093, 44, 12086-12093, 2005.09.
68. Shimomura Y, Takahashi Y, Kakuta Y, Fukuyama K., Crystal structure of Escherichia coli YfhJ protein, a member of the ISC machinery involved in assembly of iron-sulfur clusters., Proteins., 10.1002/prot.20481, 60, 3, 566-569, 60(3):566-569., 2005.08.
69. Kakuta Y, Tahara M, Maetani S, Yao M, Tanaka I, Kimura M., Crystal structure of the regulatory subunit of archaeal initiation factor 2B (aIF2B) from hyperthermophilic archaeon Pyrococcus horikoshii OT3: a proposed structure of the regulatory subcomplex of eukaryotic IF2B, Biochem. Biophys. Res. Commun, 10.1016/j.bbrc.2004.05.045, 319, 3, 725-732, 319, 725-732, 2004.07.
70. Numata T, Ishimatsu I, Kakuta Y, Tanaka I, Kimura M., Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29., RNA., 10.1261/rna.7560904, 10, 9, 1423-1432, 10(9):1423-1432., 2004.09.
71. Kimura K, Numata T, Kakuta Y, Kimura M., Amino acids conserved at the C-terminal half of the ribonuclease T2 family contribute to protein stability of the enzymes., Biosci Biotechnol Biochem., 10.1271/bbb.68.1748, 68, 8, 1748-1757, 68(8):1748-1757, 2004.08.
72. Takagi H, Watanabe M, Kakuta Y, Kamachi R, Numata T, Tanaka I, Kimura M., Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3., Biochem Biophys Res Commun., 10.1016/j.bbrc.2004.05.055, 319, 3, 787-794, 319(3):787-794., 2004.07.
73. Taguchi Y, Hoseki J, Kakuta Y, Fukuyama K., Overproduction, crystallization and preliminary X-ray diffraction analysis of probable ATP sulfurylase from Thermus thermophilus HB8, Acta. Crystallogr. D, 59, 1645-1647, 2003.09.
74. Kakuta Y, Li L, Pedersen LC, Pedersen LG, Negishi M., Heparan sulphate N-sulphotransferase activity: reaction mechanism and substrate recognition, Biochem. Soc. Trans, 31, 331-334, 2003.04.
75. Numata T, Suzuki A, Kakuta Y, Kimura K, Yao M, Tanaka I, Yoshida Y, Ueda T, Kimura M., Crystal Structures of the Ribonuclease MC1 Mutants N71T and N71S in Complex with 5’-GMP: Structural Basis for Alterations in Substrate Specificity, Biochemistry, 10.1021/bi034103g, 42, 18, 5270-5278, 42, 5270-5278, 2003.05.
76. Shimomura Y, Kakuta Y, Fukuyama K. , Crystal Structures of the Quinone Oxidoreductase from Thermus thermophilus HB8 and Its Complex with NADPH: Implication for NADPH and Substrate Recognition, J. Bacteriol., 10.1128/JB.185.14.4211.4218.2003, 185, 14, 4211-4218, 185, 4211-4218, 2003.07.
77. 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.
78. Kawano S., Kakuta Y., and Kimura M., Guanine binding site of the Nicotiana glutinosa ribonuclease NW revealed by X-ray crystallography., Biochemistry, 10.1021/bi0262471, 41, 51, 15195-15202, 41, 15195-15202, 2002.01.
79. Sugishima M., Sakamoto H., Kakuta Y., Omata Y., Hayashi S., Noguchi M., Fukuyama K., Crystal Structure of Rat Apo-Heme Oxygenase-1 (HO-1): Mechanism of Heme Binding in HO-1 Inferred from Structural Comparison of the Apo and Heme Complex Forms., Biochemistry, 41(23), 7293-7300, 2002.01.
80. Fukuyama K., Okada T., Kakuta Y., Takahashi Y., Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms: systematic distortion of [4Fe-4S] cluster in the protein., Journal of Molecular Biology, 315(5), 1155-1166, 2002.01.
81. Yamagata A., Masui R., Kakuta Y., Kuramitsu S., Fukuyama K., Overexpression, purification and characterization of RecJ protein from Thermus thermophilus HB8 and its core domain., Nucleic Acids Research, 29(22), 4617-4624, 2001.01.
82. King RS, Sharma V., Pedersen L.C., Kakuta Y., Negishi M., and Duffel MW., Structure-Function Modeling of the Interactions of N-Alkyl-N-hydroxyanilines with Rat Hepatic Aryl Sulfotransferase IV., Chem Res Toxicol, 13, 1251-1258, 2000.01.
83. Sugishima M., Omata Y., Kakuta Y., Sakamoto H., Noguchi M., and Fukuyama K., Crystal structure of rat heme oxygenase-1 in complex with heme., FEBS Letter, 471, 61-66, 2000.01.
84. Petrotchenko EV, Doerflein ME, Kakuta Y., Pedersen L.C., and Negishi M., Substrate gating confers steroid specificity to estrogen sulfotransferase., The Journal of Biological Chemistry, 274, 30019-30022, 1999.01.
85. 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.
86. Bidwell LM, McManus ME, Gaedigk A, Kakuta Y., Negishi M., Pedersen L., and Martin JL., Crystal structure of human catecholamine sulfotransferase., Journal of Molecular Biology, 293(3), 521-530, 1999.01.
87. Bartolotti, L., Kakuta, Y., Pedersen, L.C., Negishi, M., and Pedersen, L.G., A quantum mechanical study of the transfer of biological sulfate., Theochem-Journal of Molecular Structure., 462, 105-111, 1999.01.
88. Marsolais, F., Laviolette, M., Kakuta, Y., Negishi, M., Pedersen, L.C., Auger, M., and Varin, L., 3'-Phosphoadenosine 5'-phosphosulfate binding site of flavonol 3-sulfotransferase srudied by affinity chromatography and 31P NMR., Biochemistry, 38(13), 4066-4071, 1999.01.
89. Kakuta, Y., Petrotchenko E.V., Pedersen, L.C., and Negishi, M., The sulfuryl transfer mechanism: Crystal structure of a vanadate complex of estrogen sulfotransferase and mutational analysis., The Journal of Biological Chemistry, 273(42), 27325-27330, 1998.01.
90. Kakuta, Y., Pedersen, L.C., Chae, K., Song, W., Leblanc, D., London, R., Carter, C.W., and Negishi, M., Mouse steroid sulfotransferases: substrate specificity and preliminary X-ray crystallographic analysis., Biochemical Pharmacology, 55, 313-317, 1998.01.
91. 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.
92. Sueyoshi, T., Kakuta, Y., Pedersen, L.C., Frances, E.W., Pedersen, L.G., and Negishi, M., A role of Lys614 in the sulfotransferase activity of human heparan sulfate N-deacetylase/N-sulfotranferase., FEBS Letter, 433, 211-214, 1998.01.
93. Kakuta Y, Pedersen LG, Carter CW, Negishi M, Pedersen LC., Crystal structure of estrogen sulphotransferase., Nature structural biology, 4(11):904-908., 1997.11.
94. Kawamura S, Kakuta Y, Tanaka I, Hikichi K, Kuhara S, Yamasaki N, Kimura M., Glycine-15 in the bend between two alpha-helices can explain the thermostability of DNA binding protein HU from Bacillus stearothermophilus., Biochemistry., 10.1021/bi951581l, 35, 4, 1195-1200, 35(4):1195-1200., 1996.01.
95. Hikichi, K., Kakuta, Y., and Katoh, T., 1H NMR study on substituent distribution of cellulose diacetate, Polymer Journal, 27, 659-663, 1995.01.
96. Kakuta Y, Hojo H, Aimoto S, Tanaka I, Hikichi K., 13C-NMR relaxation study on mobility of the DNA-binding arm of HU., J Biochem (Tokyo)., 116(5):1153-1155., 1994.11.
97. Hojo H., Kwon Y.,Kakuta Y.,Tsuda S.,Tanaka I.,Hikichi K., and Aimoto S., Development of a Linker with an Enhanced Stability for the Preparation of Peptide Thioesters and Its Application to the Synthesis of Stable-Isotope-Labelled HU-Type DNA-Binding Protein, Bull. Chem. Soc. Jpn, 66, 2700-2706, 1993.09.