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User:Takatsugu Miyazaki

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Takatsugu Miyazaki is an Associate Professor of Research Institute of Green Science and Technology (RIGST) and Department of Agriculture, Graduate School of Integrated Science and Technology, at Shizuoka University. He obtained his PhD under the supervision of Takashi Tonozuka at Tokyo University of Agriculture and Technology. He is interested in structures and functions of CAZymes, especially glycoside hydrolases and glycosyltransferases from microorganisms and insects. He has contributed to the crystal structure determination of

  • GH6 Coprinopsis cinerea cellobiohydrolase CcCel6C [1]
  • GH6 Coprinopsis cinerea cellobiohydrolase CcCel6A [2]
  • GH13_17 Bombyx mori sucrose hydrolase BmSUH [3]
  • GH16_16 Microbulbifer thermotolerans β-agarase [4]
  • GH27 Arthrobacter globiformis isomalto-dextranase [5]
  • GH31_14 Pseudopedobacter saltans α-galactosidase Subfamily First [6]
  • GH31_15 Lactococcus lactis subsp. cremoris α-1,3-glucosidase Subfamily First [7]
  • GH31_18 Enterococcus faecalis exo-acting protein-α-N-acetylgalactosaminidase Subfamily First [8, 9]
  • GH31_19 Bacteroides salyersiae and Flavihumibacter petaseus α-1,4-galactosidases Subfamily First [10]
  • GH32 Bombyx mori β-fructofuranosidase BmSUC1 [11]
  • GH49 Aspergillus brasiliensis isopullulanase (N-glycan-deficient variant) [12]
  • GH62 Coprinopsis cinerea α-L-arabinofuranosidase CcAbf62A [13]
  • GH63 Escherichia coli α-glycosidase YgjK (glycosynthase mutant) [14, 15]
  • GH63 Thermus thermophillus mannosylglycerate hydrolase [16]
  • GH65 Flavobacterium johnsoniae kojibiose hydrolase [17, 18]
  • GH66 Flavobacterium johnsoniae dextranase [18]
  • GH68 Microbacterium saccharophilum β-fructofuranosidase [19] and its thermostabilized mutants [20]
  • GH92 Enterococcus faecalis α-1,2-mannosidase (Michaelis complex) [21]
  • GH97 Flavobacterium johnsoniae glucodextranase [22]
  • GH131 Coprinopsis cinerea CcGH131A Family First [23]
  • CBM94 C-terminal domains of Homo sapiens GT54 N-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A) and Bombyx mori ortholog Family First [24]

He also has contributed to identification and characterization of

  • GH29 Bombyx mori α-L-fucosidase [25]
  • GH31 Flavobacterium johnsoniae dextranase [18, 26]
  • GH31_10 Paenibacillus sp. 598K 6-α-glucosyltransferase [27]
  • GH31_14 Pedobacter heparinus α-galactosidase [6]
  • GH31_15 Cordyceps militaris α-1,3-glucosidase [7]
  • GH31_18 Bombyx mori exo-acting protein-α-N-acetylgalactosaminidase [28]
  • GH63 Aspergillus brasiliensis mannosyl-oligosaccharide glucosidase [29]
  • GH65 Microbacterium dextranolyticum dextran α-1,2-debranching enzyme [30]
  • GH66 Paenibacillus sp. 598K dextranase [31]
  • GH99 Shewanella amazonensis endo-α-1,2-mannosidase [32]
  • GT7 Bombyx mori β-1,4-N-acetylgalactosaminyltransferase [33]
  • GT16 Homo sapiens β-1,2-N-acetylglucosaminyltransferase II recombinantly expressed in Bombyx mori [34]
  • GT16 Bombyx mori β-1,2-N-acetylglucosaminyltransferase II [35]
  • PL21 Pedobacter heparinus heparin lyase II (mutants) [36]

  1. Liu Y, Yoshida M, Kurakata Y, Miyazaki T, Igarashi K, Samejima M, Fukuda K, Nishikawa A, and Tonozuka T. (2010). Crystal structure of a glycoside hydrolase family 6 enzyme, CcCel6C, a cellulase constitutively produced by Coprinopsis cinerea. FEBS J. 2010;277(6):1532-42. DOI:10.1111/j.1742-4658.2010.07582.x | PubMed ID:20148970 [Liu2010]
  2. Tamura M, Miyazaki T, Tanaka Y, Yoshida M, Nishikawa A, and Tonozuka T. (2012). Comparison of the structural changes in two cellobiohydrolases, CcCel6A and CcCel6C, from Coprinopsis cinerea--a tweezer-like motion in the structure of CcCel6C. FEBS J. 2012;279(10):1871-82. DOI:10.1111/j.1742-4658.2012.08568.x | PubMed ID:22429290 [Tamura2012]
  3. Miyazaki T and Park EY. (2020). Structure-function analysis of silkworm sucrose hydrolase uncovers the mechanism of substrate specificity in GH13 subfamily 17 exo-α-glucosidases. J Biol Chem. 2020;295(26):8784-8797. DOI:10.1074/jbc.RA120.013595 | PubMed ID:32381508 [Miyazaki2020a]
  4. Takagi E, Hatada Y, Akita M, Ohta Y, Yokoi G, Miyazaki T, Nishikawa A, and Tonozuka T. (2015). Crystal structure of the catalytic domain of a GH16 β-agarase from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94. Biosci Biotechnol Biochem. 2015;79(4):625-32. DOI:10.1080/09168451.2014.988680 | PubMed ID:25483365 [Takagi2015]
  5. Okazawa Y, Miyazaki T, Yokoi G, Ishizaki Y, Nishikawa A, and Tonozuka T. (2015). Crystal Structure and Mutational Analysis of Isomalto-dextranase, a Member of Glycoside Hydrolase Family 27. J Biol Chem. 2015;290(43):26339-49. DOI:10.1074/jbc.M115.680942 | PubMed ID:26330557 [Okazawa2015]
  6. Miyazaki T, Ishizaki Y, Ichikawa M, Nishikawa A, and Tonozuka T. (2015). Structural and biochemical characterization of novel bacterial α-galactosidases belonging to glycoside hydrolase family 31. Biochem J. 2015;469(1):145-58. DOI:10.1042/BJ20150261 | PubMed ID:25942325 [Miyazaki2015a]
  7. Ikegaya M, Moriya T, Adachi N, Kawasaki M, Park EY, and Miyazaki T. (2022). Structural basis of the strict specificity of a bacterial GH31 α-1,3-glucosidase for nigerooligosaccharides. J Biol Chem. 2022;298(5):101827. DOI:10.1016/j.jbc.2022.101827 | PubMed ID:35293315 [Ikegaya2022]
  8. Miyazaki T and Park EY. (2020). Crystal structure of the Enterococcus faecalis α-N-acetylgalactosaminidase, a member of the glycoside hydrolase family 31. FEBS Lett. 2020;594(14):2282-2293. DOI:10.1002/1873-3468.13804 | PubMed ID:32367553 [Miyazaki2020b]
  9. Miyazaki T, Ikegaya M, and Alonso-Gil S. (2022). Structural and mechanistic insights into the substrate specificity and hydrolysis of GH31 α-N-acetylgalactosaminidase. Biochimie. 2022;195:90-99. DOI:10.1016/j.biochi.2021.11.007 | PubMed ID:34826537 [Miyazaki2022a]
  10. Ikegaya M, Park EY, and Miyazaki T. (2023). Structure-function analysis of bacterial GH31 α-galactosidases specific for α-(1→4)-galactobiose. FEBS J. 2023;290(20):4984-4998. DOI:10.1111/febs.16904 | PubMed ID:37438884 [Ikegaya2023]
  11. Miyazaki T, Oba N, and Park EY. (2020). Structural insight into the substrate specificity of Bombyx mori β-fructofuranosidase belonging to the glycoside hydrolase family 32. Insect Biochem Mol Biol. 2020;127:103494. DOI:10.1016/j.ibmb.2020.103494 | PubMed ID:33132139 [Miyazaki2020c]
  12. Miyazaki T, Yashiro H, Nishikawa A, and Tonozuka T. (2015). The side chain of a glycosylated asparagine residue is important for the stability of isopullulanase. J Biochem. 2015;157(4):225-34. DOI:10.1093/jb/mvu065 | PubMed ID:25359784 [Miyazaki2015b]
  13. Tonozuka T, Tanaka Y, Okuyama S, Miyazaki T, Nishikawa A, and Yoshida M. (2017). Structure of the Catalytic Domain of α-L-Arabinofuranosidase from Coprinopsis cinerea, CcAbf62A, Provides Insights into Structure-Function Relationships in Glycoside Hydrolase Family 62. Appl Biochem Biotechnol. 2017;181(2):511-525. DOI:10.1007/s12010-016-2227-0 | PubMed ID:27589854 [Tonozuka2017]
  14. Miyazaki T, Ichikawa M, Yokoi G, Kitaoka M, Mori H, Kitano Y, Nishikawa A, and Tonozuka T. (2013). Structure of a bacterial glycoside hydrolase family 63 enzyme in complex with its glycosynthase product, and insights into the substrate specificity. FEBS J. 2013;280(18):4560-71. DOI:10.1111/febs.12424 | PubMed ID:23826932 [Miyazaki2013a]
  15. Miyazaki T, Nishikawa A, and Tonozuka T. (2016). Crystal structure of the enzyme-product complex reveals sugar ring distortion during catalysis by family 63 inverting α-glycosidase. J Struct Biol. 2016;196(3):479-486. DOI:10.1016/j.jsb.2016.09.015 | PubMed ID:27688023 [Miyazaki2016]
  16. Miyazaki T, Ichikawa M, Iino H, Nishikawa A, and Tonozuka T. (2015). Crystal structure and substrate-binding mode of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8. J Struct Biol. 2015;190(1):21-30. DOI:10.1016/j.jsb.2015.02.006 | PubMed ID:25712767 [Miyazaki2015c]
  17. Nakamura S, Nihira T, Kurata R, Nakai H, Funane K, Park EY, and Miyazaki T. (2021). Structure of a bacterial α-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases. J Biol Chem. 2021;297(6):101366. DOI:10.1016/j.jbc.2021.101366 | PubMed ID:34728215 [Nakamura2021]
  18. Nakamura S, Kurata R, Tonozuka T, Funane K, Park EY, and Miyazaki T. (2023). Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria. J Biol Chem. 2023;299(7):104885. DOI:10.1016/j.jbc.2023.104885 | PubMed ID:37269952 [Nakamura2023]
  19. Tonozuka T, Tamaki A, Yokoi G, Miyazaki T, Ichikawa M, Nishikawa A, Ohta Y, Hidaka Y, Katayama K, Hatada Y, Ito T, and Fujita K. (2012). Crystal structure of a lactosucrose-producing enzyme, Arthrobacter sp. K-1 β-fructofuranosidase. Enzyme Microb Technol. 2012;51(6-7):359-65. DOI:10.1016/j.enzmictec.2012.08.004 | PubMed ID:23040392 [Tonozuka2012]
  20. Ohta Y, Hatada Y, Hidaka Y, Shimane Y, Usui K, Ito T, Fujita K, Yokoi G, Mori M, Sato S, Miyazaki T, Nishikawa A, and Tonozuka T. (2014). Enhancing thermostability and the structural characterization of Microbacterium saccharophilum K-1 β-fructofuranosidase. Appl Microbiol Biotechnol. 2014;98(15):6667-77. DOI:10.1007/s00253-014-5645-3 | PubMed ID:24633372 [Ohta2014]
  21. Alonso-Gil S, Parkan K, Kaminský J, Pohl R, and Miyazaki T. (2022). Unlocking the Hydrolytic Mechanism of GH92 α-1,2-Mannosidases: Computation Inspires the use of C-Glycosides as Michaelis Complex Mimics. Chemistry. 2022;28(14):e202200148. DOI:10.1002/chem.202200148 | PubMed ID:35049087 [Alonso-Gil2022]
  22. Nakamura S, Kurata R, and Miyazaki T. (2024). Structural insights into α-(1→6)-linkage preference of GH97 glucodextranase from Flavobacterium johnsoniae. FEBS J. 2024. DOI:10.1111/febs.17139 | PubMed ID:38661728 [Nakamura2024]
  23. Miyazaki T, Yoshida M, Tamura M, Tanaka Y, Umezawa K, Nishikawa A, and Tonozuka T. (2013). Crystal structure of the N-terminal domain of a glycoside hydrolase family 131 protein from Coprinopsis cinerea. FEBS Lett. 2013;587(14):2193-8. DOI:10.1016/j.febslet.2013.05.041 | PubMed ID:23711369 [Miyazaki2013b]
  24. Oka N, Mori S, Ikegaya M, Park EY, and Miyazaki T. (2022). Crystal structure and sugar-binding ability of the C-terminal domain of N-acetylglucosaminyltransferase IV establish a new carbohydrate-binding module family. Glycobiology. 2022;32(12):1153-1163. DOI:10.1093/glycob/cwac058 | PubMed ID:36106687 [Oka2022]
  25. Nakamura S, Miyazaki T, and Park EY. (2020). α-L-Fucosidase from Bombyx mori has broad substrate specificity and hydrolyzes core fucosylated N-glycans. Insect Biochem Mol Biol. 2020;124:103427. DOI:10.1016/j.ibmb.2020.103427 | PubMed ID:32561391 [Nakamura2020]
  26. Gozu Y, Ishizaki Y, Hosoyama Y, Miyazaki T, Nishikawa A, and Tonozuka T. (2016). A glycoside hydrolase family 31 dextranase with high transglucosylation activity from Flavobacterium johnsoniae. Biosci Biotechnol Biochem. 2016;80(8):1562-7. DOI:10.1080/09168451.2016.1182852 | PubMed ID:27170214 [Gozu2016]
  27. Ichinose H, Suzuki R, Miyazaki T, Kimura K, Momma M, Suzuki N, Fujimoto Z, Kimura A, and Funane K. (2017). Paenibacillus sp. 598K 6-α-glucosyltransferase is essential for cycloisomaltooligosaccharide synthesis from α-(1 → 4)-glucan. Appl Microbiol Biotechnol. 2017;101(10):4115-4128. DOI:10.1007/s00253-017-8174-z | PubMed ID:28224195 [Ichinose2017]
  28. Ikegaya M, Miyazaki T, and Park EY. (2021). Biochemical characterization of Bombyx mori α-N-acetylgalactosaminidase belonging to the glycoside hydrolase family 31. Insect Mol Biol. 2021;30(4):367-378. DOI:10.1111/imb.12701 | PubMed ID:33742736 [Ikegaya2021]
  29. Miyazaki T, Matsumoto Y, Matsuda K, Kurakata Y, Matsuo I, Ito Y, Nishikawa A, and Tonozuka T. (2011). Heterologous expression and characterization of processing α-glucosidase I from Aspergillus brasiliensis ATCC 9642. Glycoconj J. 2011;28(8-9):563-71. DOI:10.1007/s10719-011-9356-z | PubMed ID:22020441 [Miyazaki2011]
  30. Miyazaki T, Tanaka H, Nakamura S, Dohra H, and Funane K. (2023). Identification and Characterization of Dextran α-1,2-Debranching Enzyme from Microbacterium dextranolyticum. J Appl Glycosci (1999). 2023;70(1):15-24. DOI:10.5458/jag.jag.JAG-2022_0013 | PubMed ID:37033117 [Miyazaki2022b]
  31. Mizushima D, Miyazaki T, Shiwa Y, Kimura K, Suzuki S, Fujita N, Yoshikawa H, Kimura A, Kitamura S, Hara H, and Funane K. (2019). A novel intracellular dextranase derived from Paenibacillus sp. 598K with an ability to degrade cycloisomaltooligosaccharides. Appl Microbiol Biotechnol. 2019;103(16):6581-6592. DOI:10.1007/s00253-019-09965-y | PubMed ID:31273396 [Mizushima2019]
  32. Matsuda K, Kurakata Y, Miyazaki T, Matsuo I, Ito Y, Nishikawa A, and Tonozuka T. (2011). Heterologous expression, purification, and characterization of an α-mannosidase belonging to glycoside hydrolase family 99 of Shewanella amazonensis. Biosci Biotechnol Biochem. 2011;75(4):797-9. DOI:10.1271/bbb.100874 | PubMed ID:21512220 [Matsuda2011]
  33. Miyazaki T, Miyashita R, Nakamura S, Ikegaya M, Kato T, and Park EY. (2019). Biochemical characterization and mutational analysis of silkworm Bombyx mori β-1,4-N-acetylgalactosaminyltransferase and insight into the substrate specificity of β-1,4-galactosyltransferase family enzymes. Insect Biochem Mol Biol. 2019;115:103254. DOI:10.1016/j.ibmb.2019.103254 | PubMed ID:31655162 [Miyazaki2019a]
  34. Miyazaki T, Kato T, and Park EY. (2018). Heterologous expression, purification and characterization of human β-1,2-N-acetylglucosaminyltransferase II using a silkworm-based Bombyx mori nucleopolyhedrovirus bacmid expression system. J Biosci Bioeng. 2018;126(1):15-22. DOI:10.1016/j.jbiosc.2018.01.011 | PubMed ID:29409697 [Miyazaki2018]
  35. Miyazaki T, Miyashita R, Mori S, Kato T, and Park EY. (2019). Expression and characterization of silkworm Bombyx mori β-1,2-N-acetylglucosaminyltransferase II, a key enzyme for complex-type N-glycan biosynthesis. J Biosci Bioeng. 2019;127(3):273-280. DOI:10.1016/j.jbiosc.2018.08.014 | PubMed ID:30253927 [Miyazaki2019b]
  36. Mori M, Ichikawa M, Kiguchi Y, Miyazaki T, Hattori M, Nishikawa A, and Tonozuka T. (2016). A Surface Loop in the N-Terminal Domain of Pedobacter heparinus Heparin Lyase II is Important for Activity. J Appl Glycosci (1999). 2016;63(1):7-11. DOI:10.5458/jag.jag.JAG-2015_019 | PubMed ID:34354475 [Mori2016]

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