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Research Interest

Selected Publications

Research articles
1. Itoh*, T., Yaguchi, M., Nakaichi, A., Yoda, M., Hibi, T. and Kimoto, H.*: Structural characterization of two solute-binding proteins for N,N’-diacetylchitobiose/N,N’,N’’-triacetylchitotoriose of the gram-positive bacterium, Paenibacillus sp. str. FPU-7. J. Struct. Biol. 10, 100049, 2021.
2. Itoh, T., Kamiya, A., Kimura, M. and Murai, K.*: Heterogeneous expression and purification of the wheat VRN1 K-box domain suggest the formation of a tetramer of the VRN1 protein. Am. J. Plant Sci. 12, 1002-1010, 2021.
3. Panti, N., Cherdvorapong, V., Itoh, T., Hibi, T., Suyotha, W., Yano, S. and Wakayama, M.*: Functional analysis of α-1,3-glucanase domain structure from Streptomyces thermodiastaticus HF3-3. J. Gen. Appl. Microbiol. 67, 85-91, 2021.
4. Hibi, T.* and Itoh, T.: Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity. J. Biochem. 169, 15-23, 2021.
5. Sano, C., Itoh, T., Phumsombat, P., Hayashi, J., Wakayama, M. * and Hibi, T. *: Mutagenesis and structure-based analysis of the role of Tryptophan525 of γ-glutamyltranspeptidase from Pseudomonas nitroreducens. Biochem. Biophys. Res. Commun. 534, 286-291, 2020.
6. Phumsombat, P., Sano, C., Ikezoe, H., Hayashi, J., Itoh, T., Hibi, T. and Wakayama, M.*: Efficient production of L-theanine using immobilized recombinant Escherichia coli cells expressing a modified γ-glutamyltranspeptidase gene from Pseudomonas nitroreducens. Adv. Biol. Chem.10, 157-171, 2020.
7. Itoh, T., Panti, N., Hayashi, J., Toyotake, Y., Matsui, D., Yano, S., Wakayama, M.* and Hibi, T.*: Crystal structure of the catalytic unit of thermostable GH87 α-1,3-glucanase from Streptomyces thermodiastaticus strain HF3-3. Biochem. Biophys. Res. Commun. 533, 1170-1176, 2020.
8. Hibi, T.* and Itoh, T.: Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity. J. Biochem. 169, 15-23, 2020.
9. Iwasaki, Y., * Itoh, T., Hagi, Y., Matuta, S., Nishiyama, A., Chaya, G., Koboyashi, Y., Miura, K. and Komatsu, S. *: Proteomics analysis of plasma membrane fractions of the root, leaf, and flower of rice. Int. J. Mol. Sci. 21: E6988, 2020.
10. Itoh, T., Intuy, R., Suyotha, W., Hayashi, J., Yano, S., Makabe, K., Wakayama, M.* and Hibi, T.*: Structural insights into substrate recognition and catalysis by glycoside hydrolase family 87 ⍺-1,3-glucanase from Paenibacillus glycanilyticus FH11. FEBS J. 287, 2524-2543, 2020.
11. Yano, S., Suyotha, W., Oguro, N., Matsui, T., Shiga, S., Itoh, T., Hibi, T., Tanaka, Y., Wakayama, M. and Makabe, K.*: Crystal structure of the catalytic unit of GH 87-type α-1,3-glucanase Agl-KA from Bacillus circulans. Sci. Rep. 9:15295, 2019.
12. Itoh, T.,* Nakagawa, E., Yoda, M., Nakaichi, A., Hibi, T. and Kimoto, H.: Structural and biochemical characterisation of a novel alginate lyase from Paenibacillus sp. str. FPU-7. Sci. Rep. 9:14870, 2019.
13. Itoh, T.,* Araki, T., Nishiyama, T., Hibi, T. and Kimoto, H. *: Structural and functional characterization of a glycoside hydrolase family 3 β-N-acetylglucosaminidase from Paenibacillus sp. str. FPU-7. J. Biochem. 166: 503-515. 2019.
14. Ogawa, N.,* Kimura, T., Umehara, F., Katayama, Y., Nagai, G., Suzuki, K., Aisaka, K., Maruyama, Y., Itoh, T., Hashimoto, W., Murata, K. and Ichimura, M.: Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis. Sci. Rep. 9: 942, 2019.
15. Hibi, T.,* Imaoka, M., Shimizu, Y., Itoh, T. and Wakayama, M. *: Crystal structure analysis and enzymatic characterization of γ-glutamyltranspeptidase from Pseudomonas nitroreducens. Biosci. Biotechnol. Biochem. 83: 262-269, 2019.
16. Intuy, R., Itoh, T., Suyotha, W., Hayashi, J., Yano, S, Makabe, K., Wakayama, M.* and Hibi, T.*: X-ray crystallographic analysis of the catalytic domain of Paenibacillus glycanilyticus α-1,3-glucanase FH1 overexpressed in Brevibacillus choshinensis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 74: 770-773, 2018.
17. Matsuta, S.,** Nishiyama, A.,** Chaya, G., Itoh, T., Miura, K. and and Iwasaki, Y.*: Characterization of heterotrimeric G protein γ4 subunit in rice. Int. J. Mol. Sci. 19: E3596, 2018.
18. Nishiyama, A.,** Matsuta, S.,** Chaya, G., Itoh, T., Miura, K. and and Iwasaki, Y.*: Identification of heterotrimeric G protein γ3 subunit in rice plasma membrane. Int. J. Mol. Sci. 19: E3591, 2018.
19. Tanaka, C., Itoh, T., Iwasaki, Y., Mizuno, N., Nasuda, S. and Murai, K.*: Direct interaction between VRN1 protein and the promoter region of the wheat FT gene. Genes Genet. Syst. 93: 25-29, 2018.
20. Rehman, A., Rehman, S., Khatoon, A., Qasim, M., Itoh, T., Iwasaki, Y., Wang, X., Sunohara, Y., Matsumoto, H. and Komatsu, S.*: Proteomic analysis of the promotive effect of plant-derived smoke on plant growth of chickpea. J. Proteomics 176: 56-70, 2018.
21. Itoh, T. *, Hibi, T., Suzuki, F., Sugimoto, I., Fujiwara, A., Inaka, K., Tanaka, H., Ohta, K., Fujii, Y., Taketo, A. and Kimoto, H.*: Crystal structure of chitinase ChiW from Paenibacillus sp. str. FPU-7 reveals a novel type of bacterial cell-surface-expressed multi-modular enzyme machinery. PLOS ONE, 11:e0167310, 2016.
22. Hibi, T.*, Kume, A., Kawamura, A., Itoh, T., Fukada, H. and Nishiya, Y.: Hyperstabilization of tetrameric Bacillus sp. TB-90 urate oxidase by introducing disulfide bonds through structural plasticity. Biochemistry 55: 724-732, 2016.
23. Maruyama, Y., Itoh, T. **, Kaneko, A., Nishitani, Y., Mikami, B., Hashimoto, W.* and Murata, K.*: Structure of a bacterial ABC transporter involved in the import of an acidic polysaccharide alginate. Structure 23: 1643-1654, 2015.
24. Katano, H.*, Takakuwa, M., Itoh, T. and Hibi, T.: Microplate assay of α-glucosidase and its inhibitors based on the direct reduction of molybdosilicate by glucose. Anal. Sci. 3:1291-1295, 2015.
25. Katano, H.*, Takakuwa, M., Itoh, T. and Hibi, T.: Colorimetric determination of fructose for the high-throughput microtiter plate assay of glucose isomerase. Biosci. Biotechnol. Biochem. 79: 1057-1060, 2015.
26. Hibi, T.*, Hayashi, Y., Fukada, H., Itoh, T., Nago, T. and Nishiya, Y.: Intersubunit salt bridges with a sulfate anion control subunit dissociation and thermal stabilization of Bacillus sp. TB-90 urate oxidase. Biochemistry 53: 3879-3888, 2014.
27. Suyotha, W., Yano, S., Itoh, T., Fujimoto, H., Hibi, T., Tachiki, T. and Wakayama, M.*: Characterization of α-1,3-glucanase isozyme from Paenibacillus glycanilyticus FH11 in a new subgroup of family 87 α-1,3-glucanase. J. Biosci. Bioeng. 118: 378-385, 2014.
28. Itoh, T., Sugimoto, I., Hibi, T., Suzuki, F., Matsuo, K., Fujii, Y., Taketo, A. and Kimoto, H.*: Overexpression, purification, and characterization of Paenibacillus cell surface-expressed chitinase ChiW with two catalytic domains. Biosci. Biotechnol. Biochem. 78: 624-634, 2014.
29. Itoh, T.*, Hibi, T., Sugimoto, I., Suzuki, F., Fujii, Y., Taketo, A. and Kimoto, H.: Crystallization and preliminary X-ray analysis of the catalytic domains of Paenibacillus sp. str. FPU-7 cell surface-expressed chitinase ChiW. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 70:350-353, 2014.
30. Itoh, T., Hibi, T., Fujii, Y., Sugimoto, I., Fujiwara, A., Suzuki, F., Iwasaki, Y., Kim, J-K., Taketo, A. and Kimoto, H.*: Cooperative degradation of chitin by extracellular and cell surface-expressed chitinases from Paenibacillus sp. FPU-7. Appl. Environ. Microbiol. 79: 7482-7490, 2013.
31. Prak, K., Mikami, B., Itoh, T., Fukuda, T., Maruyama, N.* and Utsumi, S.: Purification, crystallization and preliminary crystallographic analysis of the soybean glycinin A1bB2. Acta Crystallogr. Sect F Struct. Biol. Cryst. Commun. 69: 937-941, 2013.
32. Nasuno, R., Hirano, Y., Itoh, T., Hakoshima, T., Hibi, T. and Takagi, H.*: Structural and functional analysis of the yeast N-acetyltransferase Mpr1 involved in oxidative stress tolerance via proline metabolism. Proc. Natl. Acad. Sci. USA. 110: 11821-11826, 2013.
33. Nishitani, Y., Maruyama, Y., Itoh, T., Mikami, B., Hashimoto, W. and Murata, K.*: Recognition of Heteropolysaccharide Alginate by Periplasmic Solute-Binding Proteins of a Bacterial ABC Transporter. Biochemistry 51: 3622-3633, 2012.
34. Maruyama, Y., Itoh, T., Nishitani, Y., Mikami, B., Hashimoto, W. and Murata, K.*: Crystallization and preliminary X-ray analysis of alginate importer from Sphingomonas sp. A1. Acta Crystallogr. Sect F Struct. Biol. Cryst. Commun. 68: 317-320, 2012.
35. Torio, M. A. O, Itoh, T., Garcia, R. N., Maruyama, N., Utsumi, S. and Tecson-Mendoza, E. M.*: Introduction of sulfhydryl groups and disulfide linkage to mungbean 8Sα globulin and effects on physicochemical and functional properties. Food Res. Int. 45: 277-282, 2012.
36. Maruyama, Y., Ochiai, A., Itoh, T., Mikami, B., Hashimoto, W. and Murata, K.*: Mutational studies of the peptidoglycan hydrolase FlgJ of Sphingomonas sp. strain A1. J. Basic. Microbiol. 50: 311-317, 2010.
37. Tandang-Silvas, M. R., Fukuda, T., Fukuda, C., Prak, K., Cabanos, C., Kimura, A., Itoh, T., Mikami, B., Utsumi, S. and Maruyama, N.*: Conservation and divergence on plant seed 11S globulins based on crystal structures. Biochim. Biophys. Acta. 1804: 1432-1442, 2010.
38. Maruyama, Y., Nakamichi, Y., Itoh, T., Mikami, B., Hashimoto, W. and Murata, K.*: Substrate specificity of streptococcal unsaturated glucuronyl hydrolases for sulfated glycosaminoglycan. J. Biol. Chem. 284: 18059-18069, 2009.
39. Hashimoto, W., Ochiai, A., He, J., Itoh, T., Mikami, B. and Murata, K.*: Crystallization and preliminary crystallographic analysis of the cell-surface alginate-binding protein Algp7 isolated from Sphingomonas sp. A1. Acta Crystallogr. Sect F Struct. Biol. Cryst. Commun. 65: 515-517, 2009.
40. Hashimoto, W., Ochiai, A., Momma, K., Itoh, T., Mikami, B., Maruyama, Y. and Murata, K.*: Crystal structure of the glycosidase family 73 peptidoglycan hydrolase FlgJ. Biochem. Biophys. Res. Commun. 381: 16-21, 2009.
41. Ochiai, A., Itoh, T., Mikami, B., Hashimoto, W. and Murata, K.*: Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases. J. Biol. Chem. 284: 10181-10189, 2009.
42. Sakurama, H., Takita, T., Mikami, B., Itoh, T., Yasukawa, K. and Inouye, K.*: Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate. J. Biochem. 145, 555-563, 2009.
43. Itoh, T., Mikami, B., Hashimoto, W. and Murata, K.*: Crystal structure of YihS in complex with D-mannose: structural annotation of Escherichia coli and Salmonella enterica yihS-encoded proteins to an aldose-ketose isomerase. J. Mol. Biol. 377: 1443-1459, 2008.
44. Takita, T., Aono, T., Sakurama, H., Itoh, T., Wada, T., Minoda, M., Yasukawa, K. and Inouye, K.*: Effects of introducing negative charges into the molecular surface of thermolysin by site-directed mutagenesis on its activity and stability. Biochim. Biophys. Acta. 1784: 481-488, 2008.
45. Ochiai, A., Itoh, T., Maruyama, Y., Kawamata, A., Mikami, B., Hashimoto, W. and Murata, K.*: A novel structural fold in polysaccharide lyases: Bacillus subtitis family 11 rhamnogalacturonan lyase YesW with an eight-braded-propeller. J. Biol. Chem. 282: 37134-37145, 2007.
46. Ochiai, A., Itoh, T., Kawamata, A., Hashimoto, W. and Murata, K.*: Plant cell wall degradation by saprophytic Bacillus subtilis: gene clusters responsible for rhamnogalacturonan depolymerization. Appl. Environ. Microbiol. 73: 3803-3813, 2007.
47. Ochiai, A., Yamasaki, M., Itoh, T., Mikami, B., Hashimoto, W. and Murata, K.*: Crystallization and preliminary X-ray analysis of the rhamnogalacturonan lyase YesW from Bacillus subtilis strain 168, a member of polysaccharide lyase family 11. Acta Crystallograph. Sect. F Struct. Biol. Cryst. Commun. 62: 438-440, 2006.
48. Malle, D., Itoh, T., Hashimoto, W., Murata, K., Utsumi, S. and Mikami, B.*: Overexpression, purification and preliminary X-ray analysis of pullulanase from Bacillus subtilis strain 168. Acta Crystallograph. Sect. F Struct. Biol. Cryst. Commun. 62: 381-384, 2006.
49. Itoh, T., Garcia, R. N., Adachi, M., Maruyama, Y., Tecson-Mendoza, E. M., Mikami, B. and Utsumi, S.*: Structure of 8Sα globulin, the major seed storage protein of mungbean. Acta Crystallograph. Sect. D Biol. Crystallogr. 62: 824-832, 2006.
50. Itoh, T., Ochiai, A., Mikami, B., Hashimoto, W. and Murata, K.*: Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate. Biochem. Biophys. Res. Commun. 347: 1021-1029, 2006.
51. Itoh, T., Hashimoto, W., Mikami, B. and Murata, K.*: Substrate recognition of unsaturated glucuronyl hydrolase from Bacillus sp. GL1. Biochem. Biophys. Res. Commun. 344: 253-262, 2006.
52. Itoh, T., Hashimoto, W., Mikami, B. and Murata, K.*: Crystal structure of unsaturated glucuronyl hydrolase complexed with substrate: molecular insights into its catalytic reaction mechanism. J. Biol. Chem. 281: 29807-29816, 2006.
53. Itoh, T., Ochiai, A., Mikami, B., Hashimoto, W. and Murata, K.*: A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide. J. Mol. Biol. 360: 573-585, 2006.
54. Itoh, T., Akao, S., Hashimoto, W., Mikami, B. and Murata, K.*: Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 Å resolution. J. Biol. Chem. 279: 31804-31812, 2004.
55. Itoh, T., Mikami, B.*, Maru, I., Ohta, Y., Hashimoto, W. and Murata, K.: Crystal structure of N-acyl-D-glucosamine 2-epimerase from porcine kidney at 2.0 Å resolution. J. Mol. Biol. 303: 733-744, 2000.

Book
1. Katano, H.*, Itoh, T., and Hibi, T. *: Colorimetric high-throughput microplate assay of xylose isomerase and its application to improve the enzyme activity.
Advances in Medicine and Biology, 153, 2020, Chapter 7, Berhardt, L.V. (Ed.), Nova Science Publishers, NY, USA.
2. Itoh, T.* and Kimoto, H.*: Bacterial chitinase system as a model of chitin biodegradation.
Targeting Chitin-containing Organisms: Advances in Experimental Medicine and Biology, 1142. 131-151, 2019, Yang, Q. and Fukamizo, T. (Eds.), Springer, Singapore.
3. Hashimoto, W., Maruyama, Y., Itoh, T., Mikami, B. and Murata, K. *: Bacterial system for alginate uptake and degradation.
Alginates: Biology and Applications, Microbiology Monographs, 13, 73-94, 2009, Rehm, B. H. A. (Ed.), Springer, Berlin, Germany.

Reviews
1. Itoh, T.: Structures and functions of carbohydrate-active enzymes of chitinolytic bacteria Paenibacillus sp. str. FPU-7.
Biosci. Biotechnol. Biochem. 85: 1314-1323, 2021.
2. Hashimoto, W., Itoh, T., Maruyama, Y., Mikami, B. and Murata, K.: Hydration of vinyl ether groups by unsaturated glycoside hydrolases and their role in bacterial pathogenesis.
Int. Microbiol. 10: 233-243, 2007.
3. Hashimoto, W., Yamasaki, M., Itoh, T., Momma, K., Mikami, B. and Murata, K.: Super-channel in bacteria: structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules.
J. Biosci. Bioeng. 98: 399-413, 2004.

Community Engagement

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Additional Information

The Japan Bioscience, Biotechnology and Agrochemistry Society Award for the Encuragement of Young Scientists, 2015.