Jump to ContentJump to Main Navigation
Show Summary Details
More options …

Amylase

Ed. by Janecek, Stefan

Open Access
Online
ISSN
2450-9728
See all formats and pricing
More options …

Mutagenesis-induced conformational change in domain B of a pullulan-hydrolyzing α-amylase TVA I

Takashi Tonozuka
  • Corresponding author
  • Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Takanori Nihira
  • Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Masahiro Mizuno
  • Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Atsushi Nishikawa
  • Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Shigehiro Kamitori
  • Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2018-03-20 | DOI: https://doi.org/10.1515/amylase-2018-0001

Abstract

An α-amylase from Thermoactinomyces vulgaris, TVA I, hydrolyzes both α-1,4- and α-1,6-glucosidic linkages. Two variants of TVA I have been previously constructed, one containing a substitution of three residues, Ala357- Gln359-Tyr360, with Val-Asn-Glu (AQY/VNE), and the other bearing a deletion of 11 residues from Ala363 to Asn373 (Del11). The activities of both AQY/VNE and Del11 for the α-1,4-glucosidic linkage of maltotriose were decreased compared to that of wild-type TVA I, while the activities of the two variants for the α-1,6-glucosidic linkage of a trisaccharide, isopanose, were less significantly altered. Here, we determined the crystal structures of AQY/VNE and Del11. The structure of AQY/VNE was almost isomorphous with that of wild-type TVA I. On the other hand, the structure of Del11 showed that a conformational change in domain B was induced by the 11-residue deletion, causing narrowing of the catalytic cleft. Taken together with the results of kinetic analysis, this narrower catalytic cleft is likely responsible for the preference of the TVA I enzyme for the α-1,6-glucosidic linkage.

Keywords : pullulan; Thermoactinomyces vulgaris; sitedirected mutagenesis; crystal structure; neopullulanase; domain B

References

  • [1] Janecek S., Svensson B., MacGregor E.A., α-Amylase: an enzyme specificity found in various families of glycoside hydrolases, Cell. Mol. Life. Sci., 2014, 71, 1149-1170.Web of ScienceGoogle Scholar

  • [2] Khemakhem B., Ben Ali M., Aghajari N., Juy M., Haser R., Bejar S., The importance of an extra loop in the B-domain of an α-amylase from B. stearothermophilus US100, Biochem. Biophys. Res. Commun., 2009, 385, 78-83.Web of ScienceGoogle Scholar

  • [3] Alikhajeh J., Khajeh K., Ranjbar B., Naderi-Manesh H., Lin YH., Liu E., et al., Structure of Bacillus amyloliquefaciens α-amylase at high resolution: implications for thermal stability, Acta Crystallogr. F Struct. Biol. Commun., 2010, 66, 121-129.Web of ScienceGoogle Scholar

  • [4] Kumar V., Analysis of the key active subsites of glycoside hydrolase 13 family members, Carbohydr. Res., 2010, 345, 893-898.Google Scholar

  • [5] Kamitori S., Kondo S., Okuyama K., Yokota T., Shimura Y., Tonozuka T., Sakano Y., Crystal structure of Thermoactinomyces vulgaris R-47 α-amylase II (TVA II) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution, J. Mol. Biol., 1999, 287, 907-921.Google Scholar

  • [6] Tonozuka T., Mogi S., Shimura Y., Ibuka A., Sakai H., Matsuzawa H., et al., Comparison of primary structures and substrate specificities of two pullulan-hydrolyzing α-amylases, TVA I and TVA II, from Thermoactinomyces vulgaris R-47, Biochim. Biophys. Acta., 1995, 1252, 35-42.Google Scholar

  • [7] Imanaka T., Kuriki T., Pattern of action of Bacillus stearothermophilus neopullulanase on pullulan, J. Bacteriol., 1989, 171, 369-374.Google Scholar

  • [8] Kuriki T., Imanaka T., The concept of the α-amylase family: structural similarity and common catalytic mechanism. J. Biosci. Bioeng., 1999, 87, 557-565.Google Scholar

  • [9] Lee H.S., Kim M.S., Cho H.S., Kim J.I., Kim T.J., Choi J.H., et al., Cyclomaltodextrinase, neopullulanase, and maltogenic amylase are nearly indistinguishable from each other, J. Biol. Chem., 2002, 277, 21891-21897.Google Scholar

  • [10] Stam M.R., Danchin E.G., Rancurel C., Coutinho P.M., Henrissat B., Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of α-amylase-related proteins. Protein Eng. Des. Sel., 2006, 19, 555-562.Google Scholar

  • [11] Oslancova A., Janecek S., Oligo-1,6-glucosidase and neopullulanase enzyme subfamilies from the α-amylase family defined by the fifth conserved sequence region. Cell. Mol. Life Sci., 2002, 59, 1945-1959.Google Scholar

  • [12] Majzlova K., Pukajova Z., Janecek S., Tracing the evolution of the α-amylase subfamily GH13_36 covering the amylolytic enzymes intermediate between oligo-1,6-glucosidases and neopullulanases. Carbohydr. Res., 2013, 367, 48-57.Web of ScienceGoogle Scholar

  • [13] Kamitori S., Abe A., Ohtaki A., Kaji A., Tonozuka T., Sakano Y., Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 α-amylase 1 (TVA I) at 1.6 A resolution and α-amylase 2 (TVA II) at 2.3 A resolution. J. Mol. Biol., 2002, 318, 443-453.Google Scholar

  • [14] Ibuka A., Tonozuka T., Matsuzawa H., Sakai H., Conversion of neopullulanase-α-amylase from Thermoactinomyces vulgaris R-47 into an amylopullulanase-type enzyme. J. Biochem., 1998, 123, 275-282.Google Scholar

  • [15] MacGregor E.A., Janecek S., Svensson B., Relationship of sequence and structure to specificity in the α-amylase family of enzymes. Biochim. Biophys. Acta, 2001, 1546, 1-20.CrossrefGoogle Scholar

  • [16] Yamamoto K., Nakayama A., Yamamoto Y., Tabata S., Val216 decides the substrate specificity of α-glucosidase in Saccharomyces cerevisiae, Eur. J. Biochem., 2004 271, 3414-3420.Google Scholar

  • [17] Ito K., Ito S., Ishino K., Shimizu-Ibuka A., Sakai H., Val326 of Thermoactinomyces vulgaris R-47 amylase II modulates the preference for α-(1,4)- and α-(1,6)-glycosidic linkages. Biochim. Biophys. Acta., 2007, 1774, 443-449.Google Scholar

  • [18] Sakano Y., Kogure M., Kobayashi T., Tamura M., Suekane, M., Enzymatic preparation of panose and isopanose from pullulan, Carbohydr. Res., 1978, 61, 175-179.Google Scholar

  • [19] Tonozuka T., Sakai H., Ohta T., Sakano Y., A convenient enzymatic synthesis of 4(2)-α-isomaltosylisomaltose using Thermoactinomyces vulgaris R-47 α-amylase II (TVA II). Carbohydr. Res., 1994, 261, 157-162.Google Scholar

  • [20] Powell H.R., Battye T.G.G., Kontogiannis L., Johnson O., Leslie A.G.W., Integrating macromolecular X-ray diffraction data with the graphical user interface iMosflm. Nat. Protoc., 2017, 12, 1310-1325.Web of ScienceCrossrefGoogle Scholar

  • [21] Vagin A., Teplyakov A., Molecular replacement with MOLREP, Acta Crystallogr. D Biol. Crystallogr., 2010, 66, 22-25.Google Scholar

  • [22] Winn M.D., Ballard C.C., Cowtan K.D., Dodson E.J., Emsley P., Evans P.R., et al., Overview of the CCP4 suite and current developments., Acta Crystallogr. D Biol. Crystallogr., 2011, 67, 235-242.Web of ScienceGoogle Scholar

  • [23] Murshudov G.N., Skubak P., Lebedev A.A., Pannu N.S., Steiner R.A., Nicholls R.A., et al., REFMAC5 for the refinement of macromolecular crystal structures, Acta Cryst. D Biol. Crystallogr., 2011, 67, 355-367.Web of ScienceGoogle Scholar

  • [24] Emsley P., Lohkamp B., Scott W.G., Cowtan K., Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr., 2010, 66, 486-501.Google Scholar

  • [25] Lovell S.C., Davis I.W., Arendall 3rd W.B., de Bakker P.I., Word J.M., Prisant M.G., et al., Structure validation by Cα geometry: φ, ψ, and Cβ deviation, Proteins, 2003, 50, 437-450.Google Scholar

  • [26] Abe A., Yoshida H., Tonozuka T., Sakano Y., Kamitori S., Complexes of Thermoactinomyces vulgaris R-47 α-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with α-(1,6) glycosidic linkages, FEBS J., 2005, 272, 6145-6153.Google Scholar

  • [27] Yamamoto K., Miyake H., Kusunoki M., Osaki S., Steric hindrance by 2 amino acid residues determines the substrate specificity of isomaltase from Saccharomyces cerevisiae, J. Biosci. Bioeng., 2011, 112, 545-550.Web of ScienceGoogle Scholar

  • [28] Yamamoto K., Miyake H., Kusunoki M., Osaki S., Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose, FEBS J., 2010, 277, 4205-4214.Web of ScienceGoogle Scholar

About the article

Received: 2017-12-20

Accepted: 2018-02-10

Published Online: 2018-03-20


Citation Information: Amylase, Volume 2, Issue 1, Pages 1–10, ISSN (Online) 2450-9728, DOI: https://doi.org/10.1515/amylase-2018-0001.

Export Citation

© 2018 Takashi Tonozuka, et al., published by De Gruyter. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

Comments (0)

Please log in or register to comment.
Log in