In Silico Evaluation of the Structural Dynamics of Beta-Amylase from Sweet Potato (Ipomoea batatas)
Asian Journal of Biotechnology and Bioresource Technology,
Background: Sweet potato tubers are invaluable crop that could serve both dietary and industrial purposes owing to its high β-amylase content. β-amylases play essential role in plant carbohydrate metabolism as well as in many industrial applications such as the malting process in the brewing and distilling industries.
Aim: This study aims at better understanding of the evolutionary and molecular properties, and structural dynamics of β-amylase of sweet potato using in silico approach.
Methodology: 16 of the 250 sequences that are at least 69% identity to the query sequence (P10537) were manually selected from UniProt database for further analysis.
Result: It has theoretical isoelectric point of 4.97 and molecular weight of 56 kDa. The root-mean-square fluctuation (RMSF) of sweet potato β-amylase showed possible conservation of the amino acid residues 105-130 and 260-345, with highest fluctuation in C-terminal loop (residues 443-498). The catalytic role of Glu187 and Thr344 in β-amylase of sweet potato has been elucidated, and it provided the missing link in the previously available mechanisms, while Cys96 is essential for the inactivation of enzyme activity.
Conclusion: Elucidation of molecular mechanisms of expression and catalytic activity, together with the understanding of physicochemical properties of β-amylase from sweet potato will help in development of useful applications that are of industrial importance.
- Sweet potato
- Ipomoea batatas
- in silico properties
How to Cite
Mohanraj R, Sivasankar S. Sweet potato (Ipomoea batatas [L.] Lam) - A valuable medicinal food: A review. J Med Food. 2013;17 (7):1–9.
Ramakrishnan S, Rathnasamy SK. β-amylase purification from sweet potato (Ipomoea batatus): Reverse micellar extraction versus ammonium sulphate precipitation. Der Pharmacia Lettre. 2016;8(16):118-125.
Fincher GB. Molecular and cellular biology associated with endosperm mobilization in germinating cereal grains. Annu. Rev. Plant Physiol. Plant Mol. Biol. 40 (1989) 305–346. DOI:10.1146/annurev.pp.40.060189.001513.
Vajravijayan S, Pletnev S, Mani N, Pletneva N, Nandhagopal N, Gunasekaran K. Structural insights on starch hydrolysis by plant β-amylase and its evolutionary relationship with bacterial enzymes. 2018;113:329-337.
Mensah EO, Ibok O, Ellis WO, Carey EE. Thermal Stability of -Amylase Activity and Sugar Profile of Sweet- Potato Varieties during Processing. J Nutr Food Sci. 2016;6:4.
Fazekas E, Szabó K, Kandra L, Gyémánt G. Unexpected mode of action of sweet potato β-amylase on maltooligomer substrates. Biochimica et Biophysica Acta. 2013;1834:1976-1981.
Thalmann M, Coiro M, Meier T, Wicker T, Zeeman SC, et al. The evolution of functional complexity within the β-amylase gene family in land plants. BMC Evol Biol. 2019;19:66.
Kaplan F, Guy CL. β-Amylase Induction and the Protective Role of Maltose during Temperature Shock. Plant Physiology. 2004;135:1674–1684.
Lombard V, Ramulu HG, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2104;42:D490-5.
Henrissat B. A classification of glycosyl hydrolases based on amino acid sequence similarities, Biochem. J. 1991;280:309–316. DOI:10.1042/bj2800309.
Cheong CG, Eom SH, Chang C, Shin DH, Song HK, Min K, et al. Crystallization, molecular replacement solution, and refinement of tetrameric β-amylase from sweet potato, Proteins. 1995;21:105–117. DOI: 10.1002/prot.340210204
Mikami B, Yoon HJ, Yoshigi N. The crystal structure of the sevenfold mutant of barley beta-amylase with increased thermostability at 2.5 A resolution. J Mol Biol. 1999a;285:1235–43.
Mikami B, Adachi M, Kage T, Sarikaya E, Nanmori T, Shinke R, et al. Structure of raw starch-digesting Bacillus cereus β-amylase complexed with maltose. J Mol Biol. 1999b;38:7050–61.
Mikami B, Degano M, Hehre EJ, Sacchettini JC. Crystal structures of soybean β-amylase reacted with β-maltose and maltal: active site components and their apparent role in catalysis. J Mol Biol. 1994;33:7779–87.
Mikami B, Hehre EJ, Sato M, Katsube Y, Hirose M, Morita Y, et al. The 2.0-A resolution structure of soybean beta-amylase complexed with alphacyclodextrin. J Mol Biol. 1993a; 32:6836–45.
Thoma JA, Koshland DE. Three amino acids at the active site of beta amylase. J. Mol. Biol. 2 1960;169–170.
Isoda Y, Nitta Y. Affinity labeling of soybean beta-amylase with 2’,3’-epoxypropyl alpha-Dglucopyranoside. J. Biochem. 99(1986)1631-7.
Kang YN, Adachi M, Utsumi S, Mikami B. The roles of Glu186 and Glu380 in the catalytic reaction of soybean β-amylase, J. Mol. Biol. 2004;339:1129–1140. DOI:10.1016/j.jmb.2004.04.029.
Monroe JD, Pope LE, Breault JS, Berndsen CE and Storm AR. Quaternary structure, salt sensitivity, and allosteric regulation of β-AMYLASE2 from Arabidopsis thaliana. Front. Plant Sci. 2018;9:1176.
Fatoki TH, Ibraheem O, Ogunyemi IO, Akinmoladun AC, Ugboko HU, Adeseko CA, Awofisayo OA, Olusegun SJ, Enibukun JM. Network analysis, sequence and structure dynamics of key proteins of coronavirus and human host, and molecular docking of selected phytochemicals of nine medicinal plants. Journal of Biomolecular Structures and Dynamics; 2020.
Kuriata A, Gierut AM, Oleniecki T, et al. CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures. Nucleic Acids Res. 2018;46:W338-W343.
Fatoki TH. Comparative evaluation of computational and experimental analysis of polyphenol oxidase from sweet potato (Ipomoea batatas). Journal of Microbiology and Biotechnology Research. 2016; 6(5):39-46.
Horton P, Park KJ, Obayashi T, Fujita N, Arada H, Adams-Collier C.J, Nakai K. WoLF PoSORT: protein localization prediction. Nucleic Acids Res. 2007;35 (web server issue): W535-7.
Alméciga-Díaz CJ, Gutierrez AM, Bahamon I, Rodríguez A, Rodríguez MA, Sánchez OF. Computational analysis of the fructosyltransferase enzymes in plants, fungi and bacteria. Gene. 2011;484:26-34.
Toda H, Nitta Y, asanami S, Kim JP, Sakiyama F. Sweet potato P-amylase primary structure and identification of the active-site glutamyl residue. Eur. J. Biochem. 2013;216:25-38.
Sanni DM, Fatoki TH, Omotoyinbo OV. Comparative evaluation of computational and experimental analysis of polyphenol oxidase from cocoa (Theobroma cacao L.). Journal of Microbiology and Biotechnology Research. 2017;7(1):18-25.
Kozlowski LP. IPC – isoelectric point calculator. Biol Direct. 2016;11:55.
Gilliland GL. A biological macromolecule crystallization database: a basis for a crystallization strategy. J. Cryst. Growth. 1988;90:51–59.
Luft JR, Wolfley JR, Snel EH. What’s in a drop? Correlating observations and outcomes to guide macromolecular crystallization experiments. Cryst. Growth. 2011;Des,11(3):651–663.
Kantardjieff KA, Rupp B. Protein isoelectric point as a predictor for increased crystallization screening efficiency. Bioinformatics. 2004;20(14):2162-8.
Hirata A, Adachi M, Sekine A, Kang Y-N, Utsumi S, Mikami B. Structural and enzymatic analysis of soybean β-Amylase mutants with increased pH optimum. Journal of Biological Chemistry. 2004; 279(8):7287–7295.
Janati-Farda F, Housaindokht MR, Monhemi H. Investigation of structural stability and enzymatic activity of glucose oxidase and its subunits. Journal of Molecular Catalysis B: Enzymatic. 2016;134:16–24.
Mikami B, Hehre JA, Sato M, Katsube Y, Hirose M, Morita Y, Sacchattini JS. Biochemistry. 1993b;32:6836–6845.
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