In silico analysis of alcohol dehydrogenase from Bacillus thuringiensis serovar israelensis using bioinformatics tools
Keywords:
Alcohol dehydrogenase, zinc-containing ADH, bioinformatics, Bacillus thuringiensis serovar israelensis, in silico analysis
Abstract
Alcohol dehydrogenases (ADH) (EC 1.1.1.1) that belong to dehydrogenase enzymes found in many organisms carry out the interconversion of alcohols and aldehydes or ketones using nicotinamide cofactor (NAD+ or NADH). Alcohol dehydrogenase from Bacillus thuringiensis serovar israelensis (BtADH) was cloned, expressed, and characterized in our previous study. This study provides the detailed comprehensive characterization of BtADH protein by using in silico tools to estimate physicochemical properties, structural characteristics, and motif patterns consisting of secondary structure prediction and functional analysis. The prediction of the secondary structure of BtADH protein was carried out by the PSIPRED protein analysis workbench and defining functional sites of BtADH was determined by InterProScan data resource. Motif scan analysis of BtADH was conducted in different databases by using the MyHits tool.
References
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2. Shain, D.H., C. Salvadore, and C.L. Denis, Evolution of the alcohol dehydrogenase (ADH) genes in yeast: characterization of a fourth ADH in Kluyveromyces lactis. Molecular and General Genetics MGG, 1992. 232(3): p. 479-488.
3. Schwartz, D. and T. Endo, ALCOHOL DEHYDROGENASE POLYMORPHISM IN MAIZE—SIMPLE AND COMPOUND LOCI. Genetics, 1966. 53(4): p. 709-715.
4. Sun, H.W. and B.V. Plapp, Progressive sequence alignment and molecular evolution of the Zncontaining alcohol dehydrogenase family. Journal of Molecular Evolution, 1992. 34(6): p. 522-535.
5. Satre, M.A., M. Zgombić-Knight, and G. Duester, The complete structure of human class IV alcohol dehydrogenase (retinol dehydrogenase) determined from the ADH7 gene. J Biol Chem, 1994. 269(22): p. 15606-12.
6. Schwartz, M., J. O'Donnell, and W. Sofer, Origin of the multiple forms of alcohol dehydrogenase from Drosophila melanogaster. Archives of Biochemistry and Biophysics, 1979. 194(2): p. 365-378.
7. Jörnvall, H., J. Hempel, and B. Vallee, Structures of Human Alcohol and Aldehyde Dehydrogenases. Enzyme, 1987. 37: p. 5-18.
8. Inoue, T., et al., Cloning and sequencing of the gene encoding the 72-kilodalton dehydrogenase subunit of alcohol dehydrogenase from Acetobacter aceti. 1989. 171(6): p. 3115-3122. 9. Doggett, N.A., et al., Complete Genome Sequence of Bacillus thuringiensis Serovar Israelensis Strain HD-78
9. Genome announcements, 2013. 1(6): p. e01023-13.
10. Méndez-López, I., R. Basurto-Ríos, and J.E. Ibarra, Bacillus thuringiensis serovar israelensis is highly toxic to the coffee berry borer, Hypothenemus hampei Ferr. (Coleoptera: Scolytidae). FEMS Microbiology Letters, 2003. 226(1): p. 73-77.
11. Çelik, A. and F. Aktaş, A new NADH-dependent, zinc containing alcohol dehydrogenase from Bacillus thuringiensis serovar israelensis involved in oxidations of short to medium chain primary alcohols. Journal of Molecular Catalysis B: Enzymatic, 2013. 89: p. 114-121.
12. Jörnvall, H., M. Landreh, and L.J. Östberg, Alcohol dehydrogenase, SDR and MDR structural stages, present update and altered era. ChemicoBiological Interactions, 2015. 234: p. 75-79.
13. Karlsson, A., et al., Tetrameric NAD-dependent alcohol dehydrogenase. Chemico-Biological Interactions, 2003. 143-144: p. 239-245.
14. Pruess, M. and R. Apweiler, Bioinformatics Resources for In Silico Proteome Analysis. J Biomed Biotechnol, 2003. 2003(4): p. 231-236.
15. Madeira, F., et al., The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic acids research, 2019. 47(W1): p. W636-W641.
16. Wilkins, M.R., et al., Protein identification and analysis tools in the ExPASy server. Methods in molecular biology (Clifton, N.J.), 1999.
17. Buchan, D.W.A. and D.T. Jones, The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Research, 2019. 47(W1): p. W402W407.
18. Zdobnov, E.M. and R. Apweiler, InterProScan – an integration platform for the signaturerecognition methods in InterPro. Bioinformatics, 2001. 17(9): p. 847-848.
19. Pagni, M., et al., MyHits: improvements to an interactive resource for analyzing protein sequences. Nucleic Acids Res, 2007. 35(Web Server issue): p. W433-7.
20. Taneja, B. and S.C. Mande, Conserved structural features and sequence patterns in the GroES fold family. Protein engineering, 1999. 12(10): p. 815818.
21. Jörnvall, H., et al., Origin and evolution of medium chain alcohol dehydrogenases. ChemicoBiological Interactions, 2013. 202(1): p. 91-96.
22. Tiwari, M.K., et al., Role of Conserved Glycine in Zinc-dependent Medium Chain Dehydrogenase/Reductase Superfamily*. Journal of Biological Chemistry, 2012. 287(23): p. 1942919439.
Published
2021-07-18
How to Cite
Aktas, F. (2021). In silico analysis of alcohol dehydrogenase from Bacillus thuringiensis serovar israelensis using bioinformatics tools. Journal of Engineering Research and Applied Science, 10(1), 1757-1763. Retrieved from http://www.journaleras.com/index.php/jeras/article/view/240
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