References
- Aghajari, N., Feller, G., Gerday, C., & Haser, R. (1998). Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor. Protein Science : Science, 7(3), 564–572. doi:10.1002/pro.5560070304
- Bahri, S. M., & Ward, J. M. (1990). Cloning and expression of an alpha-amylase gene from Streptomyces thermoviolaceus CUB74 in Escherichia coli JM107 and S. lividans TK24. Journal of General Microbiology, 136(5), 811–818. doi:10.1099/00221287-136-5-811
- Baneyx, F., & Mujacic, M. (2004). Recombinant protein folding and misfolding in Escherichia coli. Nature Biotechnology, 22(11), 1399–1408. doi:10.1038/nbt1029
- Bano, S., Qader, S. A. U., Aman, A., Syed, M. N., & Azhar, A. (2011). Purification and characterization of novel alpha amylase from Bacillus subtilis KIBGE HAS. AAPS Pharmscitech, 12(1), 255–261. doi:10.1208/s12249-011-9586-1
- Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. F., Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977). The Protein Data Bank: A computer-based archival file for macromolecular structures. Journal of Molecular Biology, 112(3), 535–542. doi:10.1016/S0022-2836(77)80200-3
- Chakraborty, S., Khopade, A., Kokare, C., Mahadik, K., & Chopade, B. (2009). Isolation and characterization of novel α-amylase from marine Streptomyces sp. D1. Journal of Molecular Catalysis B: Enzymatic, 58(1-4), 17–23. doi:10.1016/j.molcatb.2008.10.011
- Chinthakunta, N., Cheemanapalli, S., Chinthakunta, S., Anuradha, C. M., & Chitta, S. K. (2018). A new insight into identification of in silico analysis of natural compounds targeting GPR120. Network Modeling and Analysis in Health Informatics and Bioinformatics, 7(1), 8. doi:10.1007/s13721-018-0166-0
- Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science : Science, 2(9), 1511–1519. doi:10.1002/pro.5560020916
- Da Lage, J. L., Maczkowiak, F., & Cariou, M. L. (2000). Molecular characterization and evolution of the amylase multigene family of Drosophila ananassae. Journal of Molecular Evolution, 51(4), 391–403. doi:10.1007/s002390010102
- DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40(1), 82–92.
- Eswar, N., Webb, B., Marti‐Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M. Y., Pieper, U., & Sali, A. (2006). Comparative protein structure modeling using Modeller. Current Protocols in Bioinformatics, 15(1), 5.6.1–6. doi:10.1002/0471250953.bi0506s15
- Fang, T. Y., Tseng, W. C., Shih, T. Y., & Wang, M. Y. (2008). Identification of the essential catalytic residues and selectivity-related residues of maltooligosyltrehalose trehalohydrolase from the thermophilic archaeon Sulfolobus solfataricus ATCC 35092. Journal of Agricultural and Food Chemistry, 56(14), 5628–5633. doi:10.1021/jf073320b
- Ganugapati, J., & Akash, S. (2017). Multi-template homology based structure prediction and molecular docking studies of protein ‘L’of Zaire ebolavirus (EBOV). Informatics in Medicine Unlocked, 9, 68–75. doi:10.1016/j.imu.2017.06.002
- Gramany, V., Khan, F. I., Govender, A., Bisetty, K., Singh, S., & Permaul, K. (2016). Cloning, expression, and molecular dynamics simulations of a xylosidase obtained from Thermomyces lanuginosus. Journal of Biomolecular Structure & Dynamics, 34(8), 1681–1692. doi:10.1080/07391102.2015.1089186
- Green Michael, R., & Sambrook, J. (2012). Molecular cloning: A laboratory manual (4th ed.). Cold Spring Harb.
- Hagenbüchle, O., Bovey, R., & Young, R. A. (1980). Tissue-specific expression of mouse α-amylase genes: Nucleotide sequence of isoenzyme mRNAs from pancreas and salivary gland. Cell, 21(1), 179–187. doi:10.1016/0092-8674(80)90125-7
- Hickey, D. A., Benkel, B. F., Boer, P. H., Genest, Y., Abukashawa, S., & Ben-David, G. (1987). Enzyme-coding genes as molecular clocks: The molecular evolution of animal alpha-amylases. Journal of Molecular Evolution, 26(3), 252–256. doi:10.1007/BF02099856
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–33. doi:10.1016/0263-7855(96)00018-5
- Hwang, S. Y., Nakashima, K., Okai, N., Okazaki, F., Miyake, M., Harazono, K., Ogino, C., & Kondo, A. (2013). Thermal stability and starch degradation profile of α-amylase from Streptomyces avermitilis. Bioscience Biotechnology Biochemistry, 77(12), 2449–2453. doi:10.1271/bbb.130556
- Ikai, A. (1980). Thermostability and aliphatic index of globular proteins. Journal of Biochemistry, 88(6), 1895–1898. doi:10.1093/oxfordjournals.jbchem.a133168
- Janeček, Š. (2002). How many conserved sequence regions are there in the α-amylase family. Biologia, 57(Suppl 11), 29–41.
- Janeček, Š., & Gabriško, M. (2016). Remarkable evolutionary relatedness among the enzymes and proteins from the α-amylase family. Cellular and Molecular Life Sciences, 73(14), 2707–2725. doi:10.1007/s00018-016-2246-6
- Janeček, Š., Mareček, F., MacGregor, E. A., & Svensson, B. (2019). Starch-binding domains as CBM families–history, occurrence, structure, function and evolution. Biotechnology Advances, 37(8), 107451. doi:10.1016/j.biotechadv.2019.107451
- Janeček, Š., & Ševčı́k, J. (1999). The evolution of starch-binding domain. FEBS Letters, 456(1), 119–125. doi:10.1016/S0014-5793(99)00919-9
- Janeček, S., Svensson, B., & MacGregor, E. A. (2003). Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain. European Journal of Biochemistry, 270(4), 635–645. doi:10.1046/j.1432-1033.2003.03404.x
- Janeček, Š., Svensson, B., & MacGregor, E. A. (2014). α-Amylase: An enzyme specificity found in various families of glycoside hydrolases. Cellular and Molecular Life Sciences : CMLS, 71(7), 1149–1170. doi:10.1007/s00018-013-1388-z
- Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118(45), 11225–11236. doi:10.1021/ja9621760
- Kar, S., Swain, M. R., & Ray, R. C. (2009). Statistical optimization of alpha-amylase production with immobilized cells of Streptomyces erumpens MTCC 7317 in Luffa cylindrica L. sponge discs. Applied Biochemistry and Biotechnology, 152(2), 177–188. https://doi:10.1007/s12010-008-8248-6 doi:10.1007/s12010-008-8248-6
- Knegtel, R. M., Strokopytov, B., Penninga, D., Faber, O. G., Rozeboom, H. J., Kalk, K. H., Dijkhuizen, L., & Dijkstra, B. W. (1995). Crystallographic studies of the interaction of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 with natural substrates and products. The Journal of Biological Chemistry, 270(49), 29256–29264. doi:10.1074/jbc.270.49.29256
- Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870–1874. doi:10.1093/molbev/msw054
- Laemmli, U. K. (1970). Cleavage of structural proteins during the assembly of the head of the bacteriophage T4. Nature, 227(5259), 680–685. doi:10.1038/227680a0
- Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. doi:10.1107/S0021889892009944
- Long, C. M., Virolle, M. J., Chang, S. Y., Chang, S. H., & Bibb, M. J. (1987). Alpha-Amylase gene of Streptomyces limosus: Nucleotide sequence, expression motifs, and amino acid sequence homology to mammalian and invertebrate alpha-amylases. Journal of Bacteriology, 169(12), 5745–5754. doi:10.1128/JB.169.12.5745-5754.1987
- Lüthy, R., Bowie, J. U., & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356(6364), 83–85. doi:10.1038/356083a0
- MacDonald, R. J., Crerar, M. M., Swain, W. F., Pictet, R. L., Thomas, G., & Rutter, W. J. (1980). Structure of a family of rat amylase genes. Nature, 287(5778), 117–122. doi:10.1038/287117a0
- Manteca, A., & Yagüe, P. (2019). Antimicrobials, Antibiotic Resistance, Antibiofilm Strategies and Activity Methods, Streptomyces as a Source of Antimicrobials: Novel Approaches to Activate Cryptic Secondary Metabolite Pathways (Kırmusaoğlu, S., Ed.). IntechOpen.
- Marchler-Bauer, A., Bo, Y., Han, L., He, J., Lanczycki, C. J., Lu, S., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., Gwadz, M. (2016). CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Research, 45(D1), D200–D203. https://doi:10.1093/nar/gkw1129 doi:10.1093/nar/gkw1129
- Martínez, L. (2015). Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PloS One, 10(3), e0119264. doi:10.1371/journal.pone.0119264
- Mellouli, L., Ghorbel, R., Kammoun, A., Mezghani, M., & Bejar, S. (1996). Characterization and molecular cloning of thermostable alpha-amylase from Streptomyces sp. Biotechnology Letters, 18(7), 809–814. doi:10.1007/BF00127894
- Nanthini, J., Chia, K. H., Thottathil, G. P., Taylor, T. D., Kondo, S., Najimudin, N., Baybayan, P., Singh, S., & Sudesh, K. (2015). Complete genome sequence of Streptomyces sp. strain CFMR 7, a natural rubber degrading actinomycete isolated from Penang. Journal of Biotechnology, 214(20), 47–48. doi:10.1016/j.jbiotec.2015.09.007
- Ohdan, K., Kuriki, T., Takata, H., Kaneko, H., & Okada, S. (2000). Introduction of raw starch-binding domains into Bacillus subtilis alpha-amylase by fusion with the starch-binding domain of Bacillus cyclomaltodextrin glucanotransferase. Applied and Environmental Microbiology, 66(7), 3058–3064. doi:10.1128/AEM.66.7.3058-3064.2000
- O'Neill, S. D., Kumagai, M. H., Majumdar, A., Huang, N., Sutliff, T. D., & Rodriguez, R. L. (1990). The α-amylase genes in Oryza sativa: Characterization of cDNA clones and mRNA expression during seed germination. Molecular and General Genetics Mgg, 221(2), 235–244. doi:10.1007/BF00261726
- Pandey, A., Nigam, P., Soccol, C. R., Soccol, V. T., Singh, D., & Mohan, R. (2000). Advances in microbial amylases. Biotechnology and Applied Biochemistry, 31(2), 135–152. doi:10.1042/BA19990073
- Pasero, L., Mazzéi-Pierron, Y., Abadie, B., Chicheportiche, Y., & Marchis-Mouren, G. (1986). Complete amino acid sequence and location of the five disulfide bridges in porcine pancreatic α-amylase. Biochimica et Biophysica Acta (Bba) - Protein Structure and Molecular Enzymology, 869(2), 147–157. doi:10.1016/0167-4838(86)90289-X
- Perlman, D., & Halvorson, H. O. (1983). A putative signal peptidase recognition site and sequence in eukaryotic and prokaryotic signal peptides. Journal of Molecular Biology, 167(2), 391–409. doi:10.1016/S0022-2836(83)80341-6
- Pospiech, A., & Neumann, B. (1995). A versatile quick-prep of genomic DNA from gram-positive bacteria. Trends in Genetics : Tig, 11(6), 217–218. doi:10.1016/S0168-9525(00)89052-6
- Sefidbakht, Y., Ranaei Siadat, O., & Taheri, F. (2017). Homology modeling and molecular dynamics study on Schwanniomyces occidentalis alpha-amylase. Journal of Biomolecular Structure and Dynamics, 35(3), 574–584. doi:10.1080/07391102.2016.1154892
- Shiburaj, S., & Abraham, T. K. (2002). Studies on the optimisation of cultural conditions of a strain of Streptomyces setonii (19 NRA1) for antibiotic production. Journal of Mycopathological Research, 40(2), 181–184.
- Strobl, S., Gomis-Rüth, F. X., Maskos, K., Frank, G., Huber, R., & Glockshuber, R. (1997). The α‐amylase from the yellow meal worm: Complete primary structure, crystallization and preliminary X‐ray analysis. FEBS Letters, 409(1), 109–114. doi:10.1016/S0014-5793(97)00451-1
- Syed, D. G., Agasar, D., & Pandey, A. (2009). Production and partial purification of α-amylase from a novel isolate Streptomyces gulbargensis. Journal of Industrial Microbiology & Biotechnology, 36(2), 189–194. doi:10.1007/s10295-008-0484-9
- Takahiro, N., Yusuke, N., Mitsuru, E., Tatsuo, Y., Michio, O., Takesada, M., & Kenichi, M. (1986). Primary structure of human salivary α-amylase gene. Gene, 41(2-3), 299–304. doi:10.1016/0378-1119(86)90110-1
- Takkinen, K., Pettersson, R. F., Kalkkinen, N., Palva, I., Söderlund, H., & Kääriäinen, L. (1983). Amino acid sequence of alpha-amylase from Bacillus amyloliquefaciens deduced from the nucleotide sequence of the cloned gene. The Journal of Biological Chemistry, 258(2), 1007–1013. doi:10.1016/0378-1119(81)90103-7
- Tsao, L. S., Lin, L. L., Chen, J. C., Chen, J. H., & Hsu, W. H. (1993). Cloning and characterization of an α-amylase gene from Streptomyces lividans. Biochimica et Biophysica Acta (Bba) - Gene Structure and Expression, 1171(3), 255–262. doi:10.1016/0167-4781(93)90063-J
- Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. doi:10.1002/jcc.20291
- Vigal, T., Gil, J. A., Daza, A., García-González, M. D., & Martín, J. F. (1991). Cloning, characterization and expression of an α-amylase gene from Streptomyces griseus IMRU3570. Molecular & General Genetics : Mgg, 225(2), 278–288. doi:10.1007/BF00269860
- Virolle, M. J., & Bibb, M. J. (1988). Cloning, characterization and regulation of an α‐amylase gene from Streptomyces limosus. Molecular Microbiology, 2(2), 197–208. doi:10.1111/j.1365-2958.1988.tb00021.x
- Virolle, M. J., Long, C. M., Chang, S., & Bibb, M. J. (1988). Cloning, characterisation and regulation of an α-amylase gene from Streptomyces venezuelae. Gene, 74(2), 321–334. doi:10.1016/0378-1119(88)90166-7
- Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407–W410. doi:10.1093/nar/gkm290
- Yang, M., Galizzi, A., & Henner, D. (1983). Nucleotide sequence of the amylase gene from Bacillus subtilis. Nucleic Acids Research, 11(2), 237–250. doi:10.1093/nar/11.2.237
- Yin, X. H., Gagnat, J., Gerbaud, C., Guérineau, M., & Virolle, M. J. (1997). Cloning and characterization of a new alpha-amylase gene from Streptomyces lividans TK24. Gene, 197(1-2), 37–45. doi:10.1016/S0378-1119(97)00231-X
- Yuukt, T., Nomura, T., Tezuka, H., Tsuboi, A., Yamagata, H., Tsukagoshi, N., & Udaka, S. (1985). Complete nucleotide sequence of a gene coding for heat-and pH-stable α-amylase of Bacillus licheniformis: Comparison of the amino acid sequences of three bacterial liquefying α-amylases deduced from the DNA sequences. The Journal of Biochemistry, 98(5), 1147–1156. doi:10.1093/oxfordjournals.jbchem.a135381