Three Dimensional Structural Modelling of Lipase Encoding Gene from Soil Bacterium Alcaligenes sp. JG3 Using Automated Protein Homology Analysis

https://doi.org/10.22146/ijc.34152

Dilin Rahayu Nataningtyas(1), Tri Joko Raharjo(2*), Endang Astuti(3)

(1) Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara BLS 21, Bulaksumur, Yogyakarta 55281, Indonesia
(2) Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara BLS 21, Bulaksumur, Yogyakarta 55281, Indonesia
(3) Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara BLS 21, Bulaksumur, Yogyakarta 55281, Indonesia
(*) Corresponding Author

Abstract


Bacterial lipases have significant potential to be used as the biocatalyst for many chemical reactions. In this study, a novel gene encoding lipase was isolated from an Alcaligenes sp. JG3. A pair of designed primer has successfully isolated 1 kb (LipJG3) that shares 98% identity towards lipase from Alcaligenes faecalis during sequence analysis. By using in silico tools, LipJG3 was related to the transporter protein sequences. Three highly conserved regions consisting of EASGSKT, VILLD, and LSGGQQQRVAIA were found. These regions were known as ATP-binding signature at Walker-A and Walker-B motifs and the S signature of ABC transporter family respectively. In addition, the 3-D structure of LipJG3 has been suggested but the role of the catalytic triad residues have been not fully understood.

Keywords


Alcaligenes; lipase gene; LipJG3; ABC transporter protein

Full Text:

Full Text PDF


References

[1] Gupta, R., Gupta, N., and Rathi, P., 2004, Bacterial lipases: An overview of production, purification and biochemical properties, Appl. Microbiol. Biotechnol., 64 (6), 763–781.

[2] Salihu, A., and Alam, Z., 2015, Solvent tolerant lipases: A review, Process Biochem., 50 (1), 86–96.

[3] Angajala, G., Pavan, P., and Subashini, R., 2016, Biocatalysis and agricultural biotechnology lipases: An overview of its current challenges and prospectives in the revolution of biocatalysis, Biocatal. Agric. Biotechnol., 7 (C), 257–270.

[4] Fischer, M., and Pleiss, J., 2003, The lipase engineering database: A navigation and analysis tool for protein families, Nucleic Acids Res., 31 (1), 319–321.

[5] Jaeger, K.E., Dijkstra, B.W., and Reetz, M.T., 1999, Bacterial biocatalysts: Molecular biology, three-dimensional structures, and biotechnological applications of lipases, Annu. Rev. Microbiol., 53, 315–351.

[6] Hasan, F., Shah, A.A., and Hameed, A., 2006, Industrial applications of microbial lipases, Enzyme Microb. Technol., 39 (2), 235–251.

[7] Aravindan, R., Anbumathi, P., and Viruthagiri, T., 2007, Lipase applications in food industry, Indian J. Biotechnol., 6 (2), 141–158.

[8] Nurosid, Oedjijono, and Lestari, P., 2008, Kemampuan Azospirillum sp. JG3 dalam menghasilkan lipase pada medium campuran dedak dengan waktu inkubasi berbeda, Molekul, 3, 1–12.

[9] Raharjo, T.J., Haryono, N.Y., Nataningtyas, D.R., Alfiraza, E.N., and Pranowo, D., 2016, Characterization of lipase gene fragment from Alcaligenes sp. JG3 bacterium, Am. J. Biochem. Mol. Biol., 6 (2), 45–52.

[10] Kaur, G., Singh, A., Sharma, R., Sharma, V., Verma, S., and Sharma, P.K., 2016, Cloning, expression, purification and characterization of lipase from Bacillus licheniformis, isolated from hot spring of Himachal Pradesh, 3 Biotech, 6 (1), 49.

[11] Kumar, S., Stecher, G., and Tamura, K., 2016, MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets, Mol. Biol. Evol., 33 (7), 1870–1874.

[12] Nataningtyas, D.R., 2017, Molecular characterization of lipase gene from Alcaligenes sp. JG3 bacterium, Thesis, Universitas Gadjah Mada, Yogyakarta, Indonesia.

[13] Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T.G., Bertoni, M., Bordoli, L., and Schwede, T., 2014, SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information, Nucleic Acids Res., 42, 252–258.

[14] Kelley, L.A., Mezulis, S., Yates, C.M., Wass, M.N., and Sternberg, M.J., 2015, The Phyre2 web portal for protein modeling, prediction and analysis, Nat. Protoc., 10 (6), 845–858.

[15] Chen, V.B., Arendall, W.B., Headd, J.J., Keedy, D.A., Immormino, R.M., Kapral, G.J., Murray, L.W., Richardson, J.S., and Richardson, D.C., 2010, MolProbity: All-atom structure validation for macromolecular crystallography, Acta Crystallogr., Sect. D: Biol. Crystallogr., 66 (Pt 1), 12–21.

[16] Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E., 2004, UCSF Chimera–a visualization system for exploratory research and analysis, J. Comput. Chem., 25 (13), 1605–1612.

[17] Lestari, P., Handayani, S.N., and Oedjijono, 2009, Sifat-sifat biokimiawi ekstrak kasar lipase ekstraseluler dari bakteri Azospirillum sp. JG3, Molekul, 4, 73–82.

[18] Vashishth, A., and Tehri, N., 2015, The role of recombinant DNA technology for human welfare, Int. J. Res. Biol. Sci., 5 (4), 35–39.

[19] Ethica, S.N., 2014, Detection of genes involved in glycerol metabolism of Alcaligenes sp. JG3, Dissertation, Universitas Gadjah Mada, Yogyakarta, Indonesia.

[20] Drancourt, M., and Raoult, D., 2005, Sequence-based identification of new Bacteria: A proposition for creation of an orphan bacterium repository, J. Clin. Microbiol., 43 (9), 4311–4315.

[21] Kim, M., Oh, H., Park, S., and Chun, J., 2014, Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes, Int. J. Syst. Evol. Microbiol., 64 (Pt 2), 346–351.

[22] Bell, P.J., Sunna, A., Gibbs, M.D., Curach, N.C., Nevalainen, H., and Bergquist, P.L., 2002, Prospecting for novel lipase genes using PCR, Microbiology, 148 (Pt 8), 2283–2291.

[23] Voget, S., Leggewie, C., Uesbeck, A., Raasch, C., Jaeger, K., and Streit, W.R., 2003, Prospecting for novel biocatalysts in a soil metagenome, Appl. Environ. Microbiol., 69 (10), 6235–6242.

[24] Wong, H., and Schotz, M.C., 2002, The lipase gene family, J. Lipid Res., 43 (7), 993–999.

[25] Berezin, C., Glaser, F., Rosenberg, J., Paz, I., Pupko, T., Fariselli, P., Casadio, R., and Ben-Tal, N., 2004, ConSeq: The identification of functionally and structurally important residues in protein sequences, Bioinformatics, 20 (8), 1322–1324.

[26] Cygler, M., Schrag, J.D., Sussman, J.L., Harel, M., Silman, I., Gentry, M.K., and Doctor, B.P., 1993, Relationship between sequence conservation and three-dimensional structure in a large family of esterases, lipases, and related proteins, Protein Sci., 2 (3), 366–382.

[27] Li, X., Tetling, S., Winkler, U.K., Jaeger, K., and Benedik, M.J., 1995, Gene cloning, sequence analysis, purification, and secretion by Escherichia coli of an extracellular lipase from Serratia marcescens, Appl. Microbiol. Biotechnol., 61 (7), 2674–2680.

[28] Park, Y., Moon, Y., Ryoo, J., Kim, N., Cho, H., and Ahn, J.H., 2012, Identification of the minimal region in lipase ABC transporter recognition domain of Pseudomonas fluorescens for secretion and fluorescence of green fluorescent protein, Microb. Cell Fact., 11, 60.

[29] Orelle, C., Dalmas, O., Gros, P., Di Pietro, A., and Jault, J.M., 2003, The conserved glutamate residue adjacent to the Walker-B motif is the catalytic base for ATP hydrolysis in the ATP-binding cassette transporter BmrA, J. Biol. Chem., 278 (47), 47002–47008.

[30] Ahn, J.H., Pan, J.G., and Rhee, J.S., 1999, Identification of the tliDEF ABC transporter specific for lipase in Pseudomonas fluorescens SIK W1, J. Bacteriol., 181 (6), 1847–1852.

[31] Binet, R., Létoffé, S., Ghigo, J.M., and Delepelaire, P., and Wandersman, C., 1997, Protein secretion by Gram-negative bacterial ABC exporters - A review, Gene, 192 (1), 7–11.

[32] Ahn, J.H., Pan, J.G., and Rhee, J.S., 2001, Homologous expression of the lipase and ABC transporter gene cluster, tliDEFA, enhances lipase secretion in Pseudomonas spp., Appl. Environ. Microbiol., 67 (12), 5506–5511.

[33] Arpigny, J.L., and Jaeger, K.E., 1999, Bacterial lipolytic enzymes: Classification and properties, Biochem. J., 343 (Pt 1), 177–183.

[34] Muneyuki, E., Noji, H., Amano, T., Masaike, T., and Yoshida, M., 2000, F0F1-ATP synthase: General structural features of 'ATP-engine' and a problem on free energy transduction, Biochim. Biophys. Acta, 1458, 467–481.

[35] Yuan, Y., Blecker, S., Martsinkevich, O., Millen, L., Thomas, P.J., and Hunt, J.F., 2001, The crystal structure of the MJ0796 ATP-binding cassette, implications for the structural consequences of ATP hydrolysis in the active site of an the ATP-bound form of the HisP ATP-binding cassette, J. Biol. Chem., 276 (34), 32313–32321.

[36] Wilkens, S., 2015, Structure and mechanism of ABC transporters, F1000Prime Rep., 7, 14.



DOI: https://doi.org/10.22146/ijc.34152

Article Metrics

Abstract views : 919 | views : 753


Copyright (c) 2019 Indonesian Journal of Chemistry

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

 


Indonesian Journal of Chemisty (ISSN 1411-9420 / 2460-1578) - Chemistry Department, Universitas Gadjah Mada, Indonesia.

Web
Analytics View The Statistics of Indones. J. Chem.