1. bookVolume 6 (2022): Issue 1 (January 2022)
Journal Details
License
Format
Journal
eISSN
2543-8050
First Published
16 Jun 2017
Publication timeframe
1 time per year
Languages
English
Open Access

Bioinformatic Characterization of a Kappa-Carrageenase from Pseudomonas fluorescens

Published Online: 22 Oct 2022
Volume & Issue: Volume 6 (2022) - Issue 1 (January 2022)
Page range: 33 - 39
Received: 01 Sep 2022
Accepted: 01 Oct 2022
Journal Details
License
Format
Journal
eISSN
2543-8050
First Published
16 Jun 2017
Publication timeframe
1 time per year
Languages
English

1. Zhu, B., Ni, F., Sun, Y., Zhu, X., Yin, H., Yao, Z., & Du, Y. (2018). Insight into carrageenases: major review of sources, category, property, purification method, structure, and applications. Critical reviews in biotechnology, 38(8), 1261-1276. DOI: 10.1080/07388551.2018.1472550 Open DOISearch in Google Scholar

2. Zhao, Y., Chi, Z., Xu, Y., Shi, N., Chi, Z., & Liu, G. (2018). High-level extracellular expression of κ- carrageenase in Brevibacillus choshinensis for the production of a series of κ-carrageenan oligosaccharides. Process biochemistry, 64, 83-92. DOI: 10.1016/j.procbio.2017.09.013 Open DOISearch in Google Scholar

3. Chauhan, P. S., & Saxena, A. (2016). Bacterial carrageenases: an overview of production and biotechnological applications. 3 Biotech, 6(2), 1-18. DOI: 10.1007/s13205-016-0461-3 Open DOISearch in Google Scholar

4. Zhao, D., Jiang, B., Zhang, Y., Sun, W., Pu, Z., & Bao, Y. (2021). Purification and characterization of a cold-adapted κ-carrageenase from Pseudoalteromonas sp. ZDY3. Protein Expression and Purification, 178, 105768. DOI: 10.1016/j.pep.2020.105768 Open DOISearch in Google Scholar

5. Van de Velde, F., Knutsen, S., Usov, A., Rollema, H., & Cerezo, A. (2002). 1H and 13C high resolution NMR spectroscopy of carrageenans: application in research and industry. Trends in Food Science & Technology, 13(3), 73-92. DOI: 10.1016/S0924-2244(02)00066-3 Open DOISearch in Google Scholar

6. Kobayashi, T., Uchimura, K., Koide, O., Deguchi, S., & Horikoshi, K. (2012). Genetic and biochemical characterization of the Pseudoalteromonas tetraodonis alkaline κ-carrageenase. Bioscience, biotechnology, and biochemistry, 76(3), 506-511. DOI: 10.1271/bbb.11080922451392 Open DOISearch in Google Scholar

7. Bakli, M., Pașcalău, R., & Șmuleac, L. (2020). Rare Codon Analysis in Affecting Recombinant Protein Expression in. Advanced Research in Life Sciences, 4(1), 30-35. DOI: 10.2478/arls-2020-0015 Open DOISearch in Google Scholar

8. Bakli, M., Karim, L., Mokhtari-Soulimane, N., Merzouk, H., & Vincent, F. (2020). Biochemical characterization of a glycosyltransferase Gtf3 from Mycobacterium smegmatis: a case study of improved protein solubilization. 3 Biotech, 10(10), 1-13. DOI: 10.1007/s13205-020-02431-x749470232999813 Open DOISearch in Google Scholar

9. Rahimnahal, S., Shams, M., Tarrahimofrad, H., & Mohammadi, Y. (2020). Analysis to describe the catalytic critical residue of keratinase mojavensis using peptidase inhibitors: A docking-based bioinformatics study. J. Bas. Res. Med. Sci, 7, 13-28. Search in Google Scholar

10. NCBI Resource Coordinators. (2017). Database resources of the national center for biotechnology information. Nucleic acids research, 46(D1), D8-D13. DOI: 10.1093/nar/gkx1095575337229140470 Open DOISearch in Google Scholar

11. Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. The proteomics protocols handbook, 571-607. DOI: 10.1385/1-59259-890-0:57110.1385/1-59259-890-0:571 Search in Google Scholar

12. Geourjon, C., & Deleage, G. (1995). SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics, 11(6), 681-684. DOI: 10.1093/bioinformatics/11.6.681 Open DOISearch in Google Scholar

13. Arnold, K., Bordoli, L., Kopp, J., & Schwede, T. (2006). The SWISS-MODEL workspace: a web-based environment for protein structure homology modeling. Bioinformatics, 22(2), 195-201. DOI: 10.1093/bioinformatics/bti770 Open DOISearch in Google Scholar

14. Xu, D., & Zhang, Y. (2011). Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical journal, 101(10), 2525-2534. DOI: 10.1016/j.bpj.2011.10.024 Open DOISearch in Google Scholar

15. 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. Open DOISearch in Google Scholar

16. DeLano, W. (2019). The PyMOL Molecular Graphics System, version 2.3. 1. Schrodinger LLC: New York, NY, USA. Search in Google Scholar

17. Yu, C. S., Chen, Y. C., Lu, C. H., & Hwang, J. K. (2006). Prediction of protein subcellular localization. Proteins: Structure, Function, and Bioinformatics, 64(3), 643-651. DOI: 10.1002/prot.21018 Open DOISearch in Google Scholar

18. Roy, A., Yang, J., & Zhang, Y. (2012). COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic acids research, 40(W1), W471-W477. DOI: 10.1093/nar/gks372 Open DOISearch in Google Scholar

19. Szklarczyk, D., Gable, A.L., Nastou, K.C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N.T., Legeay, M., Fang, T., and Bork, P. (2021). The STRING database in 2021: customizable protein–protein networks, and functional characterization of useruploaded gene/measurement sets. Nucleic acids research, 49(D1), D605-D612. DOI: 10.1093/nar/gkaa1074 Open DOISearch in Google Scholar

20. Østgaard, K., Wangen, B., Knutsen, S., & Aasen, I. (1993). Large-scale production and purification of κ-carrageenase from Pseudomonas carrageenovora for applications in seaweed biotechnology. Enzyme and microbial technology, 15(4), 326-333. DOI: 10.1016/0141-0229(93)90159-Y Open DOISearch in Google Scholar

21. Ziayoddin, M., Lalitha, J., & Shinde, M. (2014). Increased production of carrageenase by Pseudomonas aeruginosa ZSL-2 using Taguchi experimental design. International Letters of Natural Sciences, 12(2). DOI: 10.18052/www.scipress.com/ILNS.17.19410.18052/www.scipress.com/ILNS.17.194 Search in Google Scholar

22. Khambhaty, Y., Mody, K., & Jha, B. (2007). Purification and characterization of κ-carrageenase from a novel γ-proteobacterium, Pseudomonas elongata (MTCC 5261) syn. Microbulbifer elongatus comb. Nov. Biotechnology and Bioprocess Engineering, 12(6), 668-675. DOI: 10.1007/BF02931084 Open DOISearch in Google Scholar

23. Ikai, A. (1980). Thermostability and aliphatic index of globular proteins. The Journal of Biochemistry, 88(6), 1895-1898. DOI: 10.1093/bioinformatics/11.6.681 Open DOISearch in Google Scholar

24. Nimrod, G., Glaser, F., Steinberg, D., Ben-Tal, N., & Pupko, T. (2005). In silico identification of functional regions in proteins. Bioinformatics, 21(suppl_1), i328-i337. DOI: 10.1093/bioinformatics/bti1023 Open DOISearch in Google Scholar

25. Viborg, A. H., Terrapon, N., Lombard, V., Michel, G., Czjzek, M., Henrissat, B., & Brumer, H. (2019). A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16). Journal of Biological Chemistry, 294(44), 15973-15986. DOI: 10.1074/jbc.RA119.010619 Open DOISearch in Google Scholar

26. Matard-Mann, M., Bernard, T., Leroux, C., Barbeyron, T., Larocque, R., Préchoux, Jeudy, A., Jam, A., Nyvall Collén, P., Michel, G., & Czjzek, M. (2017). Structural insights into marine carbohydrate degradation by family GH16 κ-carrageenases. Journal of Biological Chemistry, 292(48), 19919-19934. DOI: 10.1074/jbc.M117.808279 Open DOISearch in Google Scholar

27. Michel, G., Chantalat, L., Duee, E., Barbeyron, T., Henrissat, B., Kloareg, B., & Dideberg, O. (2001). The κ-carrageenase of P. carrageenovora features a tunnel-shaped active site: a novel insight in the evolution of Clan-B glycoside hydrolases. Structure, 9(6), 513-525. DOI: 10.1016/S0969-2126(01)00612-8. Open DOISearch in Google Scholar

Recommended articles from Trend MD

Plan your remote conference with Sciendo