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Active Site Characterization of Proteases Sequences from Different Species of Aspergillus

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Abstract

A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

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References

  1. Rawlings, N. D., & Barrett, A. J. (1999). MEROPS: the peptidase database. Nucleic Acids Research, 27(1), 325–331.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Morya, V. K., Yadav, S., Kim, E. K., & Yadav, D. (2012). In silico characterization of alkaline proteases from different species of Aspergillus. Applied Biochemistry and Biotechnology, 166(1), 243–257.

    Article  CAS  PubMed  Google Scholar 

  3. Rawlings, N. D., Morton, F. R., & Barrett, A. J. (2007). In A. P. MacCabe & J. Polaina (Eds.), Industrial enzymes structure, function and applications (pp. 161–180). The Netherlands: Springer.

    Google Scholar 

  4. Rawlings, N. D., Barrett, A. J., & Bateman, A. (2010). MEROPS: the peptidase database. Nucleic Acids Research, 38, D227–D233.

    Article  CAS  PubMed  Google Scholar 

  5. Polgar, L. (2004). Catalytic mechanisms of serine and threonine peptidases. In A. J. Barrett, N. D. Rawlings, & J. F. Woessner (Eds.), Handbook of Proteolytic Enzymes (pp. 1440–1448). London: Elsevier.

    Google Scholar 

  6. James, M. N. G. (2004). Catalytic pathway of aspartic peptidases. In A. J. Barrett, N. D. Rawlings, & J. F. Woessner (Eds.), Handbook of proteolytic enzymes (pp. 12–19). London: Elsevier.

    Chapter  Google Scholar 

  7. Auld, D. (2004). Catalytic mechanisms of metallopeptidases. In A. J. Barrett, N. D. Rawlings, & J. F. Woessner (Eds.), Handbook of proteolytic enzymes (pp. 268–289). London: Elsevier.

    Chapter  Google Scholar 

  8. Gutteridge, A., Bartlett, G. J., & Thornton, J. M. (2003). Using a neural network and spatial clustering to predict the location of active sites in enzymes. Journal of Molecular Biology, 330, 719–734.

    Article  CAS  PubMed  Google Scholar 

  9. Shapiro, L., & Harris, T. (2000). Finding function through structural genomics. Current Opinion in Biotechnology, 11, 31–35.

    Article  CAS  PubMed  Google Scholar 

  10. Ofran, Y., Punta, M., Schneider, R., & Rost, B. (2005). Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery. Drug Discovery Today, 10, 1475–1482.

    Article  CAS  PubMed  Google Scholar 

  11. Bartlett, G. J., Porter, C. T., Borkakoti, N., & Thornton, J. M. (2002). Analysis of catalytic residues in enzyme active sites. Journal of Molecular Biology, 324, 105–121.

    Article  CAS  PubMed  Google Scholar 

  12. Chou, K. C., & Cai, Y. D. (2004). A novel approach to predict active sites of enzyme molecules. Proteins, 55, 77–82.

    Article  CAS  PubMed  Google Scholar 

  13. Todd, A. E., Orengo, C. A., & Thornton, J. M. (2001). Evolution of function in protein superfamilies, from a structural perspective. Journal of Molecular Biology, 307, 1113–1143.

    Article  CAS  PubMed  Google Scholar 

  14. Rost, B. (2002). Crystal structure of cleaved human α1-antichymotrypsin at 2.7 å resolution and its comparison with other serpins. Journal of Molecular Biology, 318, 595–608.

    Article  CAS  PubMed  Google Scholar 

  15. Tian, W., & Skolnick, J. (2003). How well is enzyme function conserved as a function of pairwise sequence identity? Journal of Molecular Biology, 333, 863–882.

    Article  CAS  PubMed  Google Scholar 

  16. Orengo, C. A., Todd, A. E., & Thornton, J. M. (1999). From protein structure to function. Current Opinion in Structural Biology, 9, 374–382.

    Article  CAS  PubMed  Google Scholar 

  17. Porter, C. T., Bartlett, G. J., & Thornton, J. M. (2004). The catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Research, 32, D129–D133.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Torrance, J. W., Bartlett, G. J., Porter, C. T., & Thornton, J. M. (2005). Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. Journal of Molecular Biology, 347, 565–581.

    Article  CAS  PubMed  Google Scholar 

  19. Zhang, Z., & Grigorov, M. (2006). Similarity networks of protein binding sites. Proteins Structure Function Genet, 62(2), 470–478.

    Article  CAS  Google Scholar 

  20. Zhang, Z., & Tang, Y. R. (2007). Genome-wide analysis of enzyme structure-function combination across three domains of life. Protein and Peptide Letters, 14, 291–297.

    Article  PubMed  Google Scholar 

  21. Yadav, P. K., Singh, V. K., Yadav, S., Yadav, K. D. S., & Yadav, D. (2009). In silico analysis of pectin lyases and pectinases based on protein sequences. Biochemistry (Moscow), 74, 1049–1055.

    Article  CAS  Google Scholar 

  22. Rao, M. B., Tanksale, A. M., Ghatge, M. S., & Deshpande, V. V. (1998). Molecular and biotechnological aspects of microbial proteases. Microbiology and Molecular Biology Reviews, 62, 597–635.

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Tamura, K., Dudley, J., Nei, M., & Kumar, S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596–1599.

    Article  CAS  Google Scholar 

  24. Rawlings, N. D., & Barrett, A. J. (1993). Evolutionary families of peptidases. Biochemical Journal, 290, 205–218.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Kato, I., Schrode, J., Kohr, W. J., & Laskowski, M. J. (1987). Chicken ovomucoid: determination of its amino acid sequence, determination of the trypsin reactive site, and preparation of all three of its domains. Biochemistry, 26, 193–201.

    Article  CAS  PubMed  Google Scholar 

  26. Laskar, A., Rodger, E. J., Chatterjee, A., & Mandal, C. (2012). Modeling and structural analysis of PA clan serine proteases. BMC Res Notes, 24(5), 256. doi:10.1186/1756-0500-5-256.

    Article  Google Scholar 

  27. Coates, L., Tuan, H. F., Tomanicek, S., Kovalevsky, A., Mustyakimov, M., Erskine, P., & Cooper, J. (2008). The catalytic mechanism of an aspartic proteinase explored with neutron and X-ray diffraction. Journal of the American Chemical Society, 130, 7235–7237.

    Article  CAS  PubMed  Google Scholar 

  28. Robbins, A. H., Dunn, B. M., Agbandje-McKenna, M., & McKenna, R. (2009). Crystallographic evidence for noncoplanar catalytic aspartic acids in plasmepsin II resides in the Protein Data Bank. Acta Crystallographica Section D: Biological Crystallography, 65, 294–296.

    Article  CAS  Google Scholar 

  29. Zou, Z., Lopez, D. L., Kanost, M. R., Evans, J. D., & Jiang, H. (2006). Comparative analysis of serine protease-related genes in the honey bee genome: possible involvement in embryonic development and innate immunity. Insect Molecular Biology, 15(5), 603–614.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

Authors VKM acknowledge the Inha University, Republic of Korea for providing the required assets and environment. Author SY and DY acknowledge the DDU Gorakhpur University Gorakhpur.

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Authors and Affiliations

  1. Department of Biological Engineering, Inha University, Incheon, 42-751, Republic of Korea

    V. K. Morya

  2. Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, 273009, India

    Sangeeta Yadav & Dinesh Yadav

  3. Department of Molecular and Cellular Engineering, SHIATS, Allahabad, India

    Virendra K. Yadav

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  1. V. K. Morya
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  2. Virendra K. Yadav
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  3. Sangeeta Yadav
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  4. Dinesh Yadav
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Correspondence to Dinesh Yadav.

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Morya, V.K., Yadav, V.K., Yadav, S. et al. Active Site Characterization of Proteases Sequences from Different Species of Aspergillus . Cell Biochem Biophys 74, 327–335 (2016). https://doi.org/10.1007/s12013-016-0750-9

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  • DOI: https://doi.org/10.1007/s12013-016-0750-9

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