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Research article

References

  1. Boonserm, P., M. Mo, C. Angsuthanasombat, and J. Lescar. 2006. Structure of the functional form of the mosquito larvicidal Cry4Aa toxin from Bacillus thuringiensis at a 2.8-angstrom resolution. J. Bacteriol. 188: 3391-3401.
    Pubmed PMC CrossRef
  2. Boonserm, P., P. Davis, D. J. Ellar, and J. Li. 2005. Crystal structure of the mosquito-larvicidal toxin Cry4Ba and its biological implications. J. Mol. Biol. 348: 363-382.
    Pubmed CrossRef
  3. Chen, X. J., M. K. Lee, and D. H. Dean. 1993. Site-directed mutations in a highly conserved region of Bacillus thuringiensis δ-endotoxin affect inhibition of short circuit current across Bombyx mori midgets. Proc. Natl. Acad. Sci. USA 90: 9041-9045.
    CrossRef
  4. Derbyshire, D. J., D. J. Ellar, and J. Li. 2001. Crystallization of the Bacillus thuringiensis toxin Cry1Ac and its complex with the receptor ligand N-acetyl-D-galactosamine. Acta Crystallogr. D 57: 1938-1944.
    CrossRef
  5. Galitsky, N., V. Cody, A. Wojtczak, D. Ghosh, J. R. Luft, W. Pangborn, and L. English. 2001. Structure of the insecticidal bacterial δ-endotoxin Cry3Bb1 of Bacillus thuringiensis. Acta Crystallogr. D 57: 1101-1109.
    CrossRef
  6. Gazit, E., P. La Rocca, M. S. P. Sansom, and Y. Shai. 1998. The structure and organization within the membrane of the helices composing the pore-forming domain of Bacillus thuringiensis δendotoxin are consistent with an “umbrella-like” structure of the pore. Proc. Natl. Acad. Sci. USA 95: 12289-12294.
    CrossRef
  7. Gutierrez, P., O. Alzate, and S. A. Orduz. 2001. A theoretical model of the tridimensional structure of Bacillus thuringiensis subsp. medellin Cry11Bb toxin deduced by homology modeling. Mem. Inst. Oswaldo Cruz 96: 357-364.
    CrossRef
  8. Hofmann, C., H. Vanderbruggen, H. Hofte, and H. Van Mellaert. 1988. Specificity of Bacillus thuringiensis delta-endotoxins is correlated with the presence of high-affinity binding sites in the brush border membrane of target insect midgets. Proc. Natl. Acad. Sci. USA 85: 7844-7848.
    CrossRef
  9. Knowles, B. H. and D. J. Ellar. 1987. Colloid osmotic lysis is a general feature of the mechanism of action of Bacillus thuringiensis delta-endotoxins with different insect specificities. Biochim. Biophys. Acta 924: 509-518.
    CrossRef
  10. Kumar, A. S. M. and A. I. Aronson. 1999. Analysis of mutations in the pore-forming region essential for insecticidal activity of a Bacillus thuringiensis δ-endotoxin. J. Bacteriol. 181: 6103-6107.
    Pubmed PMC
  11. Laskowski, R. A., M. W. MacArthur, D. S. Moss, and J. M. Thornton. 1993. PROCHECK: A program to check the stereo chemical quality of protein structures. J. Appl. Cryst. 26: 283-291.
    CrossRef
  12. Li, J., J. Carroll, and D. J. Ellar. 1991. Crystal structures of insecticidal δ-endotoxin from Bacillus thuringiensis at 2.5 Åresolutions. Nature 353: 815-821.
    Pubmed CrossRef
  13. Lovell, S. C., I. W. Davis, W. B. Arendall III, P. I. W. de Bakker, J. M. Word, M. G. Prisant, et al. 2002. Structure validation by C alpha geometry: Phi, psi and C beta deviation. Proteins 50: 437-450
    Pubmed CrossRef
  14. Min, Z. X., X. L. Qui, D. X. Zhi, and W. F. Xiang. 2009. The theoretical three-dimensional structure of Bacillus thuringiensis Cry5Aa and its biological implications. Protein J. 28: 104-110.
    Pubmed CrossRef
  15. Morse, R. J., T. Yamamoto, and R. M. Stroud. 2001. Structure of Cry2Aa suggests an unexpected receptor binding epitope. Structure 9: 409-417.
    CrossRef
  16. Sali, A., L. Potterton, F. Yuan, H. van Vlijmen and M. Karplus. 1995. Evaluation of comparative protein modeling by MODELLER. Proteins 23: 318-326.
    Pubmed CrossRef
  17. Schnepf, E., N. Crickmore, J. van Rie, D. Lereclus, J. Baum, J. Feitelson, et al. 1998. Bacillus thuringiensis and its pesticidal crystal proteins. Microbiol. Mol. Biol. Rev. 62: 772-806.
  18. Schwartz, J. L., L. Potvin, X. J. Chen, R. Brousseau, R. Laprade, and D. H. Dean. 1997. Single-site mutations in the conserved alternating-arginine region affect ion channels formed by CryIAa, a Bacillus thuringiensis toxin. Appl. Environ. Microbiol. 63: 3978-3984.
    Pubmed PMC
  19. Xia, L. Q., X. M. Zhao, X. Z. Ding, F. X. Wang, and Y. J. Sun. 2008. The theoretical 3D structure of Bacillus thuringiensis Cry5Ba. J. Mol. Model. 14: 843-848.
    Pubmed CrossRef

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Article

Research article

J. Microbiol. Biotechnol. 2012; 22(6): 788-792

Published online June 28, 2012 https://doi.org/10.4014/jmb.1106.06034

Copyright © The Korean Society for Microbiology and Biotechnology.

Computational Tridimensional Protein Modeling of Cry1Ab19 Toxin from Bacillus thuringiensis BtX-2

Sudhanshu Kashyap 1*, B. D. Singh 2 and D. V. Amla 3

1National Bureau of Agriculturally Important Microorganisms (ICAR), Kusmaur, Kaithauli, Mau Nath Bhanjan-275101, (U. P.) India, 2School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi 221005, (U. P.) India, 3Molecular Biology and Genetic Engineering Division, National Botanical Research Institute, Rana Pratap Marg, P.B. #436, Lucknow 226001, (U. P.) India

Received: June 15, 2011; Accepted: February 2, 2012

Abstract

We report the computational structural simulation of the
Cry1Ab19 toxin molecule from B. thuringiensis BtX-2
based on the structure of Cry1Aa1 deduced by x-ray
diffraction. Validation results showed that 93.5% of
modeled residues are folded in a favorable orientation
with a total energy Z-score of -8.32, and the constructed
model has an RMSD of only 1.13Å. The major differences
in the presented model are longer loop lengths and
shortened sheet components. The overall result supports
the hierarchical three-domain structural hypothesis of
Cry toxins and will help in better understanding the
structural variation within the Cry toxin family along with
facilitating the design of domain-swapping experiments
aimed at improving the toxicity of native toxins.

Keywords: Three-dimensional structure, Homology modeling, Cry1Ab19, Bacillus thuringiensis BtX-2, third part annotation

References

  1. Boonserm, P., M. Mo, C. Angsuthanasombat, and J. Lescar. 2006. Structure of the functional form of the mosquito larvicidal Cry4Aa toxin from Bacillus thuringiensis at a 2.8-angstrom resolution. J. Bacteriol. 188: 3391-3401.
    Pubmed KoreaMed CrossRef
  2. Boonserm, P., P. Davis, D. J. Ellar, and J. Li. 2005. Crystal structure of the mosquito-larvicidal toxin Cry4Ba and its biological implications. J. Mol. Biol. 348: 363-382.
    Pubmed CrossRef
  3. Chen, X. J., M. K. Lee, and D. H. Dean. 1993. Site-directed mutations in a highly conserved region of Bacillus thuringiensis δ-endotoxin affect inhibition of short circuit current across Bombyx mori midgets. Proc. Natl. Acad. Sci. USA 90: 9041-9045.
    CrossRef
  4. Derbyshire, D. J., D. J. Ellar, and J. Li. 2001. Crystallization of the Bacillus thuringiensis toxin Cry1Ac and its complex with the receptor ligand N-acetyl-D-galactosamine. Acta Crystallogr. D 57: 1938-1944.
    CrossRef
  5. Galitsky, N., V. Cody, A. Wojtczak, D. Ghosh, J. R. Luft, W. Pangborn, and L. English. 2001. Structure of the insecticidal bacterial δ-endotoxin Cry3Bb1 of Bacillus thuringiensis. Acta Crystallogr. D 57: 1101-1109.
    CrossRef
  6. Gazit, E., P. La Rocca, M. S. P. Sansom, and Y. Shai. 1998. The structure and organization within the membrane of the helices composing the pore-forming domain of Bacillus thuringiensis δendotoxin are consistent with an “umbrella-like” structure of the pore. Proc. Natl. Acad. Sci. USA 95: 12289-12294.
    CrossRef
  7. Gutierrez, P., O. Alzate, and S. A. Orduz. 2001. A theoretical model of the tridimensional structure of Bacillus thuringiensis subsp. medellin Cry11Bb toxin deduced by homology modeling. Mem. Inst. Oswaldo Cruz 96: 357-364.
    CrossRef
  8. Hofmann, C., H. Vanderbruggen, H. Hofte, and H. Van Mellaert. 1988. Specificity of Bacillus thuringiensis delta-endotoxins is correlated with the presence of high-affinity binding sites in the brush border membrane of target insect midgets. Proc. Natl. Acad. Sci. USA 85: 7844-7848.
    CrossRef
  9. Knowles, B. H. and D. J. Ellar. 1987. Colloid osmotic lysis is a general feature of the mechanism of action of Bacillus thuringiensis delta-endotoxins with different insect specificities. Biochim. Biophys. Acta 924: 509-518.
    CrossRef
  10. Kumar, A. S. M. and A. I. Aronson. 1999. Analysis of mutations in the pore-forming region essential for insecticidal activity of a Bacillus thuringiensis δ-endotoxin. J. Bacteriol. 181: 6103-6107.
    Pubmed KoreaMed
  11. Laskowski, R. A., M. W. MacArthur, D. S. Moss, and J. M. Thornton. 1993. PROCHECK: A program to check the stereo chemical quality of protein structures. J. Appl. Cryst. 26: 283-291.
    CrossRef
  12. Li, J., J. Carroll, and D. J. Ellar. 1991. Crystal structures of insecticidal δ-endotoxin from Bacillus thuringiensis at 2.5 Åresolutions. Nature 353: 815-821.
    Pubmed CrossRef
  13. Lovell, S. C., I. W. Davis, W. B. Arendall III, P. I. W. de Bakker, J. M. Word, M. G. Prisant, et al. 2002. Structure validation by C alpha geometry: Phi, psi and C beta deviation. Proteins 50: 437-450
    Pubmed CrossRef
  14. Min, Z. X., X. L. Qui, D. X. Zhi, and W. F. Xiang. 2009. The theoretical three-dimensional structure of Bacillus thuringiensis Cry5Aa and its biological implications. Protein J. 28: 104-110.
    Pubmed CrossRef
  15. Morse, R. J., T. Yamamoto, and R. M. Stroud. 2001. Structure of Cry2Aa suggests an unexpected receptor binding epitope. Structure 9: 409-417.
    CrossRef
  16. Sali, A., L. Potterton, F. Yuan, H. van Vlijmen and M. Karplus. 1995. Evaluation of comparative protein modeling by MODELLER. Proteins 23: 318-326.
    Pubmed CrossRef
  17. Schnepf, E., N. Crickmore, J. van Rie, D. Lereclus, J. Baum, J. Feitelson, et al. 1998. Bacillus thuringiensis and its pesticidal crystal proteins. Microbiol. Mol. Biol. Rev. 62: 772-806.
  18. Schwartz, J. L., L. Potvin, X. J. Chen, R. Brousseau, R. Laprade, and D. H. Dean. 1997. Single-site mutations in the conserved alternating-arginine region affect ion channels formed by CryIAa, a Bacillus thuringiensis toxin. Appl. Environ. Microbiol. 63: 3978-3984.
    Pubmed KoreaMed
  19. Xia, L. Q., X. M. Zhao, X. Z. Ding, F. X. Wang, and Y. J. Sun. 2008. The theoretical 3D structure of Bacillus thuringiensis Cry5Ba. J. Mol. Model. 14: 843-848.
    Pubmed CrossRef