전체메뉴
검색
Article Search

JMB Journal of Microbiolog and Biotechnology

QR Code QR Code

Research article

References

  1. Bernhardt, R. 1996. Cytochrome P450: Structure, function, and generation of reactive oxygen species. Rev. Physiol. Biochem. Pharmacol. 127: 137-221.
    CrossRef
  2. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4: 187-217.
    CrossRef
  3. Cupp-Vickery, J., R. Anderson, and Z. Hatziris. 2000. Crystal structures of ligand complexes of P450eryF exhibiting homotropic cooperativity. Proc. Natl. Acad. Sci. USA 97: 3050-3055.
    Pubmed CrossRef
  4. Discovery Studio 3.1. 2011. Accelrys Inc., San Diego, CA, USA. Available from: http://www.accelrys.com.
  5. Gotoh, O. 1992. Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. J. Biol. Chem. 267: 83-90.
    Pubmed
  6. Hamdane, D., H. Zhang, and P. Hollenberg. 2008. Oxygen activation by cytochrome P450 monooxygenase. Photosynthes. Res. 98: 657-666.
    Pubmed PMC CrossRef
  7. Hasemann, C. A., S. S. Kurumbail, S. S. Boddupalli, J. A. Peterson, and J. Deisenhofer. 1995. Structure and function of cytochrome P450: A comparative analysis of three crystal structures. Structure 2: 41-62.
    CrossRef
  8. Hayashi, K., H. Sugimoto, R. Shinkyo, M. Yamada, S. Ikeda, S. Ikushiro, M. Kamakura, Y. Shiro, and T. Sakaki. 2008. Structure-based design of highly active vitamin D hydroxylase from Streptomyces griseolus CYP105A1. Biochemistry 47:11964-11972.
    Pubmed CrossRef
  9. Lewis, D. F., E. Watson, and B. G. Lake. 1998. Evolution of the cytochrome P450 super-family: Sequence alignments and pharmacogenetics. Mutat. Res. 410: 245-270.
    CrossRef
  10. Lovell, S. C., I. Q. Davis, W. B. Arendall III, P. I. De Bakker, J. M. Word, M. G. Prisant, J. C. Richardson, and D. C. Richardson. 2003. Structure validation by C alpha geometry:Phi, psi and C beta deviation. Proteins 50: 437-450.
    Pubmed CrossRef
  11. Maiti, R., G. H. Van Domselaar, H. Zhang, and D. S. Wishart. 2004. SuperPose: A simple server for sophisticated structural superposition. Nucleic Acids Res. 32: W590-W594.
    Pubmed PMC CrossRef
  12. Mars, A. E., J. P. Gorissen, I. van den Beld, and G. Eggink. 2001. Bioconversion of limonene to increased concentrations of perillic acid by Pseudomonas putida GS1 in a fed-batch reactor. Appl. Microbiol. Biotechnol. 56: 101-107.
    Pubmed CrossRef
  13. Nelson, D. R., L. Koymans, T. Kamataki, J. J. Stegeman, R. Feyereisen, D. J. Waxman, et al. 1996. P450 superfamily:Update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics 6: 1-42.
    Pubmed CrossRef
  14. Oriel, P. J., S. Savithiry, and H. C. Chang. 1997. Process for the preparation of monoterpenes using bacterium containing recombinant DNA. U.S. patent 5,688,673.
  15. Ortiz de Montellano, P. R. 2004. Cytochrome P450 structure, mechanism, and biochemistry, pp. 183-247. In P. R. Ortiz de Montellano and De J. J. Voss. (eds.). Substrate Oxidation by Cytochrome P450 Enzymes. Kluwer Academic/PlenumPublishers, NewYork
  16. Sali, A., L. Pottertone, F. Yuan, H. Van Vlijmen, and M. Karplus. 1995. Evaluation of comparative protein modeling by MODELLER. Prot. Struct. Funct. Genet. 23: 318-326.
    Pubmed CrossRef
  17. Seifert, A., M. Antonovici, B. Hauer, and J. Pleiss. 2011. An efficient route to selective bio-oxidation catalysts: An iterative approach comprising modeling, diversification, and screening, based on CYP102A1. ChemBioChem 12: 1346-1351.
    Pubmed CrossRef
  18. Sherman, D. H., L. Shengying, L. V. Yermalitskaya, Y. Kim, J. A. Smith, M. R. Waterman, and L. M. Podust. 2006. The structural basis for substrate anchoring, active site selectivity, and product formation by P450 PikC from Streptomyces venezuelae. J. Biol. Chem. 281: 26289-26297.
    Pubmed PMC CrossRef
  19. Sippl, M. J. 1993. Recognition of errors in three-dimensional structures of proteins. Proteins 17: 355-362.
    Pubmed CrossRef
  20. The ExPASy (Expert ProteinAnalysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB). Available from: http://ca.expasy.org.
  21. Venkatachalam, C. M., X. Jiang, T. Oldeld, and M. Waldman. 2003. LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph. Model. 21: 289-307.
    CrossRef
  22. Wagner, K. H. and I. Elmadfa. 2003. Biological relevance of terpenoids. Ann. Nutr. Metab. 47: 95–106.
    Pubmed CrossRef
  23. Yasutake, Y., Y. Fujii, T. Nishioka, W. K. Cheon, A. Arisawa, and T. Tamura. 2010. Structural evidence for enhancement of sequential vitamin D3 hydroxylation activities by directed evolution of cytochrome P450 vitamin D3 hydroxylase. J. Biol. Chem. 285: 31193-31201.

Related articles in JMB

More Related Articles

Article

Research article

J. Microbiol. Biotechnol. 2012; 22(7): 917-922

Published online July 28, 2012 https://doi.org/10.4014/jmb.1112.12053

Copyright © The Korean Society for Microbiology and Biotechnology.

Homology Modeling and Docking Studies of Streptomyces peucetius CYP147F1 as Limonene Hydroxylase

Saurabh Bhattarai 1, Kwangkyoung Liou 1 and Tae-Jin Oh 1*

Institute of Biomolecule Reconstruction (iBR), Department of Pharmaceutical Engineering, SunMoon University, Asansi, Chungnam 336-708, Korea

Received: December 21, 2011; Accepted: February 23, 2012

Abstract

Homology modeling of Streptomyces peucetius CYP147F1
was constructed using three cytochrome P450 structures,
CYP107L1, CYPVdh, and CYPeryF, as templates. The
lowest energy SPCYP147F1 model was then assessed for
stereochemical quality and side-chain environment by
Accelrys Discovery Studio 3.1 software. Further activesite
optimization of the SPCYP147F1 was performed by
molecular dynamics to generate the final SPCYP147F1
model. The substrate limonene was then docked into the
model. The model-limonene complex was used to validate
the active-site architecture, and functionally important
residues within the substrate recognition site were identified
by subsequent characterization of the secondary structure.
The docking of limonene suggested that SPCYP147F1
would have broad specificity with the ligand based on the
two different orientations of limonene within the active
site facing to the heme. Limonene with C7 facing the heme
with distance of 3.4 Å from the Fe was predominant.

Keywords: Cytochrome P450, homology modeling, limonene, molecular docking, Streptomyces peucetius

References

  1. Bernhardt, R. 1996. Cytochrome P450: Structure, function, and generation of reactive oxygen species. Rev. Physiol. Biochem. Pharmacol. 127: 137-221.
    CrossRef
  2. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4: 187-217.
    CrossRef
  3. Cupp-Vickery, J., R. Anderson, and Z. Hatziris. 2000. Crystal structures of ligand complexes of P450eryF exhibiting homotropic cooperativity. Proc. Natl. Acad. Sci. USA 97: 3050-3055.
    Pubmed CrossRef
  4. Discovery Studio 3.1. 2011. Accelrys Inc., San Diego, CA, USA. Available from: http://www.accelrys.com.
  5. Gotoh, O. 1992. Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. J. Biol. Chem. 267: 83-90.
    Pubmed
  6. Hamdane, D., H. Zhang, and P. Hollenberg. 2008. Oxygen activation by cytochrome P450 monooxygenase. Photosynthes. Res. 98: 657-666.
    Pubmed KoreaMed CrossRef
  7. Hasemann, C. A., S. S. Kurumbail, S. S. Boddupalli, J. A. Peterson, and J. Deisenhofer. 1995. Structure and function of cytochrome P450: A comparative analysis of three crystal structures. Structure 2: 41-62.
    CrossRef
  8. Hayashi, K., H. Sugimoto, R. Shinkyo, M. Yamada, S. Ikeda, S. Ikushiro, M. Kamakura, Y. Shiro, and T. Sakaki. 2008. Structure-based design of highly active vitamin D hydroxylase from Streptomyces griseolus CYP105A1. Biochemistry 47:11964-11972.
    Pubmed CrossRef
  9. Lewis, D. F., E. Watson, and B. G. Lake. 1998. Evolution of the cytochrome P450 super-family: Sequence alignments and pharmacogenetics. Mutat. Res. 410: 245-270.
    CrossRef
  10. Lovell, S. C., I. Q. Davis, W. B. Arendall III, P. I. De Bakker, J. M. Word, M. G. Prisant, J. C. Richardson, and D. C. Richardson. 2003. Structure validation by C alpha geometry:Phi, psi and C beta deviation. Proteins 50: 437-450.
    Pubmed CrossRef
  11. Maiti, R., G. H. Van Domselaar, H. Zhang, and D. S. Wishart. 2004. SuperPose: A simple server for sophisticated structural superposition. Nucleic Acids Res. 32: W590-W594.
    Pubmed KoreaMed CrossRef
  12. Mars, A. E., J. P. Gorissen, I. van den Beld, and G. Eggink. 2001. Bioconversion of limonene to increased concentrations of perillic acid by Pseudomonas putida GS1 in a fed-batch reactor. Appl. Microbiol. Biotechnol. 56: 101-107.
    Pubmed CrossRef
  13. Nelson, D. R., L. Koymans, T. Kamataki, J. J. Stegeman, R. Feyereisen, D. J. Waxman, et al. 1996. P450 superfamily:Update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics 6: 1-42.
    Pubmed CrossRef
  14. Oriel, P. J., S. Savithiry, and H. C. Chang. 1997. Process for the preparation of monoterpenes using bacterium containing recombinant DNA. U.S. patent 5,688,673.
  15. Ortiz de Montellano, P. R. 2004. Cytochrome P450 structure, mechanism, and biochemistry, pp. 183-247. In P. R. Ortiz de Montellano and De J. J. Voss. (eds.). Substrate Oxidation by Cytochrome P450 Enzymes. Kluwer Academic/PlenumPublishers, NewYork
  16. Sali, A., L. Pottertone, F. Yuan, H. Van Vlijmen, and M. Karplus. 1995. Evaluation of comparative protein modeling by MODELLER. Prot. Struct. Funct. Genet. 23: 318-326.
    Pubmed CrossRef
  17. Seifert, A., M. Antonovici, B. Hauer, and J. Pleiss. 2011. An efficient route to selective bio-oxidation catalysts: An iterative approach comprising modeling, diversification, and screening, based on CYP102A1. ChemBioChem 12: 1346-1351.
    Pubmed CrossRef
  18. Sherman, D. H., L. Shengying, L. V. Yermalitskaya, Y. Kim, J. A. Smith, M. R. Waterman, and L. M. Podust. 2006. The structural basis for substrate anchoring, active site selectivity, and product formation by P450 PikC from Streptomyces venezuelae. J. Biol. Chem. 281: 26289-26297.
    Pubmed KoreaMed CrossRef
  19. Sippl, M. J. 1993. Recognition of errors in three-dimensional structures of proteins. Proteins 17: 355-362.
    Pubmed CrossRef
  20. The ExPASy (Expert ProteinAnalysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB). Available from: http://ca.expasy.org.
  21. Venkatachalam, C. M., X. Jiang, T. Oldeld, and M. Waldman. 2003. LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph. Model. 21: 289-307.
    CrossRef
  22. Wagner, K. H. and I. Elmadfa. 2003. Biological relevance of terpenoids. Ann. Nutr. Metab. 47: 95–106.
    Pubmed CrossRef
  23. Yasutake, Y., Y. Fujii, T. Nishioka, W. K. Cheon, A. Arisawa, and T. Tamura. 2010. Structural evidence for enhancement of sequential vitamin D3 hydroxylation activities by directed evolution of cytochrome P450 vitamin D3 hydroxylase. J. Biol. Chem. 285: 31193-31201.