Publication Cover
Xenobiotica
the fate of foreign compounds in biological systems
Volume 32, 2002 - Issue 4
95
Views
62
CrossRef citations to date
0
Altmetric
Research Article

Homology modelling of human CYP2 family enzymes based on the CYP2C5 crystal structure

Pages 305-323 | Published online: 22 Sep 2008

References

  • ANDREWS, P. R., CRAIK, D. J. and MARTIN, J. L., 1984, Functional group contributions to drug—receptor interactions. Journal of Medicinal Chemistry, 28, 1648–1657.
  • ANZENBACHER, P. and ANZENBACHEROVA, E., 2001, Cytochromes P450 and metabolism of xenobiotics. Cellular and Molecular Life Sciences, 58, 737–747.
  • BOUM, H.-J., 1994, The development of a simple empirical scoring function to estimate the binding constant for a protein ligand of known 3-dimensional structure. Journal of Computer-Aided Molecular Design, 8, 243–256.
  • CHANG, Y. T., STIFFELMAN, O. B., VASKER, I. A., LOEW, G. H., BRIDGES, A. and WASKEL L., 1997, Construction of a 3D model of cytochrome P4502B4. Protein Engineering, 10, 119–129.
  • CHEN, C.-D. and KEMPER, B., 1996, Different structural requirements at specific proline residue positions in the conserved proline-rich region of cytochrome P450 2C2, Journal of Biological Chemistry, 271, 28607–28611.
  • DE, R., PINCUS, M. R. and FRIEDMAN, F. K., 2000, Molecular modelling of mammalian cytochrome P450s. Cellular and Molecular Life Sciences, 57, 487–499.
  • DE GROOT, M. J., ACKLAND, M. J., HORNE, V. A., ALEX, A. A. and JoNEs, B. C., 1999, Novel approach to predicting P450-mediated drug metabolism: development of a combined protein and pharmacophore model for CYP2D6. Journal of Medicinal Chemistry, 42, 1515–1524.
  • ELLIS, S. W., HAYHURST, G. P., SMITH, G., LIGHTFOOT, R., WONG, M. M. S., SIMULA, A. P., ACKLAND, M. J., STERNBERG, M. J. E., LENNARD, M. S., TUCKER, G. T. and WOLF, C. R., 1995, Evidence that aspartic acid 301 is a critical substate-contact residue in the active site of cytochrome P450 2D6. Journal of Biological Chemistry, 270, 29055–29058.
  • FALETTO, M. B., LINKO, P. and GOLDSTEIN, J. A., 1992, A single amino acid mutation, Ser180, Cys, determines the polymorphism in cytochrome P450g, P4502C13, by altering protein stability, Journal of Biological Chemistry, 267, 2032–2037.
  • GOTOH, O., 1992, Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences, Journal of Biological Chemistry, 267, 83–90.
  • HAINING, R. L., JONES, J. P., HENNE, K. R., FISHER, M. B. and KOOP, D. R., 1999, Enzymatic determinants of the substrate specificity of CYP2C9: role of B-C loop residues in providing the pi-stacking anchor site for warfarin binding. Biochemistry, 38, 3225–3292.
  • HANIOKA, N., GONZALEZ, F. J., LINDBERG, N. A., Liu, G., GELBOIN, H. V. and KORZEKWA, K. R., 1992, Site-directed mutagenesis of cytochrome P450s CYP2A1 and CYP2A2: influence of the distal helix on the kinetics of testosterone metabolism. Biochemistry, 31, 3364–3370.
  • HSU, M.-H., GRIFFIN, K. J., WANG, Y., KEMPER, B. and JOHNSON, E. F., 1993, A single amino acid substitution confers progesterone 6, -hydroxylase activity to rabbit cytochrome P450 2C3, Journal of Biological Chemistry, 268, 6939–6944.
  • IBEANU, G. C., GHANAYEN, B. I., LINKO, P., Li, L., PEDERSEN, L. G. and GOLDSTEIN, J. A., 1996, Identification of residues 99, 220, and 221 of human cytochrome P450 2C19 as key determinants of omeprazole hydroxylase activity, Journal of Biological Chemistry, 271, 12496–12501.
  • IMM, Y. and NAKAMURA, M., 1989, Point mutations at threonine-301 modify substrate specificity of rabbit liver microsomal cytochromes P-450 (laurate, co-1) -hydroxylase and testosterone 16a-hydroxylase), Biochemical and Biophysical Research Communications, 158, 717–722.
  • KAMINSKY, L. S. DE MORAIS, S. M. F. FALETTO, M. B., DUNBAR, D. A. and GOLDSTEIN, J. A., 1993, Correlation of human cytochrome P4502C substrate specificities with primary structure: warfarin as a probe, Molecular Pharmacology, 43, 234–239.
  • KRONBACH, T., LARABEE, T. M. and JOHNSON, E. F., 1989, Hybrid cytochromes P-450 identify a substrate binding domain in P-450I105 and P450I1C4, Proceedings of the National Academy of Sciences, USA, 86, 8262–8265.
  • LEWIS, D. F. V., 1996, Cytochromes P450: Structure, Function and Mechanism (London: Taylor & Francis).
  • LEWIS, D. F. V., 1998, The CYP2 family: models, mutants and interactions. Xenobiotica, 28, 617–661.
  • LEWIS, D. F. V., 2000, On the recognition of mammalian microsomal cytochrome P450 substrates and their characteristics. Biochemical Pharmacology, 60, 293–306.
  • LEWIS, D. F. V., 2001, Guide to Cytochromes P450 Structure and Function (London: Taylor & Francis).
  • LEWIS, D. F. V., DICKINS, M., EDDERSHAW, P. J., GOLDFARB, P. S. and TARBIT, M. H., 1998, Molecular modelling of human CYP2C subfamily enzymes CYP2C9 and CYP2C19: rationalization of substrate specificity and site-directed mutagenesis experiments in the CYP2C subfamily. Xenobiotica, 28, 235–268.
  • LEWIS, D. F. V., DICKINS, M., LAKE, B. G., EDDERSHAW, P. J., TABIT, M. H. and GOLDFARB, P. S., 1999c, Molecular modelling of the human cytochrome P450 isoforrn CYP2A6 and investigations of CYP2A substrate selectivity. Toxicology, 133, 1–33.
  • LEWIS, D. F. V., EDDERSHAW, P. J., GOLDFARB, P. S. and TARBIT, M. H., 1996, Molecular modelling of CYP3A4 from an alignment with CYP102: identification of key interactions between putative active site residues and CYP3A-specific chemicals. Xenobiotica, 26, 1067–1086.
  • LEWIS, D. V. F., EDDERSHAW, P. J., GOLDFARB, P. S. and TARBIT, M. H., 1997, Molecular modelling of cytochrome P4502D6 (CYP2D6) based on an alignment with CYP102: Structural studies on specific CYP2D6 substrate metabolism. Xenobiotica, 27, 319–340.
  • LEWIS, D. F. V., LAKE, B. G., BIRD, M. G., DICKINS, M., EDDERSHAW, P. J., TARBIT, M. H. and GOLDFARB, P. S., 2000, Molecular modelling of human CYP2E1 by homology with the CYP102 haemoprotein domain: investigation of the interactions of substrates and inhibitors within the putative active site of the CYP2E1 isoform. Xenobiotica, 30, 1–25.
  • LEWIS, D. F. V., LAKE, B. G., DICKENS, M., EDDERSHAW, P. J., TARBIT, M. H. and GOLDFARB, P. S., 1999a, Molecular modelling of the phenobarbital-inducible P450 isoforms: CYP2B1, CYP2B4 and CYP2B6 by homology with the substrate-bound CYP102 crystal structure, and evaluation of CYP2B substrate binding affinity. Xenobiotica, 29, 361–393.
  • LEWIS, D. F. V., LAKE, B. G., GEORGE, S. G., DICKINS, M., BERESFORD, A. P., EDDERSHAW, P. J., TARBIT, M. H., GOLDFARB, P. S. and GUENGERICH, F. P., 1999b, Molecular modelling of CYP1 family isoforms: CYP1A1, CYP1A2, CYP1A6 and CYP1B1 based on sequence homology with CYP102. Toxicology, 139, 53–79.
  • LEWIS, D. F. V., MODI, S. and DICKINS, M., 2002, Structure-activity relationships for human cytochrome P450 substrates and inhibitors. Drug Metabolism Reviews (in press).
  • Li, H. and Potmos, T. L., 1997, The structure of the cytochrome P450BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid. Nature and Structural Biology, 4, 140–146.
  • LINDBERG, R. L. P. and NEGISHI, M., 1989, Alteration of mouse cytochrome P450coh substrate specificity by mutation of a single amino acid residue. Nature, 339, 632–674.
  • OHGIYA, S., KOMORI, M., OHI, H., SHIRAMATSU, K., SHINRIKI, N. and KAMATAKI, T., 1992, Six-base deletion occurring in messages of human cytochrome P-450 in the CYP2C subfamily results in reduction of tolbutamide hydroxylase activity, Biochemistry International, 27, 1073–1081.
  • RAMARAO, M. K., STRAUB, P. and KEMPER, B., 1995, Identification by in vitro mutagenesis of the interaction of two segments of C2MstC1, a chimera of cytochromes P450 2C2 and P450 2C1, Journal of Biological Chemistry, 270, 1873–1880.
  • RAVICHANDRAN, K. G., BODDUPALLI, S. S., HASEMANN, C. A., PETERSON, J. A. and DEISENHOFER, J., 1993, Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450s. Science, 261, 731–736.
  • RENDIC, S. and DICARLo, F. J., 1997, Human cytochrome P450 enzymes: a status report summarizing their reactions, substrates, inducers and inhibitors. Drug Metabolism Reviews, 29, 413–580.
  • RICHARDSON, T. H. and JOHNSON, E. F., 1994, Alterations of the regiospecificity of progesterone metabolism by the mutagenesis of two key amino acid residues in rabbit cytochrome P450 2C3v. Journal of Biological Chemistry, 269, 23927–23943.
  • RICHARDSON, T. H. and JOHNSON, E. F., 1996, The CYP2C subfamily. In C. Ioannides (ed.), Cytochromes P450: Metabolic and Toxicological Aspects (Boca Raton: CRC Press) pp. 161–181.
  • RIDDERSTROM, M., MASIMIREMBARA, C., TRUMP-KALLMEYER, S., AHLEFELT, M., OTTER, C. and ANDERSSON, T. B., 2000, Arginines 97 and 108 in CYP2C9 are important determinants of the catalytic function. Biochemical and Biophysical Research Communications, 270, 983–987.
  • SMITH, G., MODI, S., PILLA I., LIAN, L.-Y., SUTCLIFFE, M. J., PRITCHARD, M. P., FRIEDBERG, T., ROBERTS, G. C. K. and WOLF, C. R., 1998, Determinants of the substrate specificity of human cytochrome P450 CYP2D6: design and construction of mutant with testosterone hydroxylase activity. Biochemical Journal, 331, 783–792.
  • STRAUB, P., JOHNSON, E. F. and KEMPER, B., 1993b, Hydrophobic side chain requirements for lauric acid and progesterone hydroxylation at amino acid 113 in cytochrome P450 2C2, a potential determinant of substrate specificity, Archives of Biochemistry and Biophysics, 306, 521–527.
  • STRAUB, P., LLOYD, M., JOHNSON, E. F. and KEMPER, B., 1993a, Cassette mutagenesis of a potential substrate recognition region of cytochrome P450 2C2, Journal of Biological Chemistry, 268, 21997–22003.
  • SZKLARZ, G. D., HE, Y. Q., KEDZIE, K. M., HALPERT, J. R. and BURNETT, V. L., 1996, Elucidation of amino acid residues critical for unique activities of rabbit cytochrome P4502B5 using hybrid enzymes and reciprocal site-directed mutagenesis with rabbit cytochrome P4502B4. Archives of Biochemistry and Biophysics, 327, 308–318.
  • VERONESE, M. E., DOECKE, C. J., MACKENZIE, P. I., McMANus, M. E., MINERS, J. O., REES, D. L. P., GASSER, R., MEYER, U. A. and BIRKETT, D. J., 1993, Site-directed mutation studies of human liver cytochrome P-450 isoenzymes in the CYP2C subfamily, Biochemical Journal, 289, 533–538.
  • VON WACHENFELDT, C. and JOHNSON, E. F., 1995, Structures of eukaryotic cytochrome P450 enzymes. In P. R. Ortiz de Montellano (ed.), Cytochronze P450 (New York: Plenum), pp. 183–244.
  • WILLIAMS, D. H., Cox, J. P. L., DOIG, A. J., GARDNER, M., GERHARD, U., KAYE, P. T., LAL, A. R., Nicuous, I. A., SALTER, C. J. and MITCHELL, R. C., 1991, Toward the semiquantitative estimation of binding constants. Journal of the American Chemical Society, 113, 7020–7030.
  • WILLIAMS, P. A., COSME, J., SRIDHAR, V., JOHNSON, E. F. and McREE, D. E., 2000, Mammalian microsomal cytochrome P450 monooxygenase: structure adaptions for membrane binding and functional diversity. Molecular Cell, 5, 121–131.
  • YAMAZAKI, S., SATO, K., SUHAKA, K., SAKAGUCHI, M., MIHARA, K. and OMURA, T., 1993, Importance of the proline-rich region following signal-anchor sequence in the formation of correct conformation of microsomal cytochrome P-450s, Journal of Biochemistry, 114, 652–657.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.