What common structural features and variations of mammalian P450s are known to date?

Biochimica et Biophysica Acta - General Subjects

Volumn 1770, Issue 3, 2007, Pages 376-389

  Otyepka, Michal ^a   Skopalík, Josef ^a   Anzenbacherová, Eva ^a   Anzenbacher, Pavel ^a  

^a PALACKÝ UNIVERSITY   (Czech Republic)

Author keywords

Active site; CYP; CYP structure; Cytochrome P450; Molecular dynamic; Substrate binding

Indexed keywords

BIFONAZOLE; COUMARIN; CYTOCHROME P450; CYTOCHROME P450 2C8; CYTOCHROME P450 2C9; DICLOFENAC; FLURBIPROFEN; HEME; METHOXSALEN; METYRAPONE; WARFARIN; WATER;

CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; DRUG STRUCTURE; ENZYME SUBSTRATE COMPLEX; HUMAN; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; REVIEW; SIMULATION; SPATIAL ORIENTATION;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CYTOCHROME P-450 ENZYME SYSTEM; HUMANS; MAMMALS; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; WATER;

MAMMALIA;

EID: 33846380189     PISSN: 03044165     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbagen.2006.09.013     Document Type: Review

References (82)

1. Nebert D.W., and Nelson D.R. P450 gene nomenclature based on evolution. Method. Enzymol. 206 (1991) 3-11
2. Nelson D.R., Koymans L., Kamataki T., Stegeman J.J., Feyereisen R., Waxman D.J., Waterman M.R., Gotoh O., Coon M.J., Estabrook R.W., Gunsalus I.C., and Nebert D.W. P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics 6 (1996) 1-42
3. Ortiz de Montellano P.R. Cytochrome P450: Structure, Mechanism, and Biochemistry. 3rd ed. (2005), Kluwer Academic, New York
4. Anzenbacher P., and Anzenbacherova E. Cytochromes P450 and metabolism of xenobiotics. Cell. Mol. Life Sci. 58 (2001) 737-747
5. Shimada T., Yamazaki H., Mimura M., Inui Y., and Guengerich F.P. Interindividual variations in human liver cytochrome-P-450 enzymes involved in the oxidation of drugs, carcinogens and toxic-chemicals-Studies with liver-microsomes of 30 Japanese and 30 Caucasians. J. Pharmacol. Exp. Ther. 270 (1994) 414-423
6. Li A.P., Kaminski D.L., and Rasmussen A. Substrates of human hepatic cytochrome P450 3A4. Toxicology 104 (1995) 1-8
7. Li A.P., Reith M.K., Rasmussen A., Gorski J.C., Hall S.D., Xu L., Kaminski D.L., and Cheng L.K. Primary human hepatocytes as a tool for the evaluation of structure-activity relationship in cytochrome P450 induction potential of xenobiotics: evaluation of rifampin, rifapentine and rifabutin. Chem.-Biol. Interact. 107 (1997) 17-30
8. Rendic S., and DiCarlo F.J. Human cytochrome P450 enzymes: a status report summarizing their reactions, substrates, inducers, and inhibitors. Drug Metab. Rev. 29 (1997) 413-580
9. Tanaka E. Clinical importance of non-genetic and genetic cytochrome P450 function tests in liver disease. J. Clin. Pharm. Ther. 23 (1998) 161-170
10. Wilkinson G.R. Cytochrome P4503A (CYP3A) metabolism: prediction of in vivo activity in humans. J. Pharmacokinet. Biopharm. 24 (1996) 475-490
11. Bernhardt R. Cytochromes P450 as versatile biocatalysts. J. Biotech. 124 (2006) 128-145
12. Schlichting I., Berendzen J., Chu K., Stock A.M., Maves S.A., Benson D.E., Sweet B.M., Ringe D., Petsko G.A., and Sligar S.G. The catalytic pathway of cytochrome P450cam at atomic resolution. Science 287 (2000) 1615-1622
13. Groves J.T. The bioinorganic chemistry of iron in oxygenases and supramolecular assemblies. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 3569-3574
14. Denisov I.G., Makris T.M., Sligar S.G., and Schlichting I. Structure and chemistry of cytochrome P450. Chem. Rev. 105 (2005) 2253-2277
15. Meunier B., de Visser S.P., and Shaik S. Mechanism of oxidation reactions catalyzed by cytochrome P450 enzymes. Chem. Rev. 104 (2004) 3947-3980
16. Shaik S., Kumar D., de Visser S.P., Altun A., and Thiel W. Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes. Chem. Rev. 105 (2005) 2279-2328
17. Ravichandran K.G., Boddupalli S.S., Hasemann C.A., Peterson J.A., and Deisenhofer J. Crystal-structure of hemoprotein domain of P450bm-3, a prototype for microsomal P450s. Science 261 (1993) 731-736
18. Li H.Y., and Poulos T.L. The structure of the cytochrome P450BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid. Nat. Struct. Biol. 4 (1997) 140-146
19. Poulos T.L., Finzel B.C., Gunsalus I.C., Wagner G.C., and Kraut J. The 2.6-A crystal-structure of Pseudomonas putida cytochrome P450. J. Biol. Chem. 260 (1985) 6122-6130
20. Poulos T.L., and Raag R. Cytochrome-P450cam-Crystallography, oxygen activation, and electron-transfer. FASEB J. 6 (1992) 674-679
21. Poulos T.L. Cytochrome P450. Curr. Opin. Struct. Biol. 5 (1995) 767-774
22. Govindaraj S., and Poulos T.L. The domain architecture of cytochrome P450BM-3. J. Biol. Chem. 272 (1997) 7915-7921
23. Cosme J., and Johnson E.F. Engineering microsomal cytochrome P4502C5 to be a soluble, monomeric enzyme-Mutations that alter aggregation, phospholipid dependence of catalysis, and membrane binding. J. Biol. Chem. 275 (2000) 2545-2553
24. Williams P.A., Cosme J., Ward A., Angova H.C., Vinkovic D.M., and Jhoti H. Crystal structure of human cytochrome P4502C9 with bound warfarin. Nature 424 (2003) 464-468
25. vonWachenfeldt C., Richardson T.H., Cosme J., and Johnson E.F. Microsomal P450 2C3 is expressed as a soluble dimer in Escherichia coli following modifications of its N-terminus. Arch. Biochem. Biophys. 339 (1997) 107-114
26. Pernecky S.J., Larson J.R., Philpot R.M., and Coon M.J. Expression of truncated forms of liver microsomal P450 cytochromes 2B4 and 2E1 in Escherichia coli-Influence of Nh2-terminal region on localization in cytosol and membranes. Proc. Natl. Acad. Sci. U. S. A. 90 (1993) 2651-2655
27. Orengo C.A., Michie A.D., Jones S., Jones D.T., Swindells M.B., and Thornton J.M. CATH-A hierarchic classification of protein domain structures. Structure 5 (1997) 1093-1108
28. Lisitsa A., Archakov A., Lewi R., and Janssen P. Bioinformatic insight into the unity and diversity of cytochromes P450. Method. Find. Exp. Clin. 25 (2003) 733-745
29. Mestres J. Structure conservation in cytochromes P450. Proteins: Struct. Funct. Bioinf. 58 (2005) 596-609
30. Williams P.A., Cosme J., Sridhar V., Johnson E.F., and McRee D.E. Microsomal cytochrome P4502C5: comparison to microbial P450s and unique features. J. Inorg. Biochem. 81 (2000) 183-190
31. Gotoh O. 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 (1992) 83-90
32. Williams P.A., Cosme J., Sridhar V., Johnson E.F., and McRee D.E. Mammalian microsomal cytochrome P450 monooxygenase: structural adaptations for membrane binding and functional diversity. Mol. Cell. 5 (2000) 121-131
33. Wester M.R., Johnson E.F., Marques-Soares C., Dijols S., Dansette P.M., Mansuy D., and Stout C.D. Structure of mammalian cytochrome P4502C5 complexed with diclofenac at 2.1 angstrom resolution: evidence for an induced fit model of substrate binding. Biochemistry 42 (2003) 9335-9345
34. Wester M.R., Johnson E.F., Marques-Soares C., Dansette P.M., Mansuy D., and Stout C.D. Structure of a substrate complex of mammalian cytochrome P4502C5 at 2.3 angstrom resolution: evidence for multiple substrate binding modes. Biochemistry 42 (2003) 6370-6379
35. Schoch G.A., Yano J.K., Wester M.R., Griffin K.J., Stout C.D., and Johnson E.F. Structure of human microsomal cytochrome P4502C8-Evidence for a peripheral fatty acid binding site. J. Biol. Chem. 279 (2004) 9497-9503
36. Wester M.R., Yano J.K., Schoch G.A., Yang C., Griffin K.J., Stout C.D., and Johnson E.F. The structure of human cytochrome P4502C9 complexed with flurbiprofen at 2.0 angstrom resolution. J. Biol. Chem. 279 (2004) 35630-35637
37. Scott E.E., White M.A., He Y.A., Johnson E.F., Stout C.D., and Halpert J.R. Structure of mammalian cytochrome P4502B4 complexed with 4-(4-chlorophenyl) imidazole at 1.9-angstrom resolution-Insight into the range of P450 conformations and the coordination of redox partner binding. J. Biol. Chem. 279 (2004) 27294-27301
38. Amadei A., Linssen A.B.M., and Berenden H.J.C. Essential dynamics of protein. Proteins: Struct. Funct. Genet. 17 (1993) 412-425
39. Schleinkofer K., Sudarko P.J., Winn S.K., and Ludemann R.C. Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?. EMBO Rep. 6 (2005) 584-589
40. Seifert A., Tatzel S., Schmid R.D., and Pleiss J. Multiple molecular dynamics simulations of human p450 monooxygenase CYP2C9: the molecular basis of substrate binding and regioselectivity toward warfarin. Proteins: Struct. Funct. Bioinf. 64 (2006) 147-155
41. Haining R.L., Jones J.P., Henne K.R., Fisher M.B., Koop D.R., Trager W.F., and Rettie A.E. 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 (1999) 3285-3292
42. Hutzler J.M., Hauer M.J., and Tracy T.S. Dapsone activation of CYP2C9-mediated metabolism: evidence for activation of multiple substrates and a two-site model. Drug Metab. Dispos. 29 (2001) 1029-1034
43. Hutzler J.M., Kolwankar D., Hummel M.A., and Tracy T.S. Activation of CYP2C9-mediated metabolism by a series of dapsone analogs: kinetics and structural requirements. Drug Metab. Dispos. 30 (2002) 1194-1200
44. Meunier B., and Bernadou J. Active iron-oxo and iron-peroxo species in cytochromes P450 and peroxidases; Oxo-hydroxo tautomerism with water-soluble metalloporphyrins. Struct. Bond. 97 (2000) 1-35
45. Hlavica P. Models and mechanisms of O-O bond activation by cytochrome P450-A critical assessment of the potential role of multiple active intermediates in oxidative catalysis. Eur. J. Biochem. 271 (2004) 4335-4360
46. Zhang Q.Y., Dunbar D., Ostrowska A., Zeisloft S., Yang J., and Kaminsky L.S. Characterization of human small intestinal cytochromes P450. Drug Metab. Dispos. 27 (1999) 804-809
47. Williams P.A., Cosme J., Vinkovic D.M., Ward A., Angove H.C., Day P.J., Vonrhein C., Tickle I.J., and Jhoti H. Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone. Science 305 (2004) 683-686
48. Yano J.K., Wester M.R., Schoch G.A., Griffin K.J., Stout C.D., and Johnson E.F. The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05 angstrom resolution. J. Biol. Chem. 279 (2004) 38091-38094
49. Scott E.E., and Halpert J.R. Structures of cytochrome P450 3A4. Trends Biochem. Sci. 30 (2005) 5-7
50. Lewis D.F.V., Eddershaw P.J., Goldfarb P.S., and Tarbit M.H. Molecular modelling of CYP3A4 from an alignment with CYP102: identification of key interactions between putative active site residues and CYP3A-specific chemicals. Xenobiotica 26 (1996) 1067-1086
51. Lewis D.F.V., Lake B.G., Dickins M., and Goldfarb P.S. Homology modelling of CYP3A4 from the CYP2C5 crystallographic template: analysis of typical CYP3A4 substrate interactions. Xenobiotica 34 (2004) 549-569
52. Scott E.E., Spatzenegger M., and Halpert J.R. A truncation of 2B subfamily cytochromes P450 yields increased expression levels, increased solubility, and decreased aggregation while retaining function. Arch. Biochem. Biophys. 395 (2001) 57-68
53. Scott E.E., He Y.A., Wester M.R., White M.A., Chin C.C., Halpert J.R., Johnson E.F., and Stout C.D. An open conformation of mammalian cytochrome P4502B4 at 1.6 angstrom resolution. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 13196-13201
54. Zhao Y.H., White M.A., Muralidhara B.K., Sun L., Halpert J.R., and Stout C.D. Structure of microsomal cytochrome P4502B4 complexed with the antifungal drug bifonazole-Insight into P450 conformational plasticity and membrane interaction. J. Biol. Chem. 281 (2006) 5973-5981
55. Harlow G.R., and Halpert J.R. Analysis of human cytochrome P450 3A4 cooperativity: construction and characterization of a site-directed mutant that displays hyperbolic steroid hydroxylation kinetics. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 6636-6641
56. Khan K.K., He Y.Q., Domanski T.L., and Halpert J.R. Midazolam oxidation by cytochrome P450 3A4 and active site mutants: an evaluation of multiple binding sites and of the metabolic pathway that leads to enzyme inactivation. Mol. Pharmacol. 61 (2002) 495-506
57. Park H., Lee S., and Suh J. Structural and dynamical basis of broad substrate specificity, catalytic mechanism, and inhibition of cytochrome P450 3A4. J. Am. Chem. Soc. 127 (2005) 13634-13642
58. Bertz R.J., and Granneman G.R. Use of in vitro and in vivo data to estimate the likelihood of metabolic pharmacokinetic interactions. Clin. Pharmacokinet. 32 (1997) 210-258
59. Rowland P., Blaney F.E., Smyth M.G., Jones J.J., Leydon V.R., Oxbrow A.K., Lewis C.J., Tennant M.G., Modi S., Eggleston D.S., Chenery R.J., and Bridges A.M. Crystal structure of human cytochrome P450 2D6. J. Biol. Chem. 281 (2006) 7614-7622
60. Muralidhara B.K., Negi S., Chin C.C., Braun W., and Halpert J.R. Conformational flexibility of mammalian cytochrome P4502B4 in binding imidazole inhibitors with different ring chemistry and side chains-Solution thermodynamics and molecular modeling. J. Biol. Chem. 281 (2006) 8051-8061
61. Hodek P., Sopko B., Antonovic L., Sulc M., Novak P., and Strobel H.W. Evaluation of comparative cytochrome P450 2B4 model by photoaffinity labeling. Gen. Physiol. Biophys. 23 (2004) 467-488
62. Malaiyandi V., Sellers E.M., and Tyndale R.F. Implications of CYP2A6 genetic variation for smoking behaviors and nicotine dependence. Clin. Pharmacol. Ther. 77 (2005) 145-158
63. Yano J.K., Hsu M.H., Griffin K.J., Stout C.D., and Johnson E.F. Structures of human microsomal cytochrome P450 2A6 complexed with coumarin and methoxsalen. Nat. Struct. Mol. Biol. 12 (2005) 822-823
64. Black S.D., Martin S.T., and Smith C.A. Membrane topology of liver microsomal cytochrome P450 2B4 determined via monoclonal antibodies directed to the halt-transfer signal. Biochemistry 33 (1994) 6945-6951
65. De Lemos-Chiarandini C., Frey A.B., Sabatini D.D., and Kreibich G. Determination of the membrane topology of the phenobarbital inducible rat liver Cytochrome P450 isoenzyme Pb4 using site-specific antibodies. J. Cell Biol. 104 (1987) 209-219
66. Bridges A., Gruenke L., Chang Y.T., Vakser I.A., Loew G., and Waskell L. Identification of the binding site on cytochrome P450 2B4 for cytochrome b(5) and cytochrome P450 reductase. J. Biol. Chem. 273 (1998) 17036-17049
67. Shank-Retzlaff M.L., Raner G.M., Coon M.J., and Sligar S.G. Membrane topology of cytochrome P450 2B4 in Langmuir-Blodgett monolayers. Arch. Biochem. Biophys. 359 (1998) 82-88
68. Lomize A.L., Pogozheva I.D., and Mosberg H.I. Quantification of helix-helix binding affinities in micelles and lipid bilayers. Protein Sci. 13 (2004) 2600-2612
69. Winn P.J., Ludemann S.K., Gauges R., Lounnas V., and Wade R.C. Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a novel functional role for a buried arginine. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 5361-5366
70. Wade R.C., Winn P.J., Schlichting E., and Sudarko. A survey of active site access channels in cytochromes P450. J. Inorg. Biochem. 98 (2004) 1175-1182
71. Wade R.C., Motiejunas D., Schleinkofer K., Sudarko, Winn P.J., Banerjee A., Kaniakin A., and Jung C. Multiple molecular recognition mechanisms. Cytochrome P450-A case study. BBA Proteins Proteom. 1754 (2005) 239-244
72. Petrek M., Otyepka M., Banas P., Kosinova P., Koca J., and Damborsky J. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 7 (2006) 316
73. Clarke T.A., Im S.C., Bidwai A., and Waskell L. The role of the length and sequence of the linker domain of cytochrome b(5) in stimulating cytochrome P4502B4 catalysis. J. Biol. Chem. 279 (2004) 36809-36818
74. Anzenbacher P., and Hudecek J. Differences in flexibility of active sites of cytochromes P450 probed by resonance Raman and UV-Vis absorption spectroscopy. J. Inorg. Biochem. 87 (2001) 209-213
75. Lange R., Frank J., Saldana J.L., and Balny C. Fourth derivative UV-spectroscopy of proteins under high pressure:1. Factors affecting the fourth derivative spectrum of the aromatic amino acids. Eur. Biophys. J. Biophys. 24 (1996) 277-283
76. Mozhaev V.V., Heremans K., Frank J., Masson P., and Balny C. High pressure effects on protein structure and function. Proteins: Struct. Funct. Genet. 24 (1996) 81-91
77. Jung C., Hoa G.H.B., Davydov D., Gill E., and Heremans K. Compressibility of the heme pocket of substrate analog complexes of cytochrome P450cam-Co the effect of hydrostatic pressure on the Soret band. Eur. J. Biochem. 233 (1995) 600-606
78. Anzenbacherova E., Bec N., Anzenbacher P., Hudecek J., Soucek P., Jung C., Munro A.W., and Lange R. Flexibility and stability of the structure of cytochromes P450 3A4 and BM-3. Eur. J. Biochem. 267 (2000) 2916-2920
79. Anzenbacherova E., Hudecek J., Murgida D., Hildebrandt P., Marchal S., Lange R., and Anzenbacher P. Active sites of two orthologous cytochromes P450 2E1: Differences revealed by spectroscopic methods. Biochem. Biophys. Res. Commun. 338 (2005) 477-482
80. Davydov D.R., Halpert J.R., Renaud J.P., and Hoa G.H.B. Conformational heterogeneity of cytochrome P450 3A4 revealed by high pressure spectroscopy. Biochem. Biophys. Res. Commun. 312 (2003) 121-130
81. Davydov D.R., Petushkova N.A., Archakov A.I., and Hoa G.H.B. Stabilization of P4502B4 by its association with P450 1A2 revealed by high-pressure spectroscopy. Biochem. Biophys. Res. Commun. 276 (2000) 1005-1012
82. Ekroos M., and Sjörgen T. Structural basis for ligand promiscuity in cytochrome P450 3A4. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 13682-13687