Homology modeling and substrate binding study of human CYP4A11 enzyme

Proteins: Structure, Function and Genetics

Volumn 34, Issue 3, 1999, Pages 403-415

  Chang, Yan Tyng ^a   Loew, Gilda H ^a  

^a MOLECULAR RESEARCH INSTITUTE   (United States)

Author keywords

hydroxylation; CYP4A11; Homology modeling; Laurie acid

Indexed keywords

CYTOCHROME P450; ENZYME; HYDROGEN; ISOENZYME; LAURIC ACID; LONG CHAIN FATTY ACID; OXYGEN; OXYGENASE;

ARTICLE; BINDING AFFINITY; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; HYDROXYLATION; MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

ALKANE 1-MONOOXYGENASE; AMINO ACID SEQUENCE; BINDING SITES; COMPUTER SIMULATION; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; CYTOCHROME P-450 ENZYME SYSTEM; HUMANS; LAURIC ACIDS; LIGANDS; MIXED FUNCTION OXYGENASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; SEQUENCE ALIGNMENT; SOFTWARE; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); MAMMALIA;

EID: 0033557287     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990215)34:3<403::AID-PROT12>3.0.CO;2-D     Document Type: Article

References (55)

1. Simpson AECM. The cytochrome P450 4 (CYP4) family. Gen Pharmacol 1997;28:351-359.
2. Nelson DR, Koymans L, Kamataki T. et al. P450 superfamily: Update on new sequences, gene mapping, accession numbers, and nomenclature. Pharmacogenetics 1996;6:1-42.
3. Johnson EF, Palmer CNA, Griffin KJ, Hsu M-H. Role of the peroxisome proliferator-activated receptor in cytochrome P450 4A gene regulation. FASEB J 1996;10:1241-1248.
4. Miura Y, Fulco AJ. ω-1, ω-2, and ω-3 hydroxylation of long-chain fatty acids, amides and alcohols by a soluble enzyme system from Bacillus megaterium. Biochim Biophys Acta 1975;388: 305-317.
5. Ho PP, Fulco AJ. Involvement of a single hydroxylase species in the hydroxylation of palmitate at the omega-1, omega-2 and omega-3 positions by a preparation from Bacillus megaterium. Biochim Biophys Acta 1976;431:249-256.
6. Ruettinger RT, Fulco AJ. Epoxidation of unsaturated fatty acids by a soluble cytochrome P450-dependent system from Bacillus megaterium. J Biol Chem 1981;256:5728-5734.
7. Capdevila JH, Falck JR, Estabrook RW. Cytochrome P450 and the arachidonate cascade. FASEB J 1992;6:731-736.
8. Laethem RM, Halpert JR, Koop DR. Epoxidation of arachidonic acid as an active-site probe of cytochrome P450 2B isoforms. Biochim Biophys Acta 1994;1206:42-48.
9. Fukuda T, Imai Y, Komori M. et al. Different mechanisms of regioselection of fatty acid hydroxylation by laurate (omega-1)-hydroxylating P450s, P450 2C2 and P450 2E1. J Biochem (Tokyo) 1994;115:338-344.
10. Imaoka S, Wedlund PJ, Ogawa H, Kimura S, Gonzalez FJ, Kim HY. Identification of CYP2C23 expressed in rat kidney as an arachidonic acid epoxygenase. J Pharmacol Exp Ther 1993;267: 1012-1016.
11. Amet Y, Berthou F, Goasduff T, Salaun JP, Ke Breton L, Menez JF. Evidence that cytochrome P450 2E1 is involved in the omega-1-hydroxylation of lauric acid in rat liver microsomes. Biochem Biophys Res Commun 1994;203:1168-1174.
12. Buhler DR, Miranda CL, Deinzer ML, Griffin DA, Henderson MC. The regiospecific hydroxylation of lauric acid by rainbow trout (Oncorhynchus mykiss) cytochrome P450s. Drug Metab Dispos 1997;25:1176-1183.
13. Ma Y-H, Gebremedhin D, Schwartzman ML. et al. 20-hydroxyeico-satetraenoic acid is an endogenous vasoconstrictor of canine renal arcuate arteries. Circ Res 1993;72:126-136.
14. Zou A-P, Ma Y-H, Sui Z-H. et al. Effects of 17-octadecynoic acid, a suicide-substrate inhibitor of cytochrome P450 fatty acid ω-hydroxylase, on renal function in rats. J Pharmacol Exp Ther 1993;268:474-481.
15. Zou A-P, Imig JD, Ortiz de Montellano PR, Sui Z-H, Falck JR, Roman RJ. Effect of P450 ω-hydroxylase metabolites of arachidonic acid on tubuloglomerular feedback. Am J Physiol 266 (Renal Fluid Electrolyte Physiol) 1994;35:F934-F941.
16. Kerr JA. Bond dissociation energies by kinetic methods. Chem Rev 1966;66:465-500.
17. Collins JR, Camper DL, Loew GH. Valproic acid metabolism by cytochrome P450: A theoretical study of stereoelectronic modulators of product distribution. J Am Chem Soc 1991;113: 2736-2743.
18. Harris D, Loew GH. Prediction of regiospecific hydroxylation of camphor analogs by cytochrome P450cam. J Am Chem Soc 1995;117:2837-2746.
19. Chang YT, Loew GH, Rettie AE, Baillie TA., Sheffels PR., Ortiz de Montellano PR. Binding of flexible ligands to proteins: Valproic acid and its interaction with cytochrome P450cam. Int J Quantum Chem:QBS. 1993;20:161-180.
20. Cook BR, Reinert TJ, Suslick KS. Shape selective alkane hydroxylation by metalloporphyrin catalysts. J Am Chem Soc 1986;108: 7281-7286.
21. Ortiz de Montellano PR, Reich NO. Specific inactivation of hepatic fatty acid hydroxylases by acetylenic fatty acids. J Biol Chem 1984;259:4136-4141.
22. Ortiz de Montellano PR, Chan WK, Tuck SF, Kaikaus RM, Bass NM, Peterson JA. Mechanism-based probes of the topology and function of fatty acid hydroxylases. FASEB J 1992;6: 695-699.
23. CaJacob CA, Chan WK, Shephard E, Ortiz de Montellano PR. The catalytic site of rat hepatic lauric acid ω-hydroxylase. J Biol Chem 1988;263:18640-18649.
24. Dierks EA, Davis SC, Ortiz de Montellano PR. Glu-320 and Asp-323 are determinants of the CYP4A1 hydroxylation regiospecificity and resistance to inactivation by 1-aminobenzotriazole. Biochemistry 1998;37:1839-1847.
25. Alterman MA, Chaurasia CS, Lu P, Hardwick JP, Hanzlik RP. Fatty acid discrimination and ω-hydroxylation by cytochrome P450 4A1 and a cytochrome P450 4A1/NADPH-P450 reductase fusion protein. Arch Biochem Biophys 1995;320:289-296.
26. Alterman MA, Chaurasia CS, Lu P, Hanzlik RP. Heteroatom substitution shifts regioselectivity of lauric acid metabolism from ω-hydroxylation to (ω-1)-oxidation. Biochem Biophys Res Comm 1995;214:1089-1094.
27. Bambal RB, Hanzlik RP. Active site structure and substrate specificity of cytochrome P450 4A1: Steric control of ligand approach perpendicular to heme plane. Biochem Biophys Res Commun 1996;219:445-449.
28. Lu P, Alterman MA, Chaurasia CS, Bambal RB, Hanzlik RP. Heme-coordinating analogs of lauric acid as inibitors of fatty acid omega hydroxylation. Arch Biochem Biophys 1997;337:1-7.
29. Lewis DFV. Three dimensional models of human and other mammalian microsomal P450s constructed from an alignment with P450102 (P450bm3). Xenobiotica 1995;25:333-366.
30. Poulos TL, Finzel BC, Howard AJ. Crystal structure of substrate-free Pseudomonas putida cytochrome P-450. Biochemistry 1986; 25:5314-5322.
31. Hasemann CA, Ravichandran KG, Peterson JA, Deisenhofer J. Crystal structure and refinement of cytochrome P450 terp at 2.3 Å resolution. J Mol Biol 1994;236:1169-1185.
32. Ravichandran KG, Boddupalli SS, Hasemann CA, Peterson JA, Deisenhofer J. Crystal structure of the hemoprotein domain of P450BM-3, a prototype for microsomal P450s. Science 1993;261: 731-736.
33. Li H, Poulos TL. Modeling protein-substrate interactions in the haem domain of cytochrome P450BM-3. Acta Crystallogr D 1995; 51:21-32.
34. Cupp-Vickery JR, Poulos TL. Structure of cytochrome P450eryF involved in erythromycin biosynthesis. Nat Struct Biol 1995;2:144-153.
35. Chang YT, Loew GH. Construction and evaluation of a three-dimensional structure of cytochrome P450choP enzyme (CYP105C1). Protein Eng 1996;9:755-766.
36. Chang YT, Stiffelman OB, Vakser IA, Loew GH, Bridges A, Waskell L. Construction of a 3D model of cytochrome P450 2B4. Protein Eng 1997;10:119-129.
37. Palmer CNA, Richardson TH, Griffin KJ. et al. Characterization of a cDNA encoding a human kidney, cytochrome P-450 4A fatty acid ω-hydroxylase and the cognate enzyme expressed in Escherichia coli. Biochim Biophys Acta 1993;1172:161-166.
38. Imaoka S, Ogawa H, Kimura S, Gonzalez FJ. Complete cDNA sequence and cDNA-directed expression of CYP4A11, a fatty acid omega-hydroxylase expressed in human kidney. DNA Cell Biol 1993;12:893-899
39. Orcutt BC, Dayhoff MO, Barker WC. ALIGN. Washington, DC: National Biomedical Foundation, Georgetown University Medical Center; 1982.
40. Rost B, Sander C. Combining evolutionary information and neural networks to predict protein secondary structures. Proteins 1994;19:55-72.
41. Hasemann CA, Kurumbail RG, Boddupalli SS, Peterson JA, Deisenhofer J. Structure and function of cytochrome P450: A comparative analysis of three crystal structures. Structure 1995;3:41-62.
42. Insight, Release 95.0. San Diego: Biosym/MSI; 1995.
43. Sippl MJ. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J Comput Aided Mol Des 1993;7:473-501.
44. Holm L, Sander C. Database algorithm for building full backbone and sidechain coordinates from a protein Cα trace. Application to model building and detection of coordinate errors. J Mol Biol 1991;218:183-194.
45. Dunbrack Jr. RL, Karplus M. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nat Struct Biol 1994;1:334-340.
46. Bower MJ, Cohen FE, Dunbrack Jr. RL. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool. J Mol Biol 1997;267:1268-1282.
47. Pearlman DA, Case DA, Caldwell JW. et al. AMBER 4.1, San Francisco: University of California; 1995.
48. Zhao D, Gilfoyle DJ, Smith AT, Loew GH. Refinement of 3D models of horseradish peroxidase isoenzyme C: Predictions of 2D NMR assignments and substrate binding sites. Proteins 1996;26: 204-216.
49. Luthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992;356:83-85.
50. Vriend G, Sander C. Quality control of protein models: Directional atomic contact analysis. J Appl Crystallogr 1993;26:47-60.
51. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. Procheck: A program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291.
52. Dierks EA, Zhang Z, Johnson EF, Ortiz de Montellano PR. The catalytic site of cytochrome P450 4A11 (CYP4A11) and its L131F mutant. J Biol Chem 1998; 273:23055-23061.
53. Li H, Poulos TL. The structure of the cytochrome P450BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid. Nat Struct Biol 1997;4:140-146.
54. Du P, Loew GH. Molecular dynamics simulations of lignin peroxidase complexes for the prediction of substrate binding sites. In: Welinder KG et al., editors. Plant peroxidases: biochemistry and physiology. Geneva: University of Geneva; 1993. p 27-30.
55. Chang YT, Veitch NC, Loew GH. A theoretical study of benzhydroxamic acid binding modes in horseradish peroxidase. J Am Chem Soc 1998;120:5168-5178.