Structural evidence for a functionally relevant second camphor binding site in P450cam: Model for substrate entry into a P450 active site

Proteins: Structure, Function and Genetics

Volumn 69, Issue 1, 2007, Pages 125-138

  Yao, Huili ^a   McCullough, Christopher R ^a   Costache, Aurora D ^a   Pullela, Phani Kumar ^a   Sem, Daniel S ^a  

^a Marquette University   (United States)

Author keywords

Access channel; Binding site; Camphor; CYP; Cytochrome P450; Docking; F G loop; NMR; Structure

Indexed keywords

CAMPHOR; CAMPHOR 5 MONOOXYGENASE; CYTOCHROME P450; HEME; IRON; PYRIDINE; THREONINE;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG STRUCTURE; ENZYME BINDING; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; ULTRAVIOLET RADIATION;

BINDING SITES; CAMPHOR; CAMPHOR 5-MONOOXYGENASE; CRYSTALLOGRAPHY, X-RAY; KINETICS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY;

DRYOBALANOPS; RUMEX;

EID: 34548309047     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21508     Document Type: Article

References (47)

1. Klingenberg M. Pigments of rat liver microsomes. Arch Biochem Biophys 1958;75:376-386.
2. Petsko GA, Ringe D. Protein structure and function. Sunderland, MA: Sinauer Associates; 2004.
3. Poulos TL, Finzel BC, Gunsalus IC, Wagner GC, Kraut J. The 26-Å crystal structure of Pseudomonas putida cytochrome P-450. J Biol Chem 1985;260:16122-16124.
4. Williams PA, Cosme J, Sridhar V, Johnson EF, McRee DE. Mammalian microsomal cytochrome P450 monooxygenase: structural adaptations for membrane binding and functional diversity. Mol Cell 2000;5:121-131.
5. Poulos TL, Finzel BC, Howard AJ. Crystal structure of substrate-free Pseudomonas putida cytochrome P-450. Biochemistry 1986;25:5314-5322.
6. Poulos TL, Finzel BC, Howard AJ. High-resolution crystal structure of cytochrome P450cam. J Mol Biol 1987;195:687-700.
7. Fedorov R, Ghosh DK, Schilichting I. Crystal structures of cyanide complexes of P450cam and the oxygenase domain of inducible nitric oxide synthase-structural models of the short-lived oxygen complexes. Arch Biochem Biophys 2003;409:25-31.
8. Raag R, Poulos TL. Crystal structure of the carbon monoxide-substrate- cytochrome P-450cam ternary complex. Biochemistry 1989;28:7586-7592.
9. Nagano S, Poulos TLJ. Crystallographic study on the dioxygen complex of wild-type and mutant cytochrome P450cam. Implications for the dioxygen activation mechanism. J Biol Chem 2005;280:31659-31663.
10. Poulos TL, Johnson EF. Structures of cytochrome P450 enzymes. In: Ortiz de Montellano P, editor. Cytochrome P450: structure, function and biochemistry, 3rd ed. New York: Plenum Press; 2005. pp. 87-114.
11. Makris TM, Denisov I, Schichting I, Sligar SG. Activation of molecular oxygen by cytochrome P450. In: Ortiz de Montellano P, editor. Cytochrome P450: structure, function and biochemistry, 3rd ed. New York: Plenum Press; 2005. pp. 149-182.
12. Winn PJ, Lüdemann SK, Gauges R, Lounnas V, Wade RC. 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. Prot Natl Acad Sci USA 2002;99:5361-5366.
13. Wade RC, Winn PJ, Schlichting I, Sudarko. A survey of active site access channels in cytochromes P450. Inorg Biochem 2004;98:1175-1182.
14. Pochapsky SS, Pochapsky TC, Wei JW. A model for effector activity in a highly specific biological electron transfer complex: the cytochrome P450cam-putidaredoxin couple. Biochemistry 2003;42: 5649-5656.
15. Modi S, Sutcliffe MJ, Primrose WU, Lian L, Roberts GCK. The catalytic mechanism of cytochrome P450 BM3 involves a 6 Å movement of the bound substrate on reduction. Nat Struct Biol 1996;3: 414-417.
16. Isin EM, Guengerich FP. Kinetics and thermodynamics of ligand binding by cytochrome P450 3A4. J Biol Chem 2006;281:9127-9136.
17. Dunn AR, Dmochowski IJ, Bilwes AM, Gray HB, Crane BR. Probing the open state of cytochrome P450cam with ruthenium-linker substrates. Proc Natl Acad Sci USA 2001;98:12420-12425.
18. Hays AM, Dunn AR, Chiu R, Gray HB, Stout CD, Goodin DB. Conformational states of cytochrome P450cam revealed by trapping of synthetic molecular wires. J Mol Biol 344;455-469.
19. Dunn AR, Dmochowski IJ, Winkler JR, Gray HB. Nanosecond photoreduction of cytochrome p450cam by channel-specific Ru-diimine electron tunneling wires. J Am Chem Soc 2003;125:12450-12456.
20. Narasimhulu S, Havran LM, Axelsen PH, Winkler JD. Interactions of substrate and product with cytochrome P450: P4502B4 versus P450cam. Arch Biochem Biophys 1998;353:228-238.
21. Marden MC, Hui Bon Hoa G. P-450 binding to substrates camphor and linalool versus pressure. Arch Biochem Biophys 1987;253:100-107.
22. Lee H, Ortiz de Montellano PR, McDermott AE. Deuterium magic angle spinning studies of substrates bound to cytochrome P450. Biochemistry 1999;38:10808-10813.
23. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP. AM1: A New General Purpose Quantum Mechanical Molecular Model. J Am Chem Soc 1985;107:3902-3909.
24. Gasteiger J, Marsili M. Iterative partial equilization of orbital electronegativity - A rapid access to atomic charges. Tetrahedron 1980;36:3219-3228.
25. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J Comput Chem 1998;19:1639-1662.
26. Sibbesen O, De Voss JJ, Ortiz de Montellano PR. Putidaredoxin reductase-putidaredoxin-cytochrome P450cam triple fusion protein. J Biol Chem 1996;271:22462-22469.
27. Nickerson DP, Wong LL. The dimerization of Pseudomonas putida cytochrome P450cam: practical consequences and engineering of a monomeric enzyme. Protein Eng 1997;10:1357-1361.
28. Gunsalus IC, Wagner GC. Bacterial P-450cam methylene monooxygenase components: cytochrome m, putidaredoxin, and putidaredoxin reductase. Methods Enzymol 1978;52:166-188.
29. Marley J, Lu M, Bracken C. A method for efficient isotopic labeling of recombinant proteins. J Biomol NMR 2001;20:71-75.
30. Lipscomb JD. Electron paramagnetic resonance detectable states of cytochrome P-450cam. Biochemistry 1980;19:3590-3599.
31. Unno M, Christian JF, Benson DE, Gerber NC, Sligar SG, Champion PM. Resonance Raman investigations of cytochrome P450cam complexed with putidaredoxin. J Am Chem Soc 1997;119:6614-6620.
32. Solomon I, Bloembergen N. Nuclear Magnetic interactions in the HF molecule. J Chem Phys 1956;25:261-266.
33. Jardetzky O, Roberts GCK. NMR in molecular biology. New York: Academic Press; 1981.
34. Yao H, Costache AD, Sem DS. Chemical proteomic tool for ligand mapping of CYP antitargets: an NMR-compatible 3D QSAR descriptor in the heme-based coordinate system. J Chem Informat Comput Sci 2004;44:1456-1465.
35. Modi S, Paine MJ, Sutcliffe MJ, Lian LY, Primrose WU, Wolf CR, Roberts GCK. A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding. Biochemistry 1996;35:4540-4550.
36. Poli-Scaife S, Attias R, Dansette PM, Mansuy D. The substrate binding site of human liver cytochrome P450 2C9: an NMR study. Biochemistry 1997;36:12672-12682.
37. Modi S, Primrose WU, Boyle JMB, Gibson CF, Lian L, Roberts GCK. NMR studies of substrate binding to cytochrome P450 BM3: comparisons to cytochrome P450cam. Biochemistry 1995;34:8982-8988.
38. Li S, Wackett LP. Reductive dehalogenation by cytochrome P450cam: substrate binding and catalysis. Biochemistry 1993;32:9355-9361.
39. 1H-NMR resonances of high-spin and low-spin ferric complexes of cytochrome P450cam using one-dimensional and two-dimensional paramagnetic signals enhancement (PASE) magnetization transfer experiments. Eur J Biochem 2000;267:216-221.
40. Griffin BW, Peterson JA. Pseudomonas putida cytochrome P-450 The effect of complexes of the ferric hemeprotein on the relaxation of solvent water protons. J Biol Chem 1975;250:6445-6451.
41. 19F nuclear magnetic resonance as a probe of the spatial relationship between the heme iron of cytochrome P-450 and its substrate. J Biol Chem 1989;264:2649-2655.
42. Wei JY, Pochapsky TC, Pochapsky SS. Detection of a high-barrier conformational change in the active site of cytochrome P450cam upon binding of putidaredoxin. J Am Chem Soc 2005;127:6874-6976.
43. Tugarinov V, Kay LE. Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins. Chembiochem 2005;6:1567-1577.
44. Pellecchia M, Meininger D, Dong Q, Chang E, Jack R, Sem DS. NMR-based structural characterization of large protein-ligand interactions. J Biomol NMR 2002;22:165-173.
45. Griffin BW, Peterson JA. Camphor binding by Pseudomonas putida cytochrome P-450. Kinetics and thermodynamics of the reaction. Biochemistry 1972;11:4740-4746.
46. Sem DS. NMR-guided fragment assembly. In: Jahnke W, Erlanson DA, editors. Fragment-based approaches in drug discovery; Weinheim: Wiley-VCH; 2006. pp 163-167.
47. Vidakovic M, Sligar SG, Li H, Poulos TL. Understanding the role of the essential Asp251 in cytochrome P450cam using site-directed mutagenesis, crystallography, and kinetic solvent isotope effects. Biochemistry 1998;37:9211-9219.