Mutants of cytochrome P450 reductase lacking either gly-141 or gly-143 destabilize its FMN semiquinone

Journal of Biological Chemistry

Volumn 291, Issue 28, 2016, Pages 14639-14661

  Rwere, Freeborn ^a   Xia, Chuanwu ^b   Im, Sangchoul ^a   Haque, Mohammad M ^c   Stuehr, Dennis J ^c   Waskell, Lucy ^a   Kim, Jung Ja P ^b  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b MEDICAL COLLEGE OF WISCONSIN   (United States)

^c LERNER RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYST ACTIVITY;

BIOCHEMICAL MECHANISMS; CYTOCHROME P450 BM3; CYTOCHROME P450 REDUCTASE; CYTOCHROMES P450; DELETION MUTANTS; ELECTRON TRANSFER; NEGATIVE POTENTIAL; STRUCTURAL BASIS;

PHENOLS;

CYTOCHROME C; CYTOCHROME P450 2B4; CYTOCHROME P450 REDUCTASE; FERRICYANIDE; FLAVINE MONONUCLEOTIDE; GLYCINE; HYDROQUINONE; NEURONAL NITRIC OXIDE SYNTHASE; QUERCETIN; SEMIQUINONE; SODIUM DITHIONITE; CYTOCHROME P450; FLAVIN MONONUCLEOTIDE SEMIQUINONE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE FERRIHEMOPROTEIN REDUCTASE;

ARTICLE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DELETION MUTANT; ELECTRON TRANSPORT; ENZYME ACTIVITY; ENZYME STRUCTURE; HYDROGEN BOND; NONHUMAN; OXIDATION REDUCTION REACTION; PH; PRIORITY JOURNAL; PROTON TRANSPORT; STEADY STATE; WILD TYPE; AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; GENE DELETION; GENETICS; METABOLISM; MOLECULAR MODEL; POINT MUTATION; PROTEIN CONFORMATION; RAT; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; ANIMALS; CYTOCHROME P-450 ENZYME SYSTEM; CYTOCHROMES C; ELECTRON TRANSPORT; FLAVIN MONONUCLEOTIDE; GLYCINE; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; NADP; NADPH-FERRIHEMOPROTEIN REDUCTASE; OXIDATION-REDUCTION; POINT MUTATION; PROTEIN CONFORMATION; RATS; SEQUENCE DELETION;

EID: 84978958357     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M116.724625     Document Type: Article

References (70)

1. Massey, V., and Hemmerich, P. (1980) Active-site probes of flavoproteins. Biochem. Soc. Trans. 8, 246-257
2. Røhr, A. K., Hersleth, H.-P., and Andersson, K. K. (2010) Tracking flavin conformations in protein crystal structures with Raman spectroscopy and QM/MM calculations. Angew. Chem. Int. Ed. Engl. 49, 2324-2327
3. Cui, D., Koder, R. L., Jr., Dutton, P. L., and Miller, A.-F. (2011) 15N solidstate NMR as a probe of flavin H-bonding. J. Phys. Chem. B 115, 7788-7798
4. Evans, E. W., Dodson, C. A., Maeda, K., Biskup, T., Wedge, C. J., and Timmel, C. R. (2013) Magnetic field effects in flavoproteins and related systems. Interface Focus 3, 20130037
5. Miura, R. (2001) Versatility and specificity in flavoenzymes: control mechanisms of flavin reactivity. Chem. Rec. 1, 183-194
6. Ghisla, S., and Massey, V. (1989) Mechanisms of flavoprotein-catalyzed reactions. Eur. J. Biochem. 181, 1-17
7. Senda, T., Senda, M., Kimura, S., and Ishida, T. (2009) Redox control of protein conformation in flavoproteins. Antioxid. Redox Signal. 11, 1741-1766
8. Ghisla, S., and Massey, V. (1986) New flavins for old: artificial flavins as active site probes of flavoproteins. Biochem. J. 239, 1-12
9. Mayhew, S. G. (1999) The effects of pH and semiquinone formation on the oxidation-reduction potentials of flavin mononucleotide: a reappraisal. Eur. J. Biochem. 265, 698-702
10. Iyanagi, T., Xia, C., and Kim, J. J. (2012) NADPH-cytochrome P450 oxidoreductase: prototypic member of the diflavin reductase family. Arch. Biochem. Biophys. 528, 72-89
11. Breinlinger, E. C., Keenan, C. J., and Rotello, V. M. (1998) Modulation of flavin recognition and redox properties through donor atom-π interactions. J. Am. Chem. Soc. 120, 8606-8609
12. Koziol, L., Kumar, N., Wong, S. E., and Lightstone, F. C. (2013) Molecular recognition of aromatic rings by flavin: electrostatics and dispersion determine ring positioning above isoalloxazine. J. Phys. Chem. A 117, 12946-12952
13. Paine, M. J., Scrutton, N. S., Munro, A. W., Gutierrez, A., Roberts, G. C. K., and Wolf, C. R. (2005) in Cytochrome P450 (Ortiz de Montellano, P. R., ed) 3rd Ed., pp. 115-148, Kluwer Academic/Plenum Publishers, New York
14. Ortiz de Montellano, P. R. (2010) Hydrocarbon hydroxylation by cytochrome P450 enzymes. Chem. Rev. 110, 932-948
15. Guengerich, F. P. (2005) in Cytochrome P450: Structure, Mechanism and Biochemistry (Ortiz de Montellano, P. R., ed.) 3rd Ed., pp. 377-463, Kluwer Academic/Plenum Publishers, New York.
16. Guengerich, F. P. (2015) in Cytochrome P450: Structure, Mechanism and Biochemistry (Ortiz de Montellano, P. R., ed) 4th Ed., pp. 523-785, Springer International Publishers, Switzerland
17. Im, S. C., and Waskell, L. (2011) The interaction of microsomal cyto-chrome P450 2B4 with its redox partners, cytochrome P450 reductase and cytochrome b5. Arch. Biochem. Biophys. 507, 144-153
18. Schacter, B. A., Nelson, E. B., Marver, H. S., and Masters, B. S. (1972) Immunochemical evidence for an association of heme oxygenase with the microsomal electron transport system. J. Biol. Chem. 247, 3601-3607
19. Guengerich, F. P. (2005) Reduction of cytochrome b5 by NADPH-cytochrome P450 reductase. Arch. Biochem. Biophys. 440, 204-211
20. Oprian, D. D., and Coon, M. J. (1982) Oxidation-reduction states of FMN and FAD in NADPH-cytochrome P-450 reductase during reduction by NADPH. J. Biol. Chem. 257, 8935-8944
21. Vermilion, J. L., Ballou, D. P., Massey, V., and Coon, M. J. (1981) Separate roles for FMN and FAD in catalysis by liver microsomal NADPH-cytochrome P-450 reductase. J. Biol. Chem. 256, 266-277
22. Porter, T. D., and Kasper, C. B. (1986) NADPH-cytochrome P450 oxidoreductase: flavin mononucleotide and flavin adenine dinucleotide domains evolved from different flavoproteins. Biochemistry 25, 1682-1687
23. Sevrioukova, I., Shaffer, C., Ballou, D. P., and Peterson, J. A. (1996) Equilibrium and transient state spectrophotometric studies of the mechanism of reduction of the flavoprotein domain of P450 BM3. Biochemistry 35, 7058-7068
24. Sevrioukova, I. F., Li, H., Zhang, H., Peterson, J. A., and Poulos, T. L. (1999) Structure of a cytochrome P450-redox partner electron-transfer complex. Proc. Natl. Acad. Sci. U.S.A. 96, 1863-1868
25. Li, H., Das, A., Sibhatu, H., Jamal, J., Sligar, S. G., and Poulos, T. L. (2008) Exploring the electron transfer properties of neuronal nitric-oxide synthase by reversal of the FMN redox potential. J. Biol. Chem. 283, 34762-34772
26. Wang, M., Roberts, D. L., Paschke, R., Shea, T. M., Masters, B. S., and Kim, J. J. (1997) Three-dimensional structure of NADPH-cytochrome P450 reductase: prototype for FMN-and FAD-containing enzymes. Proc. Natl. Acad. Sci. U.S.A. 94, 8411-8416
27. Hubbard, P. A., Shen, A. L., Paschke, R., Kasper, C. B., and Kim, J. J. (2001) NADPH-cytochrome P450 oxidoreductase. Structural basis for hydride and electron transfer. J. Biol. Chem. 276, 29163-29170
28. Xia, C., Panda, S. P., Marohnic, C. C., Martásek, P., Masters, B. S., and Kim, J.-J. (2011) Structural basis for human NADPH-cytochrome P450 oxidoreductase deficiency. Proc. Natl. Acad. Sci. U.S.A. 108, 13486-13491
29. Munro, A. W., Noble, M. A., Robledo, L., Daff, S. N., and Chapman, S. K. (2001) Determination of the redox properties of human NADPH-cytochrome P450 reductase. Biochemistry 40, 1956-1963
30. Zhou, Z., and Swenson, R. P. (1995) Electrostatic effects of surface acidic amino acid residues on the oxidation-reduction potentials of the flavodoxins from Desulfovibrio vulgaris. (Hildenborough). Biochemistry 34, 3183-3192
31. O'Farrell, P. A., Walsh, M. A., McCarthy, A. A., Higgins, T. M., Voordouw, G., and Mayhew, S. G. (1998) Modulation of the redox potentials of FMN in Desulfovibrio vulgaris flavodoxin: thermodynamic properties and crystal structures of glycine-61 mutants. Biochemistry 37, 8405-8416
32. Garcin, E. D., Bruns, C. M., Lloyd, S. J., Hosfield, D. J., Tiso, M., Gachhui, R., Stuehr, D. J., Tainer, J. A., and Getzoff, E. D. (2004) Structural basis for isozyme-specific regulation of electron transfer in nitric-oxide synthase. J. Biol. Chem. 279, 37918-37927
33. Hoover, D. M., Drennan, C. L., Metzger, A. L., Osborne, C., Weber, C. H., Pattridge, K. A., and Ludwig, M. L. (1999) Comparisons of wild type and mutant flavodoxins from Anacystis nidulans. Structural determinants of the redox potentials. J. Mol. Biol. 294, 725-743
34. Ludwig, M. L., Pattridge, K. A., Metzger, A. L., Dixon, M. M., Eren, M., Feng, Y., and Swenson, R. P. (1997) Control of oxidation-reduction potentials in flavodoxin from Clostridium beijerinckii: The role of conformation changes. Biochemistry 36, 1259-1280
35. Watt, W., Tulinsky, A., Swenson, R. P., and Watenpaugh, K. D. (1991) Comparison of the crystal structures of a flavodoxin in its three oxidation states at cryogenic temperatures. J. Mol. Biol. 218, 195-208
36. Kasim, M., Chen, H. C., and Swenson, R. P. (2009) Functional characterization of the re-face loop spanning residues 536-541 and its interactions with the cofactor in the flavin mononucleotide-binding domain of flavocytochrome P450 from Bacillus megaterium. Biochemistry 48, 5131-5141
37. Hamdane, D., Xia, C., Im, S. C., Zhang, H., Kim, J. J., and Waskell, L. (2009) Structure and function of an NADPH-cytochrome P450 oxidoreductase in an open conformation capable of reducing cytochrome P450. J. Biol. Chem. 284, 11374-11384
38. Miroux, B., and Walker, J. E. (1996) Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels. J. Mol. Biol. 260, 289-298
39. Kurzban, G. P., and Strobel, H. W. (1986) Preparation and characterization of FAD-dependent NADPH-cytochrome P-450 reductase. J. Biol. Chem. 261, 7824-7830
40. Saribas, A. S., Gruenke, L., and Waskell, L. (2001) Overexpression and purification of the membrane-bound cytochrome P450 2B4. Protein Expr. Purif. 21, 303-309
41. Bridges, A., Gruenke, L., Chang, Y. T., Vakser, I. A., Loew, G., and Waskell, L. (1998) Identification of the binding site on cytochrome P450 2B4 for cytochrome b5 and cytochrome P450 reductase. J. Biol. Chem. 273, 17036-17049
42. Dutton, P. L. (1978) Redox potentiometry: determination of midpoint potentials of oxidation-reduction components of biological electrontransfer systems. Methods Enzymol. 54, 411-435
43. Chen, H. C., and Swenson, R. P. (2008) Effect of the insertion of a glycine residue into the loop spanning residues 536-541 on the semiquinone state and redox properties of the flavin mononucleotide-binding domain of flavocytochrome P450BM-3 from Bacillus megaterium. Biochemistry 47, 13788-13799
44. McPherson, A. (1999) Crystallization of Biological Macromolecules, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
45. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326
46. Brunger, A. T. (2007) The Crystallography and NMR System. Version 1.2. Nat. Protoc. 2, 2728-2733
47. Emsley, P., and Cowtan, K. (2004) Coot: Model-building Tool for Molecular Graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132
48. Xia, C., Hamdane, D., Shen, A. L., Choi, V., Kasper, C. B., Pearl, N. M., Zhang, H., Im, S. C., Waskell, L., and Kim, J. J. (2011) Conformational changes of NADPH-cytochrome P450 oxidoreductase are essential for catalysis and cofactor binding. J. Biol. Chem. 286, 16246-16260
49. Hutchinson, E. G., and Thornton, J. M. (1994) A revised set of potentials for β-turn formation in proteins. Protein Sci. 3, 2207-2216
50. Luschinsky, C. L., Dunham, W. R., Osborne, C., Pattridge, K. A., and Ludwig, M. L. (1991) in Flavins and Flavoproteins (Curti, B. S., Ronchi, S., and Zanetti, G., eds) pp. 409-413, Walter de Gruyter, Berlin
51. Chang, F. C., and Swenson, R. P. (1999) The midpoint potentials for the oxidized-semiquinone couple for GLY57 mutants of the Clostridium beijerinckii flavodoxin correlate with changes in the hydrogen-bonding interaction with the proton on N(5) of the reduced flavin mononucleotide cofactor as measured by NMR chemical shift temperature dependencies. Biochemistry 38, 7168-7176
52. Goñi, G., Serrano A., Frago, S., Hervás, M., Peregrina J. R., De la Rosa, M. A., Gómez-Moreno, C., Navarro, J. A., and Medina, M. (2008) Flavodoxin-mediated electron transfer from photosystem I to ferredoxin-NADP+ reductase in anabaena: role of flavodoxin hydrophobic residues in protein-protein interactions. Biochemistry 47, 1207-1217
53. Deane, C. M., Allen, F. H., Taylor, R., and Blundell, T. L. (1999) Carbonyl-carbonyl interactions stabilize the partially allowed Ramachandran conformations of asparagine and aspartic acid. Protein Eng. 12, 1025-1028
54. Yang, A. S., Hitz, B., and Honig, B. (1996) Free energy determinants of secondary structure formation: III. β-turns and their role in protein folding. J. Mol. Biol. 259, 873-882
55. Johansson L. B., Davidsson, A., Lindblom, G., and Naqvi, K. R. (1979) Electronic transitions in the isoalloxazine ring and orientation of the flavin in the model membranes studied by polarized light spectroscopy. Biochemistry 18, 4249-4253
56. Nishimoto, K., Watanabe, Y., and Yagi, K. (1978) Hydrogen bonding of flavoprotein. I. Effect of hydrogen bonding on electronic spectra of flavoprotein. Biochim. Biophys. Acta. 526, 34-41
57. Iyanagi, T., Makino, N., and Mason, H. S. (1974) Redox properties of the reduced nicotinamide adenine dinucleotide phosphate-cyto-chrome P-450 and reduced nicotinamide adenine dinucleotide-cytochrome b5 reductases. Biochemistry 13, 1701-1710
58. Das, A., and Sligar, S. G. (2009) Modulation of the cytochrome P450 reductase redox potential by the phospholipid bilayer. Biochemistry 48, 12104-12112
59. Wolthers, K. R., Basran, J., Munro, A. W., and Scrutton, N. S. (2003) Molecular dissection of human methionine synthase reductase: determination of the flavin redox potentials in full-length enzyme isolate flavinbinding domains. Biochemistry 42, 3911-3920
60. Zhang, H., Gruenke, L., Arscott, D., Shen, A., Kasper, C., Harris, D. L., Glavanovich, M., Johnson, R., and Waskell, L. (2003) Determination of the rate of reduction of oxyferrous cytochrome P450 2B4 by 5-deazaFAD T491V cytochrome P450 reductase. Biochemistry 42, 11594-11603
61. Draper, R. D., and Ingraham, L. L. (1968) A potentiometric study of the flavin semiquinone equilibrium. Arch. Biochem. Biophys. 125, 802-808
62. Anderson, R. F. (1983) Energetics of the one-electron reduction steps of riboflavin, FMN and FAD to their fully reduced forms. Biochim. Biophys. Acta 722, 158-162
63. Sevrioukova, I., Truan, G., and Peterson, J. A. (1996) The flavoprotein domain of P450 BM3: expression, purification, and properties of the flavin adenine dinucleotide-and flavin mononucleotide-binding subdomains. Biochemistry 35, 7528-7535
64. Shen, A. L., Porter, T. D., Wilson, T. E., and Kasper, C. B. (1989) Structural analysis of the FMN binding domain of NADPH-cytochrome P-450 oxidoreductase by site-directed mutagenesis. J. Biol. Chem. 264, 7584-7589
65. Massey, V. (1994) Activation of molecular oxygen by flavins and flavoproteins. J. Biol. Chem. 269, 22459-22462
66. Edmondson, D. E., Barman, B., and Tollin, G. (1972) On the importance of the N-5 position in flavin coenzymes, properties of free and proteinbound 5-deaza analogs. Biochemistry 11, 1133-1138
67. Massey, V. (2002) The reactivity of oxygen with flavoproteins. International Congress Series 1233, 3-11
68. Hanley, S. C., Ost, T. W., and Daff, S. (2004) The unusual redox properties of flavocytochrome P450 BM3 flavodoxin domain. Biochem. Biophys. Res. Commun. 325, 1418-1423
69. Chang, C. W., He, T. F., Guo, L., Stevens, J. A., Li, T., Wang, L., and Zhong, D. (2010) Mapping solvation dynamics at the function site of flavodoxin in three redox states. J. Am. Chem. Soc. 132, 12741-12747
70. Leenders, R., van Gunsteren, W. F., Berendsen, H. J., and Visser, A. J. (1994) Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin. Biophys. J. 66, 634-645