Abstract
Structures of nitric oxide reductase (NOR) in the ferric resting and the ferrous CO states have been solved at 2.0 Å resolution. These structures provide significant new insights into how NO is reduced in biological systems. The haem distal pocket is open to solvent, implicating this region as a possible NADH binding site. In combination with mutagenesis results, a hydrogen-bonding network from the water molecule adjacent to the iron ligand to the protein surface of the distal pocket through the hydroxyl group of Ser 286 and the carboxyl group of Asp 393 can be assigned to a pathway for proton delivery during the NO reduction reaction.
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References
Culotta, E. & Koshland, D.E. Jr. NO news is good news. Science 258, 1862–1865 (1992).
Stamler, J.S., Singel, D.S., Loscalzo, J. Biochemistry of nitric oxide and its redox-activated forms. Science 258, 1898–1902 (1992).
Coyne, M.S., Arunakumari, A.A., Averill, R.A., Tiedje, J.M. Immunological identification and distribution of dissimilatory heme cd1 and nonheme copper nitrite reductases in denitrifying bacteria. Appl. Environ. Microbiol. 55, 2924–2931 (1989).
Ferguson, S.J. Denitrification: a question of the control and organization of electron and ion transport. Trends Biochem. Sci. 12, 354–357 (1987).
Knowles, R. Denitrification. Microbiol. Rev. 46, 43–70 (1982).
Carr, G.J. & Ferguson, S.J. The nitric oxide reductase of Paracoccus denitrificans. Biochem. J. 269, 423–429 (1990).
Turk, T. & Hollocher, T.C. Oxidation of dithiothreitol during turnover of nitric oxide reductase: evidence for generation of nitroxyl with the enzyme from Paracoccus denitrificans. Biochem. Biophys. Res. Commun. 183, 983–988 (1992).
Kastrau, D.H.W., Heiss, B., Kroneck, P.M.H., Zumft, W.G. Nitric oxide reductase from Pseudomonas stutzeri, a novel cytochrome be complex, Phospholipid requirement, electron paramagnetic resonance and redox properties. Eur. J. Biochem. 222, 293–303 (1994).
Shoun, H., Suyama, W., Yasui, T. Soluble, nitrate/nitrite-inducible cytochrome P450 of the fungus Fusarium oxysporum. FEBS Lett. 244, 11–14 (1989).
Shoun, H. & Tanimoto, T. Denitrification by the fungus Fusarium oxysporum and involvement of cytochrome P450 in the respiratory nitrite reduction. J. Biol. Chem. 266, 11078–11082 (1991).
Nakahara, K., Tanimoto, T., Hatano, K., Usuda, K., Shoun, H. Cytochrome P450 55A1 (P450dNIR) acts as nitric oxide reductase employing NADH as the direct electron donor. J. Biol. Chem. 268, 8350–8355 (1993).
Kizawa, H., Tomura, D., Oda, M., Fukamizu, A., Hoshino, T., Gotoh, O., Yasui, T., Shoun, H. Nucleotide sequence of the unique nitrate/nitrite-inducible cytochrome P450 cDNA from Fusarium oxysporum. J. Biol. Chem. 266, 10632–10637 (1991).
Shiro, Y., Fujii, M., lizuka, T., Adachi, S., Tsukamoto, K., Nakahara, K., Shoun, H. Spectroscopic and kinetic studies on reaction of cytochrome P450nor with nitric oxide. J. Biol. Chem. 270, 1617–1623 (1995).
Poulos, T.L., Finzel, B.C., Howard, A. J. High-resolution crystal structure of cytochrome P450cam. J. Mol. Biol. 195, 687–700 (1987).
Raag, R. & Poulos, T.L. Crystal structure of the carbon monoxide-substrate-cytochrome P450cam ternary complex. Biochemistry 28, 7586–7592 (1989).
Ravichandran, K.G., Boddupalli, S.S., Hasemann, C.A., Peterson, J.A., Deisenhofer, J. Crystal structure of hemoprotein domain of P450BM3, a prototype for microsomal P450's. Science 261, 731–736 (1993).
Hasemann, C.A., Ravichandran, K.G., Peterson, J.A., Deisenhofer, J. Crystal structure and refinement of cytochrome P450terp at 2.3 Å resolution. J. Mol. Biol. 236, 1169–1185 (1994).
Cupp-Vickery, J.R. & Poulos, T.L. Structure of cytochrome P450eryF involved in erythromycin biosynthesis. Nature Struct. Biol. 2, 144–153 (1995).
Cupp-Vickery, J.R., Han, O., Hutchinson, C.R., Poulos, T. L. Substrate-assisted catalysis in cytochrome P450eryF. Nature Struct. Biol. 3, 632–637 (1996).
Collaborative computing project No. 4 The CCP4 suite: programs for protein crystallography. Acta crystallogr. D50, 760–763 (1994).
Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thronton, J.M. PROCHECK: a program to check the stereochemical quality of protein structure. J. Appl. Crystallogr. 26, 283–291 (1993).
Poulos, T.L., Cupp-Vickery, J., Li, H. Cytochrome P450. structure, mechanism, and biochemistry (2nd Ed.). (ed. Ortiz de Montellano, P. R.) 125–150 (Plenum Press, New York; 1995).
Peterson, J.A. & Graham-Lorence, S.E. Cytochrome P450. structure, mechanism, and biochemistry (2nd Ed.). (ed, Ortiz de Montellano, P. R.) 151–180 (Plenum Press, New York; 1995).
Hasemann, C.A., Ravichandran, K.G., Boddupalli, S.S., Peterson, J.A., Deisenhofer, J. Structure and function of cytochrome P450: a comparative analysis of three crystal structures. Structure 3, 41–62 (1995).
Shiro, Y., Kato, M., lizuka, T., Nakahara, K., Shoun, H. Kinetics and thermodynamics of CO binding to cytochrome P450nor. Biochemistry 33, 8673–8677 (1994).
Shiro, Y., Fujii, M., Isogai, Y., Adachi, S., lizuka, T., Obayashi, E., Makino, R., Nakahara, R., Shoun, H. Iron-ligand structure and iron redox property of nitric oxide reductase cytochrome P450nor from Fusarium oxysporum: relevance to Its NO reduction activity. Biochemistry 34, 9052–9058 (1995).
Usuda, K., Toritsuka, N., Matsuo, Y., Kim, D.-H., Shoun, H. Denitrification by the fungus Cylindrocarpon tonkinense: anaerobic cell growth and two isozyme forms of cytochrome P450nor. Appl. Environ. Microbiol. 61, 883–889 (1995).
Toritsuka, N., Shoun, H., Singh, U.P., Park, S.-Y., Iizuka, T., Shiro, Y. Functional and structural comparison of nitric oxide reductases from denitrifying Cylindrocarpon tonkinense and Fusarium oxysporum. Biochim. Biophys. Acta 1338, 93–99 (1997).
Imai, M., Shimada, H., Watanabe, Y., Matsushima-Hibiya, Y., Makino, R., Koga, H., Horiuchi, T., Ishimura, Y. Uncoupling of the cytochrome P-450cam monooxygenase reaction by a single mutation, threonine-252 to alanine or valine: A possible role of the hydroxy amino acid in oxygen activation. Proc. Natl. Acad. Sci. USA 86, 7823–7827 (1989).
Raag, R., Martinis, S.A., Sligar, S.G., Poulos, T.L. Crystal structure of the cytochrome P- 450cam active site mutant Thr252Ala. Biochemistry 30, 11420–11429 (1991).
Gerber, N.C. & Sligar, S.G. Catalytic mechanism of cytochrome P450: evidence for a distal charge relay. J. Am. Chem. Soc. 114, 8742–8743 (1992).
Gerber, N.C. & Sligar, S.G. A role for Asp-251 in cytochrome P450cam oxygen activation. J. Biol. Chem. 269, 4260–4266 (1994).
Yeom, H., Sligar, S.G., Li, H., Poulos, T.L., Fulco, A.J. The role of Thr268 in oxygen activation of cytochrome P450BM3. Biochemistry 34, 14733–14740 (1995).
Harris, D.L. & Loew, G.H.J. Investigation of the proton-assisted pathway to formation of the catalytically active, ferryl species of P450s by molecular dynamics studies of P450eryF. J. Am. Chem. Soc. 118, 6377–6387 (1996).
Park, S.-Y., Shimizu, H., Adachi, S.-i., Shiro, Y., Iizuka, T., Nakagawa, A., Tanaka, I., Shoun, H., Hori, H. Crystallization, Preliminary Diffraction and Electron Paramagnetic Resonance Studies of a Single Crystal of Cytochrome P450nor. FEBS Lett. 412, 346–350 (1997).
Sakabe, N. A focusing weissenberg camera with multi-layer-line screens for macromolecular crystallography. J. Appl. Crystallogr. 16, 542–547 (1983).
Otwinowski, Z. Oscillation data reduction program. In Data collection and processing (L. Sawyer, N. Isaace & S. Bailey, eds) 56–62 (SERC Daresbury Laboratory, Warrington, UK; 1993).
Abrahams, J.P., Leliew, A.G.W., Lutter, R., Walker, J.E. Structure at 2.8 Å resolution of F1-ATPase fom bovine heart mitochondria. Nature 370, 621–628 (1994).
Jones, T.A., Zou, J.Y., Cowan, S.W., Kjeldgaard, M. Improved method for building protein models in electron density maps and location of errors in these models. Acta Crystallogr. A47, 110–119 (1991).
Brünger, A.T. X-PLOR, a system for X-ay crystallography and NMR. Version 3.1 (Yale University Press, New Haven, Connecticut; 1992).
Kraulis, P.J. MOLSCRIPT: a program to protuce both de tailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).
Evans, S.V. SETOR: hardware lighted three-dimentional solid model representations of macromolecules. J. Mol. Graphics 11, 134–1338 (1993).
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Park, SY., Shimizu, H., Adachi, Si. et al. Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum. Nat Struct Mol Biol 4, 827–832 (1997). https://doi.org/10.1038/nsb1097-827
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DOI: https://doi.org/10.1038/nsb1097-827
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