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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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Pardhe BD, Do H, Jeong CS, Kim KH, Lee JH, Oh TJ. Characterization of high-H 2O 2-tolerant bacterial cytochrome P450 CYP105D18: insights into papaverine N-oxidation. IUCRJ 2021; 8:684-694. [PMID: 34258016 PMCID: PMC8256718 DOI: 10.1107/s2052252521005522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/28/2021] [Indexed: 06/13/2023]
Abstract
The bacterial CYP105 family is involved in secondary metabolite biosynthetic pathways and plays essential roles in the biotransformation of xenobiotics. This study investigates the newly identified H2O2-mediated CYP105D18 from Streptomyces laurentii as the first bacterial CYP for N-oxidation. The catalytic efficiency of CYP105D18 for papaverine N-oxidation was 1.43 s-1 µM -1. The heme oxidation rate (k) was low (<0.3 min-1) in the presence of 200 mM H2O2. This high H2O2 tolerance capacity of CYP105D18 led to higher turnover prior to heme oxidation. Additionally, the high-resolution papaverine complexed structure and substrate-free structure of CYP105D18 were determined. Structural analysis and activity assay results revealed that CYP105D18 had a strong substrate preference for papaverine because of its bendable structure. These findings establish a basis for biotechnological applications of CYP105D18 in the pharmaceutical and medicinal industries.
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Affiliation(s)
- Bashu Dev Pardhe
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 31460, Republic of Korea
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Chang-Sook Jeong
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Ki-Hwa Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 31460, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 31460, Republic of Korea
- Genome-based BioIT Convergence Institute, Asan 31460, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan 31460, Republic of Korea
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Riplinger C, Bill E, Daiber A, Ullrich V, Shoun H, Neese F. New Insights into the Nature of Observable Reaction Intermediates in Cytochrome P450 NO Reductase by Using a Combination of Spectroscopy and Quantum Mechanics/Molecular Mechanics Calculations. Chemistry 2014; 20:1602-14. [DOI: 10.1002/chem.201302443] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 11/04/2013] [Indexed: 11/08/2022]
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Evaluation of structural features in fungal cytochromes P450 predicted to rule catalytic diversification. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:205-20. [DOI: 10.1016/j.bbapap.2012.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/17/2012] [Accepted: 09/18/2012] [Indexed: 01/11/2023]
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5
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Riplinger C, Neese F. The reaction mechanism of Cytochrome P450 NO reductase: a detailed quantum mechanics/molecular mechanics study. Chemphyschem 2011; 12:3192-203. [PMID: 22095732 DOI: 10.1002/cphc.201100523] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/10/2011] [Indexed: 11/09/2022]
Abstract
A detailed QM/MM study on the reaction mechanism of Cytochrome P450 NO reductase is reported. Two reaction pathways connecting the two well-characterized intermediates as well as two putative intermediates that represent the unknown third intermediate are explored, with emphasis on the unusual direct reduction of the enzymatic active site by the cofactor NADH. Activation barriers and kinetic isotope effect are calculated and reveal that reduction of the NO-bound species occurs in form of a hydride ion transfer. Furthermore, the impact of different hydrogen bonds in the active site to binding and reactivity of NADH is explored. The calculated kinetic and thermodynamic properties for both modelled pathways are used for the kinetic simulation of the entire reaction course. It is thus shown that the unknown key intermediate is the singlet diradical Fe(III)-NHOH(⋅). It is also found that the mechanism of the N-N bond formation is spin-recoupling, which is only possible due to the diradical character of the key intermediate.
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Affiliation(s)
- Christoph Riplinger
- MPI for Bioinorganic Chemistry, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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Sabbadin F, Jackson R, Haider K, Tampi G, Turkenburg JP, Hart S, Bruce NC, Grogan G. The 1.5-A structure of XplA-heme, an unusual cytochrome P450 heme domain that catalyzes reductive biotransformation of royal demolition explosive. J Biol Chem 2009; 284:28467-28475. [PMID: 19692330 PMCID: PMC2788895 DOI: 10.1074/jbc.m109.031559] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 08/10/2009] [Indexed: 11/06/2022] Open
Abstract
XplA is a cytochrome P450 of unique structural organization, consisting of a heme-domain that is C-terminally fused to its native flavodoxin redox partner. XplA, along with flavodoxin reductase XplB, has been shown to catalyze the breakdown of the nitramine explosive and pollutant hexahydro-1,3,5-trinitro-1,3,5-triazine (royal demolition explosive) by reductive denitration. The structure of the heme domain of XplA (XplA-heme) has been solved in two crystal forms: as a dimer in space group P2(1) to a resolution of 1.9 A and as a monomer in space group P2(1)2(1)2 to a resolution of 1.5 A, with the ligand imidazole bound at the heme iron. Although it shares the overall fold of cytochromes P450 of known structure, XplA-heme is unusual in that the kinked I-helix that traverses the distal face of the heme is broken by Met-394 and Ala-395 in place of the well conserved Asp/Glu plus Thr/Ser, important in oxidative P450s for the scission of the dioxygen bond prior to substrate oxygenation. The heme environment of XplA-heme is hydrophobic, featuring a cluster of three methionines above the heme, including Met-394. Imidazole was observed bound to the heme iron and is in close proximity to the side chain of Gln-438, which is situated over the distal face of the heme. Imidazole is also hydrogen-bonded to a water molecule that sits in place of the threonine side-chain hydroxyl exemplified by Thr-252 in Cyt-P450cam. Both Gln-438 --> Ala and Ala-395 --> Thr mutants of XplA-heme displayed markedly reduced activity compared with the wild type for royal demolition explosive degradation when combined with surrogate electron donors.
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Affiliation(s)
- Federico Sabbadin
- York Structural Biology Laboratory, Department of Biology, University of York, York YO10 5YW, United Kingdom; Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, United Kingdom
| | - Rosamond Jackson
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, United Kingdom
| | - Kamran Haider
- York Structural Biology Laboratory, Department of Biology, University of York, York YO10 5YW, United Kingdom
| | - Girish Tampi
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, United Kingdom
| | - Johan P Turkenburg
- York Structural Biology Laboratory, Department of Biology, University of York, York YO10 5YW, United Kingdom
| | - Sam Hart
- York Structural Biology Laboratory, Department of Biology, University of York, York YO10 5YW, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, United Kingdom
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Biology, University of York, York YO10 5YW, United Kingdom.
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Purification and functional analysis of fungal nitric oxide reductase cytochrome P450nor. Methods Enzymol 2008. [PMID: 18433626 DOI: 10.1016/s0076-6879(07)37007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Cytochrome P450nor (P450nor) is a nitric oxide (NO) reductase involved in fungal denitrification. Denitrification is a biological process in which nitrate or nitrite is reduced to gaseous nitrogen, the reverse reaction of nitrogen fixation. It therefore plays an important role in maintaining global environmental homeostasis. The involvement of P450nor in fungal denitrification indicates that denitrification not only occurs in prokaryotic bacteria, but also in eukaryotic fungi. In addition, the reduction of NO to nitrous oxide catalyzed by P450nor has added new insight into the function of cytochrome P450s, which are usually monooxygenases. Currently, five isozymes of P450nor have been isolated from the subdivisions of eumycota, and studies on the function and structure of P450nor have provided important information for both molecular mechanisms of P450 reactions and wastewater treatment. This chapter describes the screening of NO reductase activities, cloning, purification, and functional analysis of P450nor.
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Bonifacio A, Groenhof AR, Keizers PHJ, de Graaf C, Commandeur JNM, Vermeulen NPE, Ehlers AW, Lammertsma K, Gooijer C, van der Zwan G. Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study. J Biol Inorg Chem 2007; 12:645-54. [PMID: 17318599 PMCID: PMC1915625 DOI: 10.1007/s00775-007-0210-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 01/23/2007] [Indexed: 11/28/2022]
Abstract
Cytochrome P450 2D6 (CYP2D6) is one of the most important cytochromes P450 in humans. Resonance Raman data from the T309V mutant of CYP2D6 show that the substitution of the conserved I-helix threonine situated in the enzyme's active site perturbs the heme spin equilibrium in favor of the six-coordinated low-spin species. A mechanistic hypothesis is introduced to explain the experimental observations, and its compatibility with the available structural and spectroscopic data is tested using quantum-mechanical density functional theory calculations on active-site models for both the CYP2D6 wild type and the T309V mutant.
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Affiliation(s)
- Alois Bonifacio
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - André R. Groenhof
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Peter H. J. Keizers
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Jan N. M. Commandeur
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Nico P. E. Vermeulen
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Andreas W. Ehlers
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Koop Lammertsma
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Cees Gooijer
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Gert van der Zwan
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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9
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Clark JP, Miles CS, Mowat CG, Walkinshaw MD, Reid GA, Daff SN, Chapman SK. The role of Thr268 and Phe393 in cytochrome P450 BM3. J Inorg Biochem 2006; 100:1075-90. [PMID: 16403573 DOI: 10.1016/j.jinorgbio.2005.11.020] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Accepted: 11/21/2005] [Indexed: 11/30/2022]
Abstract
In flavocytochrome P450 BM3 there are several active site residues that are highly conserved throughout the P450 superfamily. Of these, a phenylalanine (Phe393) has been shown to modulate heme reduction potential through interactions with the implicitly conserved heme-ligand cysteine. In addition, a distal threonine (Thr268) has been implicated in a variety of roles including proton donation, oxygen activation and substrate recognition. Substrate binding in P450 BM3 causes a shift in the spin state from low- to high-spin. This change in spin-state is accompanied by a positive shift in the reduction potential (DeltaE(m) [WT+arachidonate (120 microM)]=+138 mV). Substitution of Thr268 by an alanine or asparagine residue causes a significant decrease in the ability of the enzyme to generate the high-spin complex via substrate binding and consequently leads to a decrease in the substrate-induced potential shift (DeltaE(m) [T268A+arachidonate (120 microM)]=+73 mV, DeltaE(m) [T268N+arachidonate (120 microM)]=+9 mV). Rate constants for the first electron transfer and for oxy-ferrous decay were measured by pre-steady-state stopped-flow kinetics and found to be almost entirely dependant on the heme reduction potential. More positive reduction potentials lead to enhanced rate constants for heme reduction and more stable oxy-ferrous species. In addition, substitutions of the threonine lead to an increase in the production of hydrogen peroxide in preference to hydroxylated product. These results suggest an important role for this active site threonine in substrate recognition and in maintaining an efficiently functioning enzyme. However, the dependence of the rate constants for oxy-ferrous decay on reduction potential raises some questions as to the importance of Thr268 in iron-oxo stabilisation.
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Affiliation(s)
- Jonathan P Clark
- EaStCHEM, School of Chemistry, University of Edinburgh, Joseph Black Building, Kings Buildings West Mains Road, Edinburgh, Lothian EH9 3JJ, United Kingdom
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Hartree–Fock and density functional theory calculations for the reaction mechanism of nitric oxide reductase cytochrome P450nor from Fusarium oxysporum. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.06.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Denisov IG, Makris TM, Sligar SG, Schlichting I. Structure and Chemistry of Cytochrome P450. Chem Rev 2005; 105:2253-77. [PMID: 15941214 DOI: 10.1021/cr0307143] [Citation(s) in RCA: 1512] [Impact Index Per Article: 79.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, 61801, USA
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Franke A, Stochel G, Suzuki N, Higuchi T, Okuzono K, van Eldik R. Mechanistic Studies on the Binding of Nitric Oxide to a Synthetic Heme−Thiolate Complex Relevant to Cytochrome P450. J Am Chem Soc 2005; 127:5360-75. [PMID: 15826174 DOI: 10.1021/ja047572u] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthetic heme-thiolate complex (SR) in methanol binds nitric oxide (k(on) = (2.7 +/- 0.2) x10(6) M(-)(1) s(-)(1) at 25 degrees C) to form SR(NO). The binding of NO to the SR complex in a noncoordinating solvent, such as toluene, was found to be almost 3 orders of magnitude faster than that in methanol. The activation parameters DeltaH(), DeltaS(), and DeltaV() for the formation of SR(NO) in methanol are consistent with the operation of a limiting dissociative mechanism, dominated by dissociation of methanol in SR(MeOH). In the presence of an excess of NO, the formation of SR(NO) is followed by subsequent slower reactions. The substantially negative activation entropy and activation volume values found for the second observed reaction step support an associative mechanism which involves attack of a second NO molecule on the thiolate ligand in the initially formed SR(NO) complex. The following slower reactions are strongly accelerated by a large excess of NO or by the presence of NO(2)(-) in the SR/NO reaction mixture. They can be accounted for in terms of dynamic equilibria between higher nitrogen oxides (NO(x)()) and reactive SR species, which lead to the formation of a nitrosyl-nitrite complex of SR(Fe(II)) as the final product. This finding is clearly supported by laser flash photolysis studies on the SR/NO reaction mixture, which do not reveal simple NO photolabilization from SR(Fe(III))(NO), but rather involve the generation of at least three photoinduced intermediates decaying with different rate constants to the starting material. The species formed along the proposed reaction pathways were characterized by FTIR and EPR spectroscopy. The results are discussed in terms of their relevance for the biological function of cytochrome P450 enzymes and in context of results for the reaction of NO with imidazole- and thiolate-ligated iron(III) hemoproteins.
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Affiliation(s)
- Alicja Franke
- Institute for Inorganic Chemistry, University of Erlangen-Nürnberg, Egerlandstrasse 1, 91058 Erlangen, Germany
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Oshima R, Fushinobu S, Su F, Zhang L, Takaya N, Shoun H. Structural evidence for direct hydride transfer from NADH to cytochrome P450nor. J Mol Biol 2004; 342:207-17. [PMID: 15313618 DOI: 10.1016/j.jmb.2004.07.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Revised: 07/02/2004] [Accepted: 07/09/2004] [Indexed: 11/26/2022]
Abstract
Nitric oxide reductase cytochrome P450nor catalyzes an unusual reaction, direct electron transfer from NAD(P)H to bound heme. Here, we succeeded in determining the crystal structure of P450nor in a complex with an NADH analogue, nicotinic acid adenine dinucleotide, which provides conclusive evidence for the mechanism of the unprecedented electron transfer. Comparison of the structure with those of dinucleotide-free forms revealed a global conformational change accompanied by intriguing local movements caused by the binding of the pyridine nucleotide. Arg64 and Arg174 fix the pyrophosphate moiety upon the dinucleotide binding. Stereo-selective hydride transfer from NADH to NO-bound heme was suggested from the structure, the nicotinic acid ring being fixed near the heme by the conserved Thr residue in the I-helix and the upward-shifted propionate side-chain of the heme. A proton channel near the NADH channel is formed upon the dinucleotide binding, which should direct continuous transfer of the hydride and proton. A salt-bridge network (Glu71-Arg64-Asp88) was shown to be crucial for a high catalytic turnover.
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Affiliation(s)
- Rieko Oshima
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657, Japan
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Podust LM, Kim Y, Arase M, Neely BA, Beck BJ, Bach H, Sherman DH, Lamb DC, Kelly SL, Waterman MR. The 1.92-A structure of Streptomyces coelicolor A3(2) CYP154C1. A new monooxygenase that functionalizes macrolide ring systems. J Biol Chem 2003; 278:12214-21. [PMID: 12519772 DOI: 10.1074/jbc.m212210200] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Evolutionary links between cytochrome P450 monooxygenases, a superfamily of extraordinarily divergent heme-thiolate proteins catalyzing a wide array of NADPH/NADH- and O(2)-dependent reactions, are becoming better understood because of availability of an increasing number of fully sequenced genomes. Among other reactions, P450s catalyze the site-specific oxidation of the precursors to macrolide antibiotics in the genus Streptomyces introducing regiochemical diversity into the macrolide ring system, thereby significantly increasing antibiotic activity. Developing effective uses for Streptomyces enzymes in biosynthetic processes and bioremediation requires identification and engineering of additional monooxygenases with activities toward a diverse array of small molecules. To elucidate the molecular basis for substrate specificity of oxidative enzymes toward macrolide antibiotics, the x-ray structure of CYP154C1 from Streptomyces coelicolor A3(2) was determined (Protein Data Bank code ). Relocation of certain common P450 secondary structure elements, along with a novel structural feature involving an additional beta-strand transforming the five-stranded beta-sheet into a six-stranded variant, creates an open cleft-shaped substrate-binding site between the two P450 domains. High sequence similarity to macrolide monooxygenases from other microbial species translates into catalytic activity of CYP154C1 toward both 12- and 14-membered ring macrolactones in vitro.
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Affiliation(s)
- Larissa M Podust
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.
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15
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Distribution, structure and function of fungal nitric oxide reductase P450nor—recent advances. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0531-5131(02)00369-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Affiliation(s)
- Graeme R A Wyllie
- The Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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