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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: 92] [Impact Index Per Article: 30.7] [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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Kroneck PMH. Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen. J Biol Inorg Chem 2021; 27:1-21. [PMID: 34865208 PMCID: PMC8840924 DOI: 10.1007/s00775-021-01921-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022]
Abstract
Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2- is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2- to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.
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Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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van Wonderen JH, Knight C, Oganesyan VS, George SJ, Zumft WG, Cheesman MR. Activation of the cytochrome cd1 nitrite reductase from Paracoccus pantotrophus. Reaction of oxidized enzyme with substrate drives a ligand switch at heme c. J Biol Chem 2007; 282:28207-15. [PMID: 17623666 DOI: 10.1074/jbc.m701242200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochromes cd(1) are dimeric bacterial nitrite reductases, which contain two hemes per monomer. On reduction of both hemes, the distal ligand of heme d(1) dissociates, creating a vacant coordination site accessible to substrate. Heme c, which transfers electrons from donor proteins into the active site, has histidine/methionine ligands except in the oxidized enzyme from Paracoccus pantotrophus where both ligands are histidine. During reduction of this enzyme, Tyr(25) dissociates from the distal side of heme d(1), and one heme c ligand is replaced by methionine. Activity is associated with histidine/methionine coordination at heme c, and it is believed that P. pantotrophus cytochrome cd(1) is unreactive toward substrate without reductive activation. However, we report here that the oxidized enzyme will react with nitrite to yield a novel species in which heme d(1) is EPR-silent. Magnetic circular dichroism studies indicate that heme d(1) is low-spin Fe(III) but EPR-silent as a result of spin coupling to a radical species formed during the reaction with nitrite. This reaction drives the switch to histidine/methionine ligation at Fe(III) heme c. Thus the enzyme is activated by exposure to its physiological substrate without the necessity of passing through the reduced state. This reactivity toward nitrite is also observed for oxidized cytochrome cd(1) from Pseudomonas stutzeri suggesting a more general involvement of the EPR-silent Fe(III) heme d(1) species in nitrite reduction.
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Affiliation(s)
- Jessica H van Wonderen
- Centre for Metalloprotein Spectroscopy and Biology, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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Teschner T, Yatsunyk L, Schünemann V, Paulsen H, Winkler H, Hu C, Scheidt WR, Walker FA, Trautwein AX. Models of the membrane-bound cytochromes: mössbauer spectra of crystalline low-spin ferriheme complexes having axial ligand plane dihedral angles ranging from 0 degree to 90 degrees. J Am Chem Soc 2006; 128:1379-89. [PMID: 16433558 PMCID: PMC1525297 DOI: 10.1021/ja056343k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystalline samples of four low-spin Fe(III) octaalkyltetraphenylporphyrinate and two low-spin Fe(III) tetramesitylporphyrinate complexes, all of which are models of the bis-histidine-coordinated cytochromes of mitochondrial complexes II, III, and IV and chloroplast complex b(6)f, and whose molecular structures and EPR spectra have been reported previously, have been investigated in detail by Mössbauer spectroscopy. The six complexes and the dihedral angles between axial ligand planes of each are [(TMP)Fe(1-MeIm)(2)]ClO(4) (0 degree), paral-[(OMTPP)Fe(1-MeIm)(2)]Cl (19.5 degrees), paral-[(TMP)Fe(5-MeHIm)(2)]ClO(4) (26 degrees, 30 degrees for two molecules in the unit cell whose EPR spectra overlap), [(OETPP)Fe(4-Me(2)NPy)(2)]Cl (70 degrees), perp-[(OETPP)Fe(1-MeIm)(2)]Cl (73 degrees), and perp-[(OMTPP)Fe(1-MeIm)(2)]Cl (90 degrees). Of these, the first three have been shown to exhibit normal rhombic EPR spectra, each with three clearly resolved g-values, while the last three have been shown to exhibit "large g(max)" EPR spectra at 4.2 K. It is found that the hyperfine coupling constants of the complexes are consistent with those reported previously for low-spin ferriheme systems, with the largest-magnitude hyperfine coupling constant, A(zz), being considerably smaller for the "parallel" complexes (400-540 kG) than for the strictly perpendicular complex (902 kG), A(xx) being negative for all six complexes, and A(zz) and A(xx) being of similar magnitude for the "parallel" complexes (for example, for [(TMP)Fe(1-MeIm)(2)]Cl, A(zz) = 400 kG, A(xx) = -400 kG). In all cases, A(yy) is small but difficult to estimate with accuracy. With results for six structurally characterized model systems, we find for the first time qualitative correlations of g(zz), A(zz), and DeltaE(Q) with axial ligand plane dihedral angle Deltavarphi.
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Walker FA. Models of the Bis-Histidine-Ligated Electron-Transferring Cytochromes. Comparative Geometric and Electronic Structure of Low-Spin Ferro- and Ferrihemes. Chem Rev 2004; 104:589-615. [PMID: 14871136 DOI: 10.1021/cr020634j] [Citation(s) in RCA: 176] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F Ann Walker
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA.
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Benda R, Schünemann V, Trautwein AX, Cai S, Reddy Polam J, Watson CT, Shokhireva TK, Walker FA. Models of the bis-histidine-coordinated ferricytochromes: Mössbauer and EPR spectroscopic studies of low-spin iron(III) tetrapyrroles of various electronic ground states and axial ligand orientations. J Biol Inorg Chem 2003; 8:787-801. [PMID: 12898323 DOI: 10.1007/s00775-003-0472-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2002] [Accepted: 05/19/2003] [Indexed: 10/26/2022]
Abstract
The EPR and magnetic Mössbauer spectra of a series of axial ligand complexes of tetrakis(2,6-dimethoxyphenyl)porphyrinatoiron(III), [(2,6-(OMe)(2))(4)TPPFeL(2)](+), where L= N-methylimidazole, 2-methylimidazole, or 4-(dimethylamino)pyridine, of one axial ligand complex of tetraphenylporphyrin, the bis(4-cyanopyridine) complex [TPPFe(4-CNPy)(2)](+), and of one axial ligand complex of tetraphenylchlorin, [TPCFe(ImH)(2)](+), where ImH=imidazole, have been investigated and compared to those of low-spin Fe(III) porphyrinates and ferriheme proteins reported in the literature. On the basis of this and previous complementary spectroscopic investigations, three types of complexes have been identified: those having (d(xy))(2)(d(xz),d(yz))(3) electronic ground states with axial ligands aligned in perpendicular planes (Type I), those having (d(xy))(2)(d(xz),d(yz))(3) electronic ground states with axial ligands aligned in parallel planes (Type II), and those having the novel (d(xz),d(yz))(4)(d(xy))(1) electronic ground state (Type III). A subset of the latter type, with planar axial ligands aligned parallel to each other or strong macrocycle asymmetry that yield rhombic EPR spectra, cannot be created using the porphyrinate ligand. Type I centers are characterized by "large g(max)" EPR spectra with g>3.2 and well-resolved, widely spread magnetic Mössbauer spectra having A(zz)/ g(N)mu(N)>680 kG, with A(xx) negative in sign but much smaller in magnitude than A(zz), while Type II centers have well-resolved rhombic EPR spectra with g(zz)=2.4-3.1 and also less-resolved magnetic Mössbauer spectra, and usually have A(zz)/ g(Nmu(N) in the range of 440-660 kG (but in certain cases as small as 180 kG) and A(xx) again negative in sign but only somewhat smaller (but occasionally larger in magnitude) than A(zz), and Type III centers have axial EPR spectra with g( upper left and right quadrants ) approximately 2.6 or smaller and g( vertical line )<1.0-1.95, but often not resolved, and less-resolved magnetic Mössbauer spectra having A(zz)/ g(N)mu(N) in the range of 270-400 kG, and A(xx) again negative in sign but much smaller in magnitude than A(zz). An exception to this rule is [TPPFe(4-CNPy)(2)](+), which has A(xx)/ g(N)mu(N)=-565 kG, A(yy)/ g(N)mu(N)=629 kG, and A(zz)/ g(N)mu(N)=4 kG. A subset of Type II complexes (Type II') have rhombicities ( V/Delta) much greater than 0.67 and A(zz)/ g(N)mu(N) ranging from 320 to 170 kG, with A(xx) also negative but with the magnitude of A(xx) significantly larger than that of A(zz). These classifications are also observed for a variety of ferriheme proteins, and they lead to linear correlations between A(zz) and either A(xx), g(zz), or V/Delta for Types I and II (but not for A(zz) versus V/Delta for Type II'). Not enough data are yet available on Type III complexes to determine what, if any, correlations may be observed.
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Affiliation(s)
- Rüdiger Benda
- Institut für Physik, Universität Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
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Wasser IM, de Vries S, Moënne-Loccoz P, Schröder I, Karlin KD. Nitric oxide in biological denitrification: Fe/Cu metalloenzyme and metal complex NO(x) redox chemistry. Chem Rev 2002; 102:1201-34. [PMID: 11942794 DOI: 10.1021/cr0006627] [Citation(s) in RCA: 355] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ian M Wasser
- Department of Chemistry, The Johns Hopkins University, Charles and 34th Streets, Baltimore, MD 21218, USA
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Abstract
The structure-function relationships in nitrite reductases, key enzymes in the dissimilatory denitrification pathway which reduce nitrite to nitric oxide (NO), are reviewed in this paper. The mechanisms of NO production are discussed in detail and special attention is paid to new structural information, such as the high resolution structure of the copper- and heme-containing enzymes from different sources. Finally, some implications relevant to regulation of the steady state levels of NO in denitrifiers are presented.
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Affiliation(s)
- F Cutruzzolà
- Dipartimento di Scienze Biochimiche, Università di Roma 'La Sapienza', P.le A. Moro, 5, 00185, Rome, Italy.
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Walker F. Magnetic spectroscopic (EPR, ESEEM, Mössbauer, MCD and NMR) studies of low-spin ferriheme centers and their corresponding heme proteins. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(99)00029-6] [Citation(s) in RCA: 234] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Cheesman MR, Ferguson SJ, Moir JW, Richardson DJ, Zumft WG, Thomson AJ. Two enzymes with a common function but different heme ligands in the forms as isolated. Optical and magnetic properties of the heme groups in the oxidized forms of nitrite reductase, cytochrome cd1, from Pseudomonas stutzeri and Thiosphaera pantotropha. Biochemistry 1997; 36:16267-76. [PMID: 9405061 DOI: 10.1021/bi971677a] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
It is shown that, in the oxidized state, heme c of Pseudomonas stutzeri (ZoBell strain) cytochrome cd1 has histidine-methionine ligation as observed for cytochrome cd1 from Pseudomonas aeruginosa [Sutherland, J., Greenwood, C., Peterson, J., and Thomson, A. J. (1986) Biochem. J. 233, 893-898]. However, the X-ray structure of Thiosphaera pantotropha cytochrome cd1 reveals bis-histidine ligation for heme c. It is confirmed by EPR and near-infrared (NIR) MCD measurements that the bis-histidine coordination remains unaltered in the solution phase. Hence, the difference between the heme c ligation states defines two distinct classes of oxidized cytochromes cd1 as isolated. A weak feature in the T. pantotropha NIR MCD at 1900 nm suggests that a small population of heme c has histidine-methionine coordination. The ligation state of heme d1 cannot be defined with the same level of confidence, because the porphyrin-to-Fe(III) charge-transfer (CT) bands are less well characterized for this class of partially reduced porphyrin ring. However, variable temperature absorption and MCD spectra show that, in the T. pantotropha enzyme, heme d1 exists in a thermal low-spin/high-spin mixture with the low-spin as the ground state, whereas in P. stutzeri cytochrome cd1, and d1 heme is low-spin at all temperatures. A weak band, assigned as the heme d1 porphyrin-pi(a1u,a2u)-to-ferric(d) charge-transfer transition has been identified for the first time at 2170 nm. Its magnetic properties show the heme d1 to have an unusual (dxz,yz)4(dxy)1 electronic ground state as is found for low-spin Fe(III) chlorins [Cheesman, M. R., and Walker, F. A. (1996) J. Am. Chem. Soc. 118, 7373-7380]. It is proposed that the localization of the Fe(III) unpaired d-electron in an orbital lying in the heme plane may decrease the affinity of the Fe(III) heme for unsaturated ligands such as NO. Although heme d1 in the enzymes from P. stutzeri and T. pantotropha shows different temperature-dependent spin properties, the positions of the low-spin Fe(III) alpha-absorption band, at approximately 640 nm, are very similar to those observed for cytochromes cd1 from eight other sources, suggesting that all have similar strength fields from the axial ligands and, hence, that all have the same coordination, namely histidine-tyrosine or possibly histidine-hydroxide at the heme.
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Affiliation(s)
- M R Cheesman
- Centre for Metalloprotein Spectroscopy and Biology, School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, U.K.
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Abstract
Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.
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Affiliation(s)
- W G Zumft
- Lehrstuhl für Mikrobiologie, Universität Fridericiana, Karlsruhe, Germany
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Electrochemistry of nitrite reductase model compounds 6. Voltammetric and spectroelectrochemical studies of iron(II) nitrosyl complexes with porphyrins, hydroprophyrins and porphinones. Inorganica Chim Acta 1997. [DOI: 10.1016/s0020-1693(96)05547-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
During microbial denitrification, NO is produced by reduction of nitrite by either the reduced high spin d1 hemes in a unique reductase (NIR) or at the expense of a blue copper protein that transfers electrons that move first to a type I copper and then to a type II copper in a unique trimeric NIR. This latter type of NIR is also produced by several denitrifying filamentous fungi. Reduction of NO is then carried out by either a specific cytochrome be complex NOR in denitrifying bacteria or a unique cytochrome P-450 in denitrifying filamentous fungi. NO is also produced by an anomalous reaction of a molybdoprotein, nitrate reductase (NAR), acting on an odd substrate, NO2-. NO is also reduced by a multiheme NIR that serves physiologically for reduction of NO2- to NH3. This type NIR reduces NO to either N2O, if only partially reduced, or NH3, if fully reduced, when it encounters NO. This multiheme NIR is very sensitive to cyanide. Transcription of the genes for NIR and NOR production in a denitrifier is activated by NO, a process that also requires the presence of the gene product, a transcriptional activator, NnrR.
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Affiliation(s)
- W J Payne
- Department of Microbiology, University of Georgia, Athens 30602, USA
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Berks BC, Ferguson SJ, Moir JW, Richardson DJ. Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1232:97-173. [PMID: 8534676 DOI: 10.1016/0005-2728(95)00092-5] [Citation(s) in RCA: 390] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- B C Berks
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich, UK
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Fülöp V, Moir JW, Ferguson SJ, Hajdu J. The anatomy of a bifunctional enzyme: structural basis for reduction of oxygen to water and synthesis of nitric oxide by cytochrome cd1. Cell 1995; 81:369-77. [PMID: 7736589 DOI: 10.1016/0092-8674(95)90390-9] [Citation(s) in RCA: 221] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cytochrome cd1-nitrite reductase is a bifunctional enzyme that catalyzes the one-electron reduction of nitrite to nitric oxide and the four-electron reduction of oxygen to water. The 1.55 A crystal structure of the dimeric enzyme from Thiosphaera pantotropha is reported here. The protein was sequenced from the X-ray structure. Each subunit contains a covalent c heme with two axial His ligands (His-17, His-69) and a unique noncovalent d1 heme ligated by Tyr-25 and His-200. The d1 heme is the mononuclear iron center where both oxygen and nitrite reduction take place. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis.
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Affiliation(s)
- V Fülöp
- Laboratory of Molecular Biophysics, University of Oxford, England
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[38] Mössbauer spectroscopy in study of cytochrome cd1 from Thiobacillus denitrificans, desulfoviridin, and iron hydrogenase. Methods Enzymol 1994. [DOI: 10.1016/0076-6879(94)43040-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Brittain T, Blackmore R, Greenwood C, Thomson AJ. Bacterial nitrite-reducing enzymes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 209:793-802. [PMID: 1425687 DOI: 10.1111/j.1432-1033.1992.tb17350.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The enzymic reduction of nitrite takes place in a wide range of bacteria and is found to occur in denitrifying, assimilatory and dissimilatory pathways. In this review we describe the major molecular characteristics of the various enzymes employed in each of these processes.
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Affiliation(s)
- T Brittain
- Department of Biochemistry, University of Auckland, New Zealand
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Ravi N, Moura I, Costa C, Teixeira M, LeGall J, Moura JJ, Huynh BH. Mössbauer characterization of the tetraheme cytochrome c3 from Desulfovibrio baculatus (DSM 1743). Spectral deconvolution of the heme components. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 204:779-82. [PMID: 1311680 DOI: 10.1111/j.1432-1033.1992.tb16694.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mössbauer spectroscopy was used to study the tetraheme cytochrome c3 from Desulfovibrio baculatus (DSM 1743). Samples with different degrees of reduction were prepared using a redoxtitration technique. In the reduced cytochrome c3, all four hemes are reduced and exhibit diamagnetic Mössbauer spectra typical for low-spin ferrous hemes (S = 0). In the oxidized protein, the hemes are low-spin ferric (S = 1/2) and exhibit overlapping magnetic Mössbauer spectra. A method of differential spectroscopy was applied to deconvolute the four overlapping heme spectra and a crystal-field model was used for data analysis. Characteristic Mössbauer spectral components for each heme group are obtained. Hyperfine and crystal-field parameters for all four hemes are determined from these deconvoluted spectra.
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Affiliation(s)
- N Ravi
- Department of Physics, Emory University, Atlanta, GA 30322
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Costa C, Moura J, Moura I, Liu M, Peck H, LeGall J, Wang Y, Huynh B. Hexaheme nitrite reductase from Desulfovibrio desulfuricans. Mössbauer and EPR characterization of the heme groups. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)77313-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Steup MB, Muhoberac BB. Preparation and spectral characterization of the heme d1.apomyoglobin complex: an unusual protein environment for the substrate-binding heme of Pseudomonas cytochrome oxidase. J Inorg Biochem 1989; 37:233-57. [PMID: 2557389 DOI: 10.1016/0162-0134(89)80045-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The heme d1 prosthetic group isolated from Pseudomonas cytochrome oxidase combines with apomyoglobin to form a stable, optically well-defined complex. Addition of ferric heme d1 quenches apomyoglobin tryptophan fluorescence suggesting association in a 1:1 molar ratio. Optical absorption maxima for heme d1.apomyoglobin are at 629 and 429 nm before, and 632 and 458 nm after dithionite reduction; they are distinct from those of heme d1 in aqueous solution but more similar to those unobscured by heme c in Pseudomonas cytochrome oxidase. Cyanide, carbon monoxide and imidazole alter the spectrum of heme d1.apomyoglobin demonstrating axial coordination to heme d1 by exogeneous ligands. The cyanide-induced optical difference spectra exhibit isosbestic points, and a Scatchard-like analysis yields a linear plot with an apparent dissociation constant of 4.2 X 10(-5) M. However, carbon monoxide induces two absorption spectra with Soret maxima at 454 or 467 nm, and this duplicity, along with a shoulder that correlates with the latter before binding, suggests multiple carbon monoxide and possibly heme d1 orientations within the globin. The 50-fold reduction in cyanide affinity over myoglobin is more consistent with altered heme pocket interactions than the intrinsic electronic differences between the two hemes. However, stability of the heme d1.apomyoglobin complex is verified further by the inability to separate heme d1 from globin during dialysis and column chromatography in excess cyanide or imidazole. This stability, together with a comparison between spectra of ligand-free and -bound derivatives of heme d1-apomyoglobin and heme d1 in solution, implies that the prosthetic group is coordinated in the heme pocket through a protein-donated, strong-field ligand. Furthermore, the visible spectrum of heme d1.apomyoglobin varies minimally with ligand exchange, in contrast to the Soret, which suggests that much spectral information concerning heme d1 coordination in the oxidase is lost by interference from heme c absorption bands. A comparison of the absorption spectra of heme d1.apomyoglobin and Pseudomonas cytochrome oxidase, together with a critical examination of the previous axial ligand assignments from magnetic resonance techniques in the latter, implies that it is premature to accept the assignment of bishistidine heme d1 coordination in oxidized, ligand-free oxidase and other iron-isobacteriochlorin-containing enzymes.
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Affiliation(s)
- M B Steup
- Department of Chemistry, Purdue University School of Science, Indiana University-Purdue University, Indianapolis
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23
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Gadsby PM, Hartshorn RT, Moura JJ, Sinclair-Day JD, Sykes AG, Thomson AJ. Redox properties of the diheme cytochrome c4 from Azotobacter vinelandii and characterisation of the two hemes by NMR, MCD and EPR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 994:37-46. [PMID: 2535788 DOI: 10.1016/0167-4838(89)90059-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
From biphasic stopped-flow kinetic studies it has been established that the two heme centres of cytochrome c4 from Azotobacter vinelandii undergo redox change with [Co(terpy)2]3+/2+ (260 mV) at different rates. Rate constants for oxidation and reduction at pH 7.5 give reduction potentials for the two heme centres in agreement with previous values from spectrophotometric titrations (263 and 317 mV). From NMR studies on the fully reduced protein two sharp methyl methionine resonances are observed at -3.16 and -3.60 ppm, consistent with axial methionine coordination. On titration with [Fe(CN)6]3- the -3.16 ppm resonance is the first to disappear, and is assigned to the less positive reduction potential. Line-broadening effects are observed on partial oxidation, which are dominated by intermolecular processes in an intermediate time-range exchange process. The hemes of the oxidised protein are distinguishable by EPR g-values of 3.64 and 3.22. The former is of interest because it is at an unusually low field for histidine/methionine coordination, and has an asymmetric or ramp shape. The latter assigned to the low potential heme is similar to that of a cytochrome c551. The MCD spectra of the fully oxidised protein are typical of low-spin Fe(III) heme centres, with a negative peak at 710 nm characteristic of methionine coordination, and an NIR peak at 1900 nm characteristic of histidine/methionine (axial) coordination. Of the four histidines per molecule only two undergo diethyl pyrocarbonate (DEPC) modification.
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Affiliation(s)
- P M Gadsby
- Department of Chemistry, University of Newcastle upon Tyne, U.K
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24
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Liu MC, Huynh BH, Payne WJ, Peck HD, Dervartanian DV, Legall J. Optical, EPR and Mössbauer spectroscopic studies on the NO derivatives of cytochrome cd1 from Thiobacillus denitrificans. EUROPEAN JOURNAL OF BIOCHEMISTRY 1987; 169:253-8. [PMID: 2826139 DOI: 10.1111/j.1432-1033.1987.tb13605.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have used optical, EPR and Mössbauer spectroscopies to study the formation of heme-NO complex upon the addition of nitrite to reduced cytochrome cd1 from Thiobacillus denitrificans. The reduced d1 heme binds NO under both alkaline and acidic conditions, but the binding of NO to the reduced c heme was strongly pH-dependent. The Mössbauer data showed unambiguously that at pH 7.6 the c heme does not complex NO, whereas at pH 5.8 approximately half of the reduced c heme binds NO. This observation was confirmed by EPR studies, which showed that the spin concentration of the heme-NO EPR signal increased from 2 spins/molecule at pH 8.0 to approximately 3 spins/molecule at pH 5.8. Optical absorption study also showed strong pH dependence in the binding of NO to the reduced c heme. We have also analyzed the Mössbauer spectra of the ferrous d1 heme-NO complex using a spin-Hamiltonian formalism. The magnetic hyperfine coupling tensor was found to be consistent with the unpaired electron residing on a sigma orbital.
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Affiliation(s)
- M C Liu
- Department of Microbiology, University of Georgia, Athens
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25
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Liu MC, Liu MY, Payne WJ, Peck HD, Le Gall J, DerVartanian DV. Comparative EPR studies on the nitrite reductases from Escherichia coli and Wolinella succinogenes. FEBS Lett 1987; 218:227-30. [PMID: 3036590 DOI: 10.1016/0014-5793(87)81051-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hexaheme nitrite reductases purified to homogeneity from Escherichia coli K-12 and Wolinella succinogenes were studied by low-temperature EPR spectroscopy. In their isolated states, the two enzymes revealed nearly identical EPR spectra when measured at 12 K. Both high-spin and low-spin ferric heme EPR resonances with g values of 9.7, 3.7, 2.9, 2.3 and 1.5 were observed. These signals disappeared upon reduction by dithionite. Reaction of reduced enzyme with nitrite resulted in the formation of ferrous heme-NO complexes with distinct EPR spectral characteristics. The heme-NO complexes formed with the two enzymes differed, however, in g values and line-shapes. When reacted with hydroxylamine, reduced enzymes also showed the formation of ferrous heme-NO complexes. These results suggested the involvement of an enzyme-bound NO intermediate during the six-electron reduction of nitrite to ammonia catalyzed by these two hexaheme nitrite reductases. Heme proteins that can either expose bound NO to reduction or release it are significant components of both assimilatory and dissimilatory metabolisms of nitrate. The different ferrous heme-NO complexes detected for the two enzymes indicated, nevertheless, their subtle variation in heme reactivity during the reduction reaction.
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26
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Huynh BH, Patil DS, Moura I, Teixeira M, Moura JJ, DerVartanian DV, Czechowski MH, Prickril BC, Peck HD, LeGall J. On the active sites of the [NiFe] hydrogenase from Desulfovibrio gigas. Mössbauer and redox-titration studies. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(19)75856-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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27
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Andersson KK, Lipscomb JD, Valentine M, Münck E, Hooper AB. Tetraheme cytochrome c-554 from Nitrosomonas europaea. Heme-heme interactions and ligand binding. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)36064-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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28
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Characterization of a sulfite reductase from Desulfovibrio vulgaris. Evidence for the presence of a low-spin siroheme and an exchange-coupled siroheme-[4Fe-4S] unit. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)42559-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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29
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Abstract
The g values from low-spin ferric hemes can be related through the t2g hole model to rhombic (V/lambda) and tetragonal (delta/lambda) ligand field components and to the lowest Kramer's doublet energy (E/lambda). The latter is also a measure of unpaired electron sharing among the iron 3d (t2g) orbitals. For a series of ligands (X), there is a monotonic increase in myoglobin complex (Mb . X) [E/lambda] values with nonheme hexacoordinate metal complex (M . X6) [eg-t2gPg] orbital separations. As the aqueous solution pKa values of the sulfurous or nitrogenous ligands in model heme complexes increase, values of V/lambda and delta/lambda increase linearly, but those of [E/lambda] decrease linearly. The greater the electron-acceptor ability of the ligand, as suggested by its position in the spectrochemical series or its pKa, the more the unpaired electron sharing among the heme t2g orbitals increases. The rate of change of [E/lambda] with V/lambda and the pKa is different with sulfurous and nitrogenous ligands, and the magnitude of both rates increases with two sulfurs less than sulfur and nitrogen less than two nitrogens bound to the heme. The maximum magnitude of this rate with V/lambda for cytochrome P-450 is four times less than that for myoglobin, which may explain, in part, the differences in ligand binding between these two hemeproteins. The perturbation of [E/lambda], V/lambda, and delta/lambda induced by strain of iron-ligand bonds is quantitated for several hemeproteins and heme models. In addition, energy level comparisons suggest that the largest-magnitude g value falls approximately along the iron-chlorin ring normal. This suggestion implies that the electron distribution of the iron at the catalytic sites of cytochrome P-450 and certain chlorin-containing enzymes is in some way similar, but distinct from that at the transport site of myoglobin.
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Mössbauer, EPR, and optical studies of the P-460 center of hydroxylamine oxidoreductase from Nitrosomonas. A ferrous heme with an unusually large quadrupole splitting. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)39803-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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31
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Moura I, Liu MC, LeGall J, Peck HD, Payne WJ, Xavier AV, Moura JJ. NMR studies of a dihaem cytochrome from Pseudomonas perfectomarinus (ATCC 14405). EUROPEAN JOURNAL OF BIOCHEMISTRY 1984; 141:297-303. [PMID: 6329753 DOI: 10.1111/j.1432-1033.1984.tb08191.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pseudomonas perfectomarinus (ATCC 14405) dihaem cytochrome c552 was studied by 300-MHz proton magnetic resonance. Some of the haem resonances were assigned in the fully reduced and fully oxidized states. No evidence was found for methionine haem axial coordination. The oxidation-reduction equilibrium was studied in detail. Due to the large difference in mid-point redox potential between the two haems (+174 mV, for haem II and -180 mV for haem I) an intermediate oxidation state could be obtained containing reduced haem I and oxidized haem II. In this way the total paramagnetic shift at different oxidation levels could be decomposed in the intrinsic and extrinsic contributions. It was found that the two haems interact. The rate of electron exchange is slow on the NMR time scale. The redox equilibria are discussed for four possible redox species in solution.
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Kim CH, Hollocher TC. Catalysis of nitrosyl transfer reactions by a dissimilatory nitrite reductase (cytochrome c,d1). J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43321-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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33
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Christner JA, Münck E, Janick PA, Siegel LM. Mössbauer evidence for exchange-coupled siroheme and [4Fe-4S] prosthetic groups in Escherichia coli sulfite reductase. Studies of the reduced states and of a nitrite turnover complex. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44398-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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