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Jasniewski AJ, Que L. Dioxygen Activation by Nonheme Diiron Enzymes: Diverse Dioxygen Adducts, High-Valent Intermediates, and Related Model Complexes. Chem Rev 2018; 118:2554-2592. [PMID: 29400961 PMCID: PMC5920527 DOI: 10.1021/acs.chemrev.7b00457] [Citation(s) in RCA: 304] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A growing subset of metalloenzymes activates dioxygen with nonheme diiron active sites to effect substrate oxidations that range from the hydroxylation of methane and the desaturation of fatty acids to the deformylation of fatty aldehydes to produce alkanes and the six-electron oxidation of aminoarenes to nitroarenes in the biosynthesis of antibiotics. A common feature of their reaction mechanisms is the formation of O2 adducts that evolve into more reactive derivatives such as diiron(II,III)-superoxo, diiron(III)-peroxo, diiron(III,IV)-oxo, and diiron(IV)-oxo species, which carry out particular substrate oxidation tasks. In this review, we survey the various enzymes belonging to this unique subset and the mechanisms by which substrate oxidation is carried out. We examine the nature of the reactive intermediates, as revealed by X-ray crystallography and the application of various spectroscopic methods and their associated reactivity. We also discuss the structural and electronic properties of the model complexes that have been found to mimic salient aspects of these enzyme active sites. Much has been learned in the past 25 years, but key questions remain to be answered.
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Affiliation(s)
- Andrew J. Jasniewski
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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2
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Farquhar ER, Emerson JP, Koehntop KD, Reynolds MF, Trmčić M, Que L. In vivo self-hydroxylation of an iron-substituted manganese-dependent extradiol cleaving catechol dioxygenase. J Biol Inorg Chem 2011; 16:589-97. [PMID: 21279661 DOI: 10.1007/s00775-011-0760-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 01/16/2011] [Indexed: 11/30/2022]
Abstract
The homoprotocatechuate 2,3-dioxygenase from Arthrobacter globiformis (MndD) catalyzes the oxidative ring cleavage reaction of its catechol substrate in an extradiol fashion. Although this reactivity is more typically associated with non-heme iron enzymes, MndD exhibits an unusual specificity for manganese(II). MndD is structurally very similar to the iron(II)-dependent homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum (HPCD), and we have previously shown that both MndD and HPCD are equally active towards substrate turnover with either iron(II) or manganese(II) (Emerson et al. in Proc. Natl. Acad. Sci. USA 105:7347-7352, 2008). However, expression of MndD in Escherichia coli under aerobic conditions in the presence of excess iron results in the isolation of inactive blue-green iron-substituted MndD. Spectroscopic studies indicate that this form of iron-substituted MndD contains an iron(III) center with a bound catecholate, which is presumably generated by in vivo self-hydroxylation of a second-sphere tyrosine residue, as found for other self-hydroxylated non-heme iron oxygenases. The absence of this modification in either the native manganese-containing MndD or iron-containing HPCD suggests that the metal center of iron-substituted MndD is able to bind and activate O(2) in the absence of its substrate, employing a high-valence oxoiron oxidant to carry out the observed self-hydroxylation chemistry. These results demonstrate that the active site metal in MndD can support two dramatically different O(2) activation pathways, further highlighting the catalytic flexibility of enzymes containing a 2-His-1-carboxylate facial triad metal binding motif.
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Affiliation(s)
- Erik R Farquhar
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455, USA
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3
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Farquhar ER, Koehntop KD, Emerson JP, Que L. Post-translational self-hydroxylation: A probe for oxygen activation mechanisms in non-heme iron enzymes. Biochem Biophys Res Commun 2005; 338:230-9. [PMID: 16165090 DOI: 10.1016/j.bbrc.2005.08.191] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Accepted: 08/25/2005] [Indexed: 10/25/2022]
Abstract
Recent years have seen considerable evolution in our understanding of the mechanisms of oxygen activation by non-heme iron enzymes, with high-valent iron-oxo intermediates coming to the forefront as formidably potent oxidants. In the absence of substrate, the generation of vividly colored chromophores deriving from the self-hydroxylation of a nearby aromatic amino acid for a number of these enzymes has afforded an opportunity to discern the conditions under which O2 activation occurs to generate a high-valent iron intermediate, and has provided a basis for a rigorous mechanistic examination of the oxygenation process. Here, we summarize the current evidence for self-hydroxylation processes in both mononuclear non-heme iron enzymes and in mutant forms of ribonucleotide reductase, and place it within the context of our developing understanding of the oxidative transformations accomplished by non-heme iron centers.
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Affiliation(s)
- Erik R Farquhar
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
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Koehntop KD, Marimanikkuppam S, Ryle MJ, Hausinger RP, Que L. Self-hydroxylation of taurine/alpha-ketoglutarate dioxygenase: evidence for more than one oxygen activation mechanism. J Biol Inorg Chem 2005; 11:63-72. [PMID: 16320009 DOI: 10.1007/s00775-005-0059-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Accepted: 10/13/2005] [Indexed: 10/25/2022]
Abstract
2-Aminoethanesulfonic acid (taurine)/alpha-ketoglutarate (alphaKG) dioxygenase (TauD) is a mononuclear non-heme iron enzyme that catalyzes the hydroxylation of taurine to generate sulfite and aminoacetaldehyde in the presence of O2, alphaKG, and Fe(II). Fe(II)TauD complexed with alphaKG or succinate, the decarboxylated product of alphaKG, reacts with O2 in the absence of prime substrate to generate 550- and 720-nm chromophores, respectively, that are interconvertible by the addition or removal of bound bicarbonate and have resonance Raman features characteristic of an Fe(III)-catecholate complex. Mutagenesis studies suggest that both reactions result in the self-hydroxylation of the active-site residue Tyr73, and liquid chromatography nano-spray mass spectrometry/mass spectrometry evidence corroborates this result for the succinate reaction. Furthermore, isotope-labeling resonance Raman studies demonstrate that the oxygen atom incorporated into the tyrosyl residue derives from H2 18O and 18O2 for the alphaKG and succinate reactions, respectively, suggesting distinct mechanistic pathways. Whereas the alphaKG-dependent hydroxylation likely proceeds via an Fe(IV) = O intermediate that is known to be generated during substrate hydroxylation, we propose Fe(III)-OOH (or Fe(V) = O) as the oxygenating species in the succinate-dependent reaction. These results demonstrate the two oxygenating mechanisms available to enzymes with a 2-His-1-carboxylate triad, depending on whether the electron source donates one or two electrons.
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Affiliation(s)
- Kevin D Koehntop
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455, USA
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Moe LA, Hu Z, Deng D, Austin RN, Groves JT, Fox BG. Remarkable aliphatic hydroxylation by the diiron enzyme toluene 4-monooxygenase in reactions with radical or cation diagnostic probes norcarane, 1,1-dimethylcyclopropane, and 1,1-diethylcyclopropane. Biochemistry 2005; 43:15688-701. [PMID: 15595825 DOI: 10.1021/bi040033h] [Citation(s) in RCA: 31] [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
Toluene 4-monooxygenase (T4MO) catalyzes the hydroxylation of toluene to yield 96% p-cresol. This diiron enzyme complex was used to oxidize norcarane (bicyclo[4.1.0]heptane), 1,1-dimethylcyclopropane, and 1,1-diethylcyclopropane, substrate analogues that can undergo diagnostic reactions upon the production of transient radical or cationic intermediates. Norcarane closely matches the shape and volume of the natural substrate toluene. Reaction of isoforms of the hydroxylase component of T4MO (T4moH) with different regiospecificities for toluene hydroxylation (k(cat) approximately 1.9-2.3 s(-)(1) and coupling efficiency approximately 81-96%) revealed similar catalytic parameters for norcarane oxidation (k(cat) approximately 0.3-0.5 s(-)(1) and coupling efficiency approximately 72%). The products included variable amounts of the un-rearranged isomeric norcaranols and cyclohex-2-enyl methanol, a product attributed to rearrangement of a radical oxidation intermediate. A ring-expansion product derived from the norcaranyl C-2 cation, cyclohept-3-enol, was not produced by either the natural enzyme or any of the T4moH isoforms tested. Comparative studies of 1,1-dimethylcyclopropane and 1,1-diethylcyclopropane, diagnostic substrates with differences in size and with approximately 50-fold slower k(cat) values, gave products consistent with both radical rearrangement and cation ring expansion. Examination of the isotopic enrichment of the incorporated O-atoms for all products revealed high-fidelity incorporation of an O-atom from O(2) in the un-rearranged and radical-rearranged products, while the O-atom found in the cation ring-expansion products was predominantly obtained by reaction with H(2)O. The results show a divergence of radical and cation pathways for T4moH-mediated hydroxylation that can be dissected by diagnostic substrate probe rearrangements and by changes in the source of oxygen used for substrate oxygenation.
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Affiliation(s)
- Luke A Moe
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin 53706-1544, USA
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Kolberg M, Logan DT, Bleifuss G, Pötsch S, Sjöberg BM, Gräslund A, Lubitz W, Lassmann G, Lendzian F. A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies. J Biol Chem 2005; 280:11233-46. [PMID: 15634667 DOI: 10.1074/jbc.m414634200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The R2 protein subunit of class I ribonucleotide reductase (RNR) belongs to a structurally related family of oxygen bridged diiron proteins. In wild-type R2 of Escherichia coli, reductive cleavage of molecular oxygen by the diferrous iron center generates a radical on a nearby tyrosine residue (Tyr122), which is essential for the enzymatic activity of RNR, converting ribonucleotides into deoxyribonucleotides. In this work, we characterize the mutant E. coli protein R2-Y122H, where the radical site is substituted with a histidine residue. The x-ray structure verifies the mutation. R2-Y122H contains a novel stable paramagnetic center which we name H, and which we have previously proposed to be a diferric iron center with a strongly coupled radical, Fe(III)Fe(III)R.. Here we report a detailed characterization of center H, using 1H/2H -14N/15N- and 57Fe-ENDOR in comparison with the Fe(III)Fe(IV) intermediate X observed in the iron reconstitution reaction of R2. Specific deuterium labeling of phenylalanine residues reveals that the radical results from a phenylalanine. As Phe208 is the only phenylalanine in the ligand sphere of the iron site, and generation of a phenyl radical requires a very high oxidation potential, we propose that in Y122H residue Phe208 is hydroxylated, as observed earlier in another mutant (R2-Y122F/E238A), and further oxidized to a phenoxyl radical, which is coordinated to Fe1. This work demonstrates that small structural changes can redirect the reactivity of the diiron site, leading to oxygenation of a hydrocarbon, as observed in the structurally similar methane monoxygenase, and beyond, to formation of a stable iron-coordinated radical.
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Affiliation(s)
- Matthias Kolberg
- Max-Volmer-Laboratory, Institute for Chemistry, PC 14, Technical University Berlin, D-10623 Berlin, Germany
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Liu P, Mehn MP, Yan F, Zhao Z, Que L, Liu HW. Oxygenase activity in the self-hydroxylation of (s)-2-hydroxypropylphosphonic acid epoxidase involved in fosfomycin biosynthesis. J Am Chem Soc 2004; 126:10306-12. [PMID: 15315444 DOI: 10.1021/ja0475050] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The last step of the biosynthesis of fosfomycin is the conversion of (S)-2-hydroxypropylphosphonic acid (HPP) to fosfomycin by HPP epoxidase (HppE), which is a mononuclear non-heme iron-dependent enzyme. The apo-HppE from Streptomyces wedmorensis is colorless, but turns green with broad absorption bands at 430 and 680 nm after reconstitution with ferrous ion under aerobic conditions. Resonance Raman studies showed that this green chromophore arises from a bidentate iron(III)-catecholate (DOPA) complex, and the most likely site of modification is at Tyr105 on the basis of site-specific mutagenesis results. It was also found that reconstitution in the presence of ascorbate leads to the formation of additional DOPA that shows (18)O-incorporation from (18)O(2). Thus, HppE can act as an oxygenase via a putative high valent iron-oxo or an iron-hydroperoxo intermediate, just like other members of the family of non-heme iron enzymes. The oxygen activation mechanism for catalytic turnover is proposed to parallel that for self-hydroxylation.
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Affiliation(s)
- Pinghua Liu
- Contribution from the Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
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Que L. The oxo/peroxo debate: a nonheme iron perspective. J Biol Inorg Chem 2004; 9:684-90. [PMID: 15300470 DOI: 10.1007/s00775-004-0574-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2004] [Accepted: 06/24/2004] [Indexed: 10/26/2022]
Abstract
The oxygen activation mechanisms proposed for nonheme iron systems generally follow the heme paradigm in invoking the involvement of iron-peroxo and iron-oxo species in their catalytic cycles. However, the nonheme ligand environments allow for end-on and side-on dioxygen coordination and impart greater flexibility in the modes of dioxygen activation. The currently available evidence for nonheme iron-peroxo and iron-oxo intermediates is summarized and discussed in light of the ongoing discussion on the nature of the oxidant(s) in heme enzymes.
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Affiliation(s)
- Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455, USA.
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Saleh L, Krebs C, Ley BA, Naik S, Huynh BH, Bollinger JM. Use of a Chemical Trigger for Electron Transfer to Characterize a Precursor to Cluster X in Assembly of the Iron-Radical Cofactor of Escherichia coli Ribonucleotide Reductase. Biochemistry 2004; 43:5953-64. [PMID: 15147179 DOI: 10.1021/bi036099e] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A key step in generation of the catalytically essential tyrosyl radical (Y122(*)) in protein R2 of Escherichia coli ribonucleotide reductase is electron transfer (ET) from the near-surface residue, tryptophan 48 (W48), to a (Fe(2)O(2))(4+) complex formed by addition of O(2) to the carboxylate-bridged diiron(II) cluster. Because this step is rapid, the (Fe(2)O(2))(4+) complex does not accumulate and, therefore, has not been characterized. The product of the ET step is a "diradical" intermediate state containing the well-characterized Fe(IV)Fe(III) cluster, X, and a W48 cation radical (W48(+)(*)). The latter may be reduced from solution to complete the two-step transfer of an electron to the buried diiron site. In this study, a (Fe(2)O(2))(4+) state that is probably the precursor to the X-W48(+)(*) diradical state in the reaction of the wild-type protein (R2-wt) has been characterized by exploitation of the observation that in R2 variants with W48 replaced with alanine (A), the otherwise disabled ET step can be mediated by indole compounds. Mixing of the Fe(II) complex of R2-W48A/Y122F with O(2) results in accumulation of an intermediate state that rapidly converts to X upon mixing with 3-methylindole (3-MI). The state comprises at least two species, of which each exhibits an apparent Mössbauer quadrupole doublet with parameters characteristic of high-spin Fe(III) ions. The isomer shifts of these complexes and absence of magnetic hyperfine coupling in their Mössbauer spectra suggest that both are antiferromagnetically coupled diiron(III) clusters. The fact that both rapidly convert to X upon treatment with a molecule (3-MI) shown in the preceding paper to mediate ET in W48A R2 variants indicates that they are more oxidized than X by one electron, which suggests that they have a bound peroxide equivalent. Their failure to exhibit either the long-wavelength absorption (at 650-750 nm) or Mössbauer doublet with high isomer shift (>0.6 mm/s) that are characteristic of the putatively mu-1,2-peroxo-bridged diiron(III) intermediates that have been detected in the reactions of methane monooxygenase (P or H(peroxo)) and variants of R2 with the D84E ligand substitution suggests that they have geometries and electronic structures different from those of the previously characterized complexes. Supporting this deduction, the peroxodiiron(III) complex that accumulates in R2-W48A/D84E is much less reactive toward 3-MI-mediated reduction than the (Fe(2)O(2))(4+) state in R2-W48A/Y122F. It is postulated that the new (Fe(2)O(2))(4+) state is either an early adduct in an orthogonal pathway for oxygen activation or, more likely, the successor to a (mu-1,2-peroxo)diiron(III) complex that is extremely fleeting in R2 proteins with the wild-type ligand set but longer lived in D84E-containing variants.
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Affiliation(s)
- Lana Saleh
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Saleh L, Kelch BA, Pathickal BA, Baldwin J, Ley BA, Bollinger JM. Mediation by Indole Analogues of Electron Transfer during Oxygen Activation in Variants of Escherichia coli Ribonucleotide Reductase R2 Lacking the Electron-Shuttling Tryptophan 48. Biochemistry 2004; 43:5943-52. [PMID: 15147178 DOI: 10.1021/bi036098m] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Activation of dioxygen by the carboxylate-bridged diiron(II) cluster in the R2 subunit of class I ribonucleotide reductase from Escherichia coli results in the one-electron oxidation of tyrosine 122 (Y122) to a stable radical (Y122*). A key step in this reaction is the rapid transfer of a single electron from a near-surface residue, tryptophan 48 (W48), to an adduct between O(2) and diiron(II) cluster to generate a readily reducible cation radical (W48(+)(*)) and the formally Fe(IV)Fe(III) intermediate known as cluster X. Previous work showed that this electron injection step is blocked in the R2 variant with W48 replaced by phenylalanine [Krebs, C., Chen, S., Baldwin, J., Ley, B. A., Patel, U., Edmondson, D. E., Huynh, B. H., and Bollinger, J. M., Jr. (2000) J. Am. Chem. Soc. 122, 12207-12219]. In this study, we show that substitution of W48 with alanine similarly disables the electron transfer (ET) but also permits its chemical mediation by indole compounds. In the presence of an indole mediator, O(2) activation in the R2-W48A variant produces approximately 1 equiv of stable Y122* and more than 1 equiv of the normal (micro-oxo)diiron(III) product. In the absence of a mediator, the variant protein generates primarily altered Fe(III) products and only one-fourth as much stable Y122* because, as previously reported for R2-W48F, most of the Y122* that is produced decays as a consequence of the inability of the protein to mediate reductive quenching of one of the two oxidizing equivalents of the initial diiron(II)-O(2) complex. Mediation of ET is effective in W48A variants containing additional substitutions that also impact the reaction mechanism or outcome. In the reaction of R2-W48A/F208Y, the presence of mediator suppresses formation of the Y208-derived diiron(III)-catecholate product (which is predominant in R2-F208Y in the absence of reductants) in favor of Y122*. In the reaction of R2-W48A/D84E, the presence of mediator affects the outcome of decay of the peroxodiiron(III) intermediate known to accumulate in D84E variants, increasing the yield of Y122* by as much as 2.2-fold to a final value of 0.75 equiv and suppressing formation of a 490 nm absorbing product that results from decay of the two-electron oxidized intermediate in the absence of a functional ET apparatus.
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Affiliation(s)
- Lana Saleh
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Lee D, Pierce B, Krebs C, Hendrich MP, Huynh BH, Lippard SJ. Functional mimic of dioxygen-activating centers in non-heme diiron enzymes: mechanistic implications of paramagnetic intermediates in the reactions between diiron(II) complexes and dioxygen. J Am Chem Soc 2002; 124:3993-4007. [PMID: 11942838 DOI: 10.1021/ja012251t] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two tetracarboxylate diiron(II) complexes, [Fe(2)(mu-O(2)CAr(Tol))(2)(O(2)CAr(Tol))(2)(C(5)H(5)N)(2)] (1a) and [Fe(2)(mu-O(2)CAr(Tol))(4)(4-(t)BuC(5)H(4)N)(2)] (2a), where Ar(Tol)CO(2)(-) = 2,6-di(p-tolyl)benzoate, react with O(2) in CH(2)Cl(2) at -78 degrees C to afford dark green intermediates 1b (lambda(max) congruent with 660 nm; epsilon = 1600 M(-1) cm(-1)) and 2b (lambda(max) congruent with 670 nm; epsilon = 1700 M(-1) cm(-1)), respectively. Upon warming to room temperature, the solutions turn yellow, ultimately converting to isolable diiron(III) compounds [Fe(2)(mu-OH)(2)(mu-O(2)CAr(Tol))(2)(O(2)CAr(Tol))(2)L(2)] (L = C(5)H(5)N (1c), 4-(t)BuC(5)H(4)N (2c)). EPR and Mössbauer spectroscopic studies revealed the presence of equimolar amounts of valence-delocalized Fe(II)Fe(III) and valence-trapped Fe(III)Fe(IV) species as major components of solution 2b. The spectroscopic and reactivity properties of the Fe(III)Fe(IV) species are similar to those of the intermediate X in the RNR-R2 catalytic cycle. EPR kinetic studies revealed that the processes leading to the formation of these two distinctive paramagnetic components are coupled to one another. A mechanism for this reaction is proposed and compared with those of other synthetic and biological systems, in which electron transfer occurs from a low-valent starting material to putative high-valent dioxygen adduct(s).
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Affiliation(s)
- Dongwhan Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Eklund H, Uhlin U, Färnegårdh M, Logan DT, Nordlund P. Structure and function of the radical enzyme ribonucleotide reductase. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 77:177-268. [PMID: 11796141 DOI: 10.1016/s0079-6107(01)00014-1] [Citation(s) in RCA: 256] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze all new production in nature of deoxyribonucleotides for DNA synthesis by reducing the corresponding ribonucleotides. The reaction involves the action of a radical that is produced differently for different classes of the enzyme. Class I enzymes, which are present in eukaryotes and microorganisms, use an iron center to produce a stable tyrosyl radical that is stored in one of the subunits of the enzyme. The other classes are only present in microorganisms. Class II enzymes use cobalamin for radical generation and class III enzymes, which are found only in anaerobic organisms, use a glycyl radical. The reductase activity is in all three classes contained in enzyme subunits that have similar structures containing active site cysteines. The initiation of the reaction by removal of the 3'-hydrogen of the ribose by a transient cysteinyl radical is a common feature of the different classes of RNR. This cysteine is in all RNRs located on the tip of a finger loop inserted into the center of a special barrel structure. A wealth of structural and functional information on the class I and class III enzymes can now give detailed views on how these enzymes perform their task. The class I enzymes demonstrate a sophisticated pattern as to how the free radical is used in the reaction, in that it is only delivered to the active site at exactly the right moment. RNRs are also allosterically regulated, for which the structural molecular background is now starting to be revealed.
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Affiliation(s)
- H Eklund
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Center, Box 590, S-751 24, Uppsala, Sweden.
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Baldwin J, Voegtli WC, Khidekel N, Moënne-Loccoz P, Krebs C, Pereira AS, Ley BA, Huynh BH, Loehr TM, Riggs-Gelasco PJ, Rosenzweig AC, Bollinger JM. Rational reprogramming of the R2 subunit of Escherichia coli ribonucleotide reductase into a self-hydroxylating monooxygenase. J Am Chem Soc 2001; 123:7017-30. [PMID: 11459480 DOI: 10.1021/ja002114g] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The outcome of O2 activation at the diiron(II) cluster in the R2 subunit of Escherichia coli (class I) ribonucleotide reductase has been rationally altered from the normal tyrosyl radical (Y122*) production to self-hydroxylation of a phenylalanine side-chain by two amino acid substitutions that leave intact the (histidine)2-(carboxylate)4 ligand set characteristic of the diiron-carboxylate family. Iron ligand Asp (D) 84 was replaced with Glu (E), the amino acid found in the cognate position of the structurally similar diiron-carboxylate protein, methane monooxygenase hydroxylase (MMOH). We previously showed that this substitution allows accumulation of a mu-1,2-peroxodiiron(III) intermediate, which does not accumulate in the wild-type (wt) protein and is probably a structural homologue of intermediate P (H(peroxo)) in O2 activation by MMOH. In addition, the near-surface residue Trp (W) 48 was replaced with Phe (F), blocking transfer of the "extra" electron that occurs in wt R2 during formation of the formally Fe(III)Fe(IV) cluster X. Decay of the mu-1,2-peroxodiiron(III) complex in R2-W48F/D84E gives an initial brown product, which contains very little Y122* and which converts very slowly (t1/2 approximately 7 h) upon incubation at 0 degrees C to an intensely purple final product. X-ray crystallographic analysis of the purple product indicates that F208 has undergone epsilon-hydroxylation and the resulting phenol has shifted significantly to become a ligand to Fe2 of the diiron cluster. Resonance Raman (RR) spectra of the purple product generated with 16O2 or 18O2 show appropriate isotopic sensitivity in bands assigned to O-phenyl and Fe-O-phenyl vibrational modes, confirming that the oxygen of the Fe(III)-phenolate species is derived from O2. Chemical analysis, experiments involving interception of the hydroxylating intermediate with exogenous reductant, and Mössbauer and EXAFS characterization of the brown and purple species establish that F208 hydroxylation occurs during decay of the peroxo complex and formation of the initial brown product. The slow transition to the purple Fe(III)-phenolate species is ascribed to a ligand rearrangement in which mu-O2- is lost and the F208-derived phenolate coordinates. The reprogramming to F208 monooxygenase requires both amino acid substitutions, as very little epsilon-hydroxyphenylalanine is formed and pathways leading to Y122* formation predominate in both R2-D84E and R2-W48F.
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Affiliation(s)
- J Baldwin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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14
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Sahlin M, Sjöberg BM. Ribonucleotide reductase. A virtual playground for electron transfer reactions. Subcell Biochem 2001; 35:405-43. [PMID: 11192729 DOI: 10.1007/0-306-46828-x_12] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- M Sahlin
- Department of Molecular Biology, Stockholm University, SE-10691 Stockholm, Sweden
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15
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Whittington DA, Lippard SJ. Crystal structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site. J Am Chem Soc 2001; 123:827-38. [PMID: 11456616 DOI: 10.1021/ja003240n] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxidation of methane to methanol is performed at carboxylate-bridged dinuclear iron centers in the soluble methane monooxygenase hydroxylase (MMOH). Previous structural studies of MMOH, and the related R2 subunit of ribonucleotide reductase, have demonstrated the occurrence of carboxylate shifts involving glutamate residues that ligate the catalytic iron atoms. These shifts are thought to have important mechanistic implications. Recent kinetic and theoretical studies have also emphasized the importance of hydrogen bonding and pH effects at the active site. We report here crystal structures of MMOH from Methylococcus capsulatus (Bath) in the diiron(II), diiron(III), and mixed-valent Fe(II)Fe(III) oxidation states, and at pH values of 6.2, 7.0, and 8.5. These structures were investigated in an effort to delineate the range of possible motions at the MMOH active site and to identify hydrogen-bonding interactions that may be important in understanding catalysis by the enzyme. Our results present the first view of the diiron center in the mixed-valent state, and they indicate an increased lability for ferrous ions in the enzyme. Alternate conformations of Asn214 near the active site according to redox state and a distortion in one of the alpha-helices adjacent to the metal center in the diiron(II) state have also been identified. These changes alter the surface of the protein in the vicinity of the catalytic core and may have implications for small-molecule accessibility to the active site and for protein component interactions in the methane monooxygenase system. Collectively, these results help to explain previous spectroscopic observations and provide new insight into catalysis by the enzyme.
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Affiliation(s)
- D A Whittington
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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16
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Solomon EI, Brunold TC, Davis MI, Kemsley JN, Lee SK, Lehnert N, Neese F, Skulan AJ, Yang YS, Zhou J. Geometric and electronic structure/function correlations in non-heme iron enzymes. Chem Rev 2000; 100:235-350. [PMID: 11749238 DOI: 10.1021/cr9900275] [Citation(s) in RCA: 1351] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
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17
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Ménage S, Galey JB, Dumats J, Hussler G, Seité M, Luneau IG, Chottard G, Fontecave M. O2 Activation and Aromatic Hydroxylation Performed by Diiron Complexes. J Am Chem Soc 1998. [DOI: 10.1021/ja981123a] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stéphane Ménage
- Contribution from the Laboratoire de Chimie et Biochimie des Centres Redox Biologiques, DBMS-CEA Grenoble/EP 1087 CNRS/ Université Joseph Fourier, 17 Rue des Martyrs 38054, Grenoble Cédex 9, France, L'Oréal Research Center, 1 avenue Eugène Schueller, 93600 Aulnay sous bois, France, L.E.D.S.S., UMR 5616, Université Joseph Fourier, 301 rue de la Chimie, 91041 Grenoble Cedex, France, and Laboratoire de Chimie des Métaux de Transition, Université Pierre et Marie Curie, F75230 Paris Cedex 05, France
| | - Jean-Baptiste Galey
- Contribution from the Laboratoire de Chimie et Biochimie des Centres Redox Biologiques, DBMS-CEA Grenoble/EP 1087 CNRS/ Université Joseph Fourier, 17 Rue des Martyrs 38054, Grenoble Cédex 9, France, L'Oréal Research Center, 1 avenue Eugène Schueller, 93600 Aulnay sous bois, France, L.E.D.S.S., UMR 5616, Université Joseph Fourier, 301 rue de la Chimie, 91041 Grenoble Cedex, France, and Laboratoire de Chimie des Métaux de Transition, Université Pierre et Marie Curie, F75230 Paris Cedex 05, France
| | - Jacqueline Dumats
- Contribution from the Laboratoire de Chimie et Biochimie des Centres Redox Biologiques, DBMS-CEA Grenoble/EP 1087 CNRS/ Université Joseph Fourier, 17 Rue des Martyrs 38054, Grenoble Cédex 9, France, L'Oréal Research Center, 1 avenue Eugène Schueller, 93600 Aulnay sous bois, France, L.E.D.S.S., UMR 5616, Université Joseph Fourier, 301 rue de la Chimie, 91041 Grenoble Cedex, France, and Laboratoire de Chimie des Métaux de Transition, Université Pierre et Marie Curie, F75230 Paris Cedex 05, France
| | - Georges Hussler
- Contribution from the Laboratoire de Chimie et Biochimie des Centres Redox Biologiques, DBMS-CEA Grenoble/EP 1087 CNRS/ Université Joseph Fourier, 17 Rue des Martyrs 38054, Grenoble Cédex 9, France, L'Oréal Research Center, 1 avenue Eugène Schueller, 93600 Aulnay sous bois, France, L.E.D.S.S., UMR 5616, Université Joseph Fourier, 301 rue de la Chimie, 91041 Grenoble Cedex, France, and Laboratoire de Chimie des Métaux de Transition, Université Pierre et Marie Curie, F75230 Paris Cedex 05, France
| | - Michel Seité
- Contribution from the Laboratoire de Chimie et Biochimie des Centres Redox Biologiques, DBMS-CEA Grenoble/EP 1087 CNRS/ Université Joseph Fourier, 17 Rue des Martyrs 38054, Grenoble Cédex 9, France, L'Oréal Research Center, 1 avenue Eugène Schueller, 93600 Aulnay sous bois, France, L.E.D.S.S., UMR 5616, Université Joseph Fourier, 301 rue de la Chimie, 91041 Grenoble Cedex, France, and Laboratoire de Chimie des Métaux de Transition, Université Pierre et Marie Curie, F75230 Paris Cedex 05, France
| | - Isabelle Gautier Luneau
- Contribution from the Laboratoire de Chimie et Biochimie des Centres Redox Biologiques, DBMS-CEA Grenoble/EP 1087 CNRS/ Université Joseph Fourier, 17 Rue des Martyrs 38054, Grenoble Cédex 9, France, L'Oréal Research Center, 1 avenue Eugène Schueller, 93600 Aulnay sous bois, France, L.E.D.S.S., UMR 5616, Université Joseph Fourier, 301 rue de la Chimie, 91041 Grenoble Cedex, France, and Laboratoire de Chimie des Métaux de Transition, Université Pierre et Marie Curie, F75230 Paris Cedex 05, France
| | - Geneviève Chottard
- Contribution from the Laboratoire de Chimie et Biochimie des Centres Redox Biologiques, DBMS-CEA Grenoble/EP 1087 CNRS/ Université Joseph Fourier, 17 Rue des Martyrs 38054, Grenoble Cédex 9, France, L'Oréal Research Center, 1 avenue Eugène Schueller, 93600 Aulnay sous bois, France, L.E.D.S.S., UMR 5616, Université Joseph Fourier, 301 rue de la Chimie, 91041 Grenoble Cedex, France, and Laboratoire de Chimie des Métaux de Transition, Université Pierre et Marie Curie, F75230 Paris Cedex 05, France
| | - Marc Fontecave
- Contribution from the Laboratoire de Chimie et Biochimie des Centres Redox Biologiques, DBMS-CEA Grenoble/EP 1087 CNRS/ Université Joseph Fourier, 17 Rue des Martyrs 38054, Grenoble Cédex 9, France, L'Oréal Research Center, 1 avenue Eugène Schueller, 93600 Aulnay sous bois, France, L.E.D.S.S., UMR 5616, Université Joseph Fourier, 301 rue de la Chimie, 91041 Grenoble Cedex, France, and Laboratoire de Chimie des Métaux de Transition, Université Pierre et Marie Curie, F75230 Paris Cedex 05, France
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18
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19
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Persson AL, Sahlin M, Sjöberg BM. Cysteinyl and substrate radical formation in active site mutant E441Q of Escherichia coli class I ribonucleotide reductase. J Biol Chem 1998; 273:31016-20. [PMID: 9812999 DOI: 10.1074/jbc.273.47.31016] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All classes of ribonucleotide reductase are proposed to have a common reaction mechanism involving a transient cysteine thiyl radical that initiates catalysis by abstracting the 3'-hydrogen atom of the substrate nucleotide. In the class Ia ribonucleotide reductase system of Escherichia coli, we recently trapped two kinetically coupled transient radicals in a reaction involving the engineered E441Q R1 protein, wild-type R2 protein, and substrate (Persson, A. L., Eriksson, M., Katterle, B., Pötsch, S., Sahlin, M., and Sjöberg, B.-M. (1997) J. Biol. Chem. 272, 31533-31541). Using isotopically labeled R1 protein or substrate, we now demonstrate that the early radical intermediate is a cysteinyl radical, possibly in weak magnetic interaction with the diiron site of protein R2, and that the second radical intermediate is a carbon-centered substrate radical with hyperfine coupling to two almost identical protons. This is the first report of a cysteinyl free radical in ribonucleotide reductase that is a kinetically coupled precursor of an identified substrate radical. We suggest that the cysteinyl radical is localized to the active site residue, Cys439, which is conserved in all classes of ribonucleotide reductase, and which, in the three-dimensional structure of protein R1, is positioned to abstract the 3'-hydrogen atom of the substrate. We also suggest that the substrate radical is localized to the 3'-position of the ribose moiety, the first substrate radical intermediate in the postulated reaction mechanism.
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Affiliation(s)
- A L Persson
- Department of Molecular Biology, Stockholm University, S-10691 Stockholm, Sweden
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20
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Schmidt PP, Rova U, Katterle B, Thelander L, Gräslund A. Kinetic evidence that a radical transfer pathway in protein R2 of mouse ribonucleotide reductase is involved in generation of the tyrosyl free radical. J Biol Chem 1998; 273:21463-72. [PMID: 9705274 DOI: 10.1074/jbc.273.34.21463] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Class I ribonucleotide reductases consist of two subunits, R1 and R2. The active site is located in R1; active R2 contains a diferric center and a tyrosyl free radical (Tyr.), both essential for enzymatic activity. The proposed mechanism for the enzymatic reaction includes the transport of a reducing equivalent, i.e. electron or hydrogen radical, across a 35-A distance between Tyr. in R2 and the active site in R1, which are connected by a hydrogen-bonded chain of conserved, catalytically essential amino acid residues. Asp266 and Trp103 in mouse R2 are part of this radical transfer pathway. The diferric/Tyr. site in R2 is reconstituted spontaneously by mixing iron-free apoR2 with Fe(II) and O2. The reconstitution reaction requires the delivery of an external reducing equivalent to form the diferric/Tyr. site. Reconstitution kinetics were investigated in mouse apo-wild type R2 and the three mutants D266A, W103Y, and W103F by rapid freeze-quench electron paramagnetic resonance with >/=4 Fe(II)/R2 at various reaction temperatures. The kinetics of Tyr. formation in D266A and W103Y is on average 20 times slower than in wild type R2. More strikingly, Tyr. formation is completely suppressed in W103F. No change in the reconstitution kinetics was found starting from Fe(II)-preloaded proteins, which shows that the mutations do not affect the rate of iron binding. Our results are consistent with a reaction mechanism using Asp266 and Trp103 for delivery of the external reducing equivalent. Further, the results with W103F suggest that an intact hydrogen-bonded chain is crucial for the reaction, indicating that the external reducing equivalent is a H. Finally, the formation of Tyr. is not the slowest step of the reaction as it is in Escherichia coli R2, consistent with a stronger interaction between Tyr. and the iron center in mouse R2. A new electron paramagnetic resonance visible intermediate named mouse X, strikingly similar to species X found in E. coli R2, was detected only in small amounts under certain conditions. We propose that it may be an intermediate in a side reaction leading to a diferric center without forming the neighboring Tyr.
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Affiliation(s)
- P P Schmidt
- Department of Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
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21
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Liu A, Sahlin M, Pötsch S, Sjöberg BM, Gräslund A. New paramagnetic species formed at the expense of the transient tyrosyl radical in mutant protein R2 F208Y of Escherichia coli ribonucleotide reductase. Biochem Biophys Res Commun 1998; 246:740-5. [PMID: 9618282 DOI: 10.1006/bbrc.1998.8701] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The highly conserved residue F208 in protein R2 of E. coli ribonucleotide reductase is close to the binuclear iron center, and found to be involved in stabilizing the tyrosyl radical Y122. in wild type R2. Upon the reconstitution reaction of the mutant R2 F208Y with ferrous iron and molecular oxygen, we observed a new EPR singlet signal (g = 2.003) formed concomitantly with decay of the transient tyrosyl radical Y122. (g = 2.005). This new paramagnetic species (denoted Z) was stable for weeks at 4 degrees C and visible by EPR only below 50 K. The EPR singlet could not be saturated by available microwave power, suggesting that Z may be a mainly metal centered species. The maximum amount of the compound Z in the protein purified from cells grown in rich medium was about 0.18 unpaired spin/R2. An identical EPR signal of Z was found also in the double mutant R2 F208Y/Y122F. In the presence of high concentration of sodium ascorbate, the amounts of both the transient Y122. and the new species Z increased considerably in the reconstitution reaction. The results suggest that Z is most likely an oxo-ferryl species possibly in equilibrium with a Y208 ligand radical.
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Affiliation(s)
- A Liu
- Department of Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
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22
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Parkin SE, Chen S, Ley BA, Mangravite L, Edmondson DE, Huynh BH, Bollinger JM. Electron injection through a specific pathway determines the outcome of oxygen activation at the diiron cluster in the F208Y mutant of Escherichia coli ribonucleotide reductase protein R2. Biochemistry 1998; 37:1124-30. [PMID: 9454605 DOI: 10.1021/bi9723717] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein R2 of ribonucleotide reductase from Escherichia coli contains a dinuclear iron cluster, which reductively activates O2 to produce the enzyme's functionally essential tyrosyl radical by one-electron oxidation of residue Y122. A key step in this reaction is the rapid injection of a single electron from an exogenous reductant (Fe2+ or ascorbate) during formation of the radical-generating intermediate, cluster X, from the diiron(II) cluster and O2. As this step leaves only one of the two oxidizing equivalents of the initial diiron(II)-O2 adduct, it commits the reaction to a one-electron oxidation outcome and precludes possible two-electron alternatives (as occur in the related diiron bacterial alkane hydroxylases and fatty acyl desaturases). In the F208Y site-directed mutant of R2, Y208 is hydroxylated (a two-electron oxidation) in preference to the normal reaction [Aberg, A., Ormö, M., Nordlund, P., & Sjöberg, B. M. (1993) Biochemistry 32, 9845-9850], implying that this substitution blocks electron injection or (more likely) introduces an endogenous reductant (Y208) that effectively competes. Here we demonstrate that O2 activation in the F208Y mutant of R2 partitions between these two-electron (Y208 hydroxylation) and one-electron (Y122 radical production) outcomes and that the latter becomes predominant under conditions which favor electron injection (namely, high concentration of the reductant ascorbate). Moreover, we show that the sensitivity of the partition ratio to ascorbate concentration is strictly dependent on the integrity of a hydrogen-bond network involving the near surface residue W48: when this residue is substituted with F, Y208 hydroxylation predominates irrespective of ascorbate concentration. These data suggest that the hydrogen-bond network involving W48 is a specific electron-transfer pathway between the cofactor site and the protein surface.
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Affiliation(s)
- S E Parkin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16802, USA
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23
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Smith JJ, Thomson AJ, Proudfoot AE, Wells TN. Identification of an Fe(III)-dihydroxyphenylalanine site in recombinant phosphomannose isomerase from Candida albicans. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 244:325-33. [PMID: 9118997 DOI: 10.1111/j.1432-1033.1997.00325.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Candida albicans phosphomannose isomerase (PMI) is a zinc metalloprotein of known crystal structure. When heterologously overexpressed in Escherichia coli, a blue protein that contains up to 0.5 iron atoms/PMI molecule could be isolated, with absorption maxima at 420 nm and 680 nm. These bands are reminiscent of ferric catecholate complexes, an assignment that has been confirmed by resonance Raman spectroscopy, and by reaction with Arnow's reagent, which is specific for the presence of 3,4-dihydroxyphenylalanine (Dopa). After enzymatic digestion of blue PMI, a peptide with the sequence DPHAXISG was isolated corresponding to residues Asp283-Gly290 in the amino acid sequence of C. albicans PMI, where the unidentified residue X287 is encoded by a tyrosine codon. It is proposed that iron and oxygen bring about hydroxylation of Tyr287 in PMI and that Fe(III) subsequently chelates the Dopa residue to give the characteristic absorption spectrum. The EPR spectrum of the blue protein suggests three iron environments in the protein, two in axial environments with E/D values approximately equal to 0.06 and 0.12 and one rhombic species. The nature of the iron co-ordination sites is discussed with the help of model systems and by comparison with other blue non-heme iron proteins.
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Affiliation(s)
- J J Smith
- Centre for Metalloprotein Spectroscopy and Biology, School of Chemical Sciences, University of East Anglia, England
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24
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Mulliez E, Fontecave M. Structure and Reactivity of the Metal Centers of Ribonucleotide Reductases. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/cber.19971300303] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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25
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Ribonucleotide reductases — a group of enzymes with different metallosites and a similar reaction mechanism. METAL SITES IN PROTEINS AND MODELS 1997. [DOI: 10.1007/3-540-62870-3_5] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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26
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Taylor SW, Chase DB, Emptage MH, Nelson MJ, Waite JH. Ferric Ion Complexes of a DOPA-Containing Adhesive Protein from Mytilus edulis. Inorg Chem 1996. [DOI: 10.1021/ic960514s] [Citation(s) in RCA: 207] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Steven W. Taylor
- Department of Chemistry/Biochemistry and College of Marine Studies, University of Delaware, Newark, Delaware 19716, and Central Research & Development Department, E. I. du Pont de Nemours and Company, Inc., Wilmington, Delaware 19880-0328
| | - D. Bruce Chase
- Department of Chemistry/Biochemistry and College of Marine Studies, University of Delaware, Newark, Delaware 19716, and Central Research & Development Department, E. I. du Pont de Nemours and Company, Inc., Wilmington, Delaware 19880-0328
| | - Mark H. Emptage
- Department of Chemistry/Biochemistry and College of Marine Studies, University of Delaware, Newark, Delaware 19716, and Central Research & Development Department, E. I. du Pont de Nemours and Company, Inc., Wilmington, Delaware 19880-0328
| | - Mark J. Nelson
- Department of Chemistry/Biochemistry and College of Marine Studies, University of Delaware, Newark, Delaware 19716, and Central Research & Development Department, E. I. du Pont de Nemours and Company, Inc., Wilmington, Delaware 19880-0328
| | - J. Herbert Waite
- Department of Chemistry/Biochemistry and College of Marine Studies, University of Delaware, Newark, Delaware 19716, and Central Research & Development Department, E. I. du Pont de Nemours and Company, Inc., Wilmington, Delaware 19880-0328
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27
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Wallar BJ, Lipscomb JD. Dioxygen Activation by Enzymes Containing Binuclear Non-Heme Iron Clusters. Chem Rev 1996; 96:2625-2658. [PMID: 11848839 DOI: 10.1021/cr9500489] [Citation(s) in RCA: 977] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bradley J. Wallar
- Department of Biochemistry, Medical School, 4-225 Millard Hall, University of Minnesota, Minneapolis, Minnesota 55455
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28
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Lendzian F, Sahlin M, MacMillan F, Bittl R, Fiege R, Pötsch S, Sjöberg BM, Gräslund A, Lubitz W, Lassmann G. Electronic Structure of Neutral Tryptophan Radicals in Ribonucleotide Reductase Studied by EPR and ENDOR Spectroscopy. J Am Chem Soc 1996. [DOI: 10.1021/ja960917r] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Friedhelm Lendzian
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Margareta Sahlin
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Fraser MacMillan
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Robert Bittl
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Robert Fiege
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Stephan Pötsch
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Britt-Marie Sjöberg
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Astrid Gräslund
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Wolfgang Lubitz
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Günter Lassmann
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
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29
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Feig AL, Becker M, Schindler S, van Eldik R, Lippard SJ. Mechanistic Studies of the Formation and Decay of Diiron(III) Peroxo Complexes in the Reaction of Diiron(II) Precursors with Dioxygen. Inorg Chem 1996; 35:2590-2601. [PMID: 11666474 DOI: 10.1021/ic951242g] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mechanistic studies of the reactions of three analogous alkoxo-bridged diiron(II) complexes with O(2) have been carried out. The compounds, which differ primarily in the steric accessibility of dioxygen to the diiron(II) center, form metastable &mgr;-peroxo intermediates when studied at low temperature. At ambient temperatures, these intermediates decay to form (&mgr;-oxo)polyiron(III) products. The effect of ligand steric constraints on the O(2) reactivity was investigated. When access to the diiron center was unimpeded, the reaction was first-order with respect to both [Fe(II)(2)] and [O(2)] and the activation parameters for O(2) addition were similar to those for O(2) reacting with the dioxygen transport protein hemerythrin. When the binding site was occluded, however, reduced order with respect to [O(2)] was observed and a two-step mechanism was required to explain the kinetic results. Decay of all three peroxide intermediates involves a bimolecular event, implying the formation of tetranuclear species in the transition state.
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Affiliation(s)
- Andrew L. Feig
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Institute for Inorganic Chemistry, University of Erlangen-Nürnberg, Egerlandstrasse 1, 91058 Erlangen, Germany
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30
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Abstract
Di-iron centers bridged by carboxylate residues and oxide/hydroxide groups have so far been seen in four classes of proteins involved in dioxygen chemistry or phosphoryl transfer reactions. The dinuclear iron centers in these proteins are coordinated by histidines and additional carboxylate ligands. Recent structural data on some of these enzymes, combined with spectroscopic and kinetic data, can now serve as a base for detailed mechanistic suggestions. The di-iron sites in the major class of hydroxylase-oxidase enzymes, which contains ribonucleotide reductase and methane monooxygenase, show significant flexibility in the geometry of their coordination of three or more carboxylate groups. This flexibility, combined with a relatively low coordination number, and a buried environment suitable for reactive oxygen chemistry, explains their efficient harnessing of the oxidation power of molecular oxygen.
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Ormö M, Regnström K, Wang Z, Que L, Sahlin M, Sjöberg BM. Residues important for radical stability in ribonucleotide reductase from Escherichia coli. J Biol Chem 1995; 270:6570-6. [PMID: 7896794 DOI: 10.1074/jbc.270.12.6570] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The R2 protein of ribonucleotide reductase contains at the side chain of tyrosine 122 a stable free radical, which is essential for enzyme catalysis. The tyrosyl radical is buried in the protein matrix close to a dinuclear iron center and a cluster of three hydrophobic residues (Phe-208, Phe-212, and Ile-234) conserved throughout the R2 family. A key step in the generation of the tyrosyl radical is the activation of molecular oxygen at the iron center. It has been suggested that the hydrophobic cluster provides an inert binding pocket for molecular oxygen bound to the iron center and that it may play a role in directing the oxidative power of a highly reactive intermediate toward tyrosine 122. We have tested these hypotheses by constructing the following mutant R2 proteins:F208Y, F212Y, F212W, and I234N. The resulting mutant proteins all have the ability to form a tyrosine radical, which indicates that binding of molecular oxygen can occur. In the case of F208Y, the yield of tyrosyl radical is substantially lower than in the wild-type case. A competing reaction resulting in hydroxylation of Tyr-208 implies that the phenylalanine at position 208 may influence the choice of target for electron abstraction. The most prominent result is that all mutant proteins show impaired radical half-life; in three of the four mutants, the half-lives are several orders of magnitude shorter than that of the wild-type radical. This suggests that the major role of the hydrophobic pocket is to stabilize the tyrosyl radical. This hypothesis is corroborated by comparative studies of the environment of other naturally occurring tyrosyl radicals.
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Affiliation(s)
- M Ormö
- Department of Molecular Biology, Stockholm University, Sweden
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Affiliation(s)
- J H Waite
- Department of Chemistry/Biochemistry, University of Delaware, Newark 19716, USA
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34
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Sjöberg BM. Structure of Ribonucleotide Reductase from Escherichia coli. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 1995. [DOI: 10.1007/978-3-642-79488-9_10] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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35
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Matsuzaki R, Fukui T, Sato H, Ozaki Y, Tanizawa K. Generation of the topa quinone cofactor in bacterial monoamine oxidase by cupric ion-dependent autooxidation of a specific tyrosyl residue. FEBS Lett 1994; 351:360-4. [PMID: 8082796 DOI: 10.1016/0014-5793(94)00884-1] [Citation(s) in RCA: 155] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The quinone of 2,4,5-trihydroxyphenylalanine (topa), recently identified as the covalently bound redox cofactor in copper amine oxidases, is encoded by a specific tyrosine codon. To elucidate the mechanism of its formation, the recombinant phenylethylamine oxidase of Arthrobacter globiformis has been overproduced in Escherichia coli and purified in a Cu(2+)-deficient form. The inactive precursor enzyme thus obtained was dramatically activated upon incubation with Cu2+, concomitantly with the formation of the topa quinone at the position corresponding to Tyr382, occurring in the tetrapeptide sequence highly conserved in this class of enzymes. The topa quinone was produced only under aerobic conditions, but its formation required no external enzymatic systems. These findings demonstrate the Cu(2+)-dependent autooxidation of a specific tyrosyl residue to generate the topa quinone cofactor.
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Affiliation(s)
- R Matsuzaki
- Institute of Scientific and Industrial Research, Osaka University, Japan
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36
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Cai D, Klinman JP. Copper amine oxidase: heterologous expression, purification, and characterization of an active enzyme in Saccharomyces cerevisiae. Biochemistry 1994; 33:7647-53. [PMID: 8011631 DOI: 10.1021/bi00190a019] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A copper amine oxidase gene from a methylotrophic yeast Hansenula polymorpha has been expressed in Saccharomyces cerevisiae under the control of the ADHI promoter and the recombinant protein purified to near homogeneity. The recombinant enzyme is as active as the native enzyme in catalyzing methylamine oxidation. We demonstrate that it is a quinoprotein by redox-cycling staining and titrations with carbonyl reagents. The absorption spectral properties of the recombinant amine oxidase and its phenylhydrazine derivative are very similar to those of other copper amine oxidases. The cofactor in the enzyme is 2,4,5-trihydroxyphenylalanine (topa) quinone, as demonstrated by the pH-dependent shift in the lambda max of the p-nitrophenylhydrazone adduct. Alignment of an active-site peptide and DNA-derived protein sequences reveals a tyrosine residue as the precursor to topa quinone, consistent with findings with other copper amine oxidases. All evidence presented herein indicates that the heterologously expressed copper amine oxidase protein is processed posttranslationally in S. cerevisiae to form an active enzyme with an intact cofactor. This occurs despite an inability of S. cerevisiae to utilize amines as a nitrogen source. The implications of this study for the mechanism of topa quinone biogenesis are discussed.
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Affiliation(s)
- D Cai
- Department of Chemistry, University of California, Berkeley 94720
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Tryptophan radicals formed by iron/oxygen reaction with Escherichia coli ribonucleotide reductase protein R2 mutant Y122F. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)32628-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Ling J, Sahlin M, Sjöberg B, Loehr T, Sanders-Loehr J. Dioxygen is the source of the mu-oxo bridge in iron ribonucleotide reductase. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37503-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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