Cytochrome P450 enzymes activate oxygen at heme iron centers to oxidize relatively inert substrate carbon-hydrogen bonds. Cysteine thiolate coordination to iron is posited to increase the pKa of compound II, an iron(IV)hydroxide complex, correspondingly lowering the one-electron reduction potential of compound I, the active catalytic intermediate, and decreasing the driving force for deleterious autooxidation of tyrosine and tryptophan residues in the enzyme’s framework. Here we report the preparation of an iron(IV)hydroxide complex in a P450 enzyme (CYP158) in ≥ 90% yield. Using rapid mixing technologies in conjunction with Mössbauer, ultraviolet/visible, and X-ray absorption spectroscopies, we determine a pKa value for this compound of 11.9. Marcus theory analysis indicates that this elevated pKa results in a >10,000 fold reduction in the rate constant for oxidations of the protein framework, making these processes noncompetitive with substrate oxidation.
Recently, we reported the spectroscopic and kinetic characterizations of cytochrome P450 compound I in CYP119A1, effectively closing the catalytic cycle of cytochrome P450-mediated hydroxylations. In this minireview, we focus on the developments that made this breakthrough possible. We examine the importance of enzyme purification in the quest for reactive intermediates and report the preparation of compound I in a second P450 (P450 ST ). In an effort to bring clarity to the field, we also examine the validity of controversial reports claiming the production of P450 compound I through the use of peroxynitrite and laser flash photolysis.A significant amount of research in the field of bioinorganic chemistry is focused on discerning the intimate details of enzyme catalysis. Critical to these efforts is the preparation of reactive intermediates that form the stations of the catalytic cycle of an enzyme. The study of these transient species is driven by the hope that insights gleaned from their electronic, structural, and kinetic characterizations will guide the design of next-generation catalysts or point the way to inhibitors that could serve as drugs for a variety of maladies. Although a thorough characterization of all the intermediates in a catalytic cycle is required for a detailed dissection of the catalytic mechanism, there are certain species that have special significance and, as such, are considered high-value targets for characterization. These species are generally the highly reactive intermediates that are ultimately responsible for the most important, difficult, or chemically interesting transformation in the catalytic mechanism.Recently, we reported the capture and characterization of one of the most highly sought intermediates in biological chemistry, P450 compound I (P450-I) 4 (1). This iron(IV)-oxo (or ferryl) radical species (7 in Fig. 1) had long been thought to be the principal intermediate in cytochrome P450 catalysis, but due to its highly reactive nature, it had eluded definitive characterization for over 40 years. The existence of P450-I was postulated based on the observation of a "shunt pathway" (Fig. 1) allowing the oxidation of substrates through the use of oxygen donors such as hydrogen peroxide and meta-chloroperbenzoic acid. These oxidants were known to generate high-valent iron-oxo species in heme peroxidases (2, 3), suggesting that a similar intermediate might be involved in P450 catalysis. However, 4 decades worth of searching for the elusive P450-I had led to questions about not only its competence as a hydroxylating agent but also its role in P450 catalysis (4 -6).Our investigations confirmed the existence and the reactive nature of the intermediate. P450-I is capable of hydroxylating unactivated C-H bonds with the remarkable rate constant of 1 ϫ 10 7 M Ϫ1 s Ϫ1 (1). Kinetic isotope effects support a mechanism in which P450-I abstracts hydrogen from substrate, forming an iron(IV)-hydroxide complex that rapidly recombines with substrate to yield hydroxylated product (7-9 in Fig. 1...
Cytochrome P450 (P450) and chloroperoxidase (CPO) are thiolate ligated heme proteins that catalyze the activation of carbon hydrogen bonds. The principal intermediate in these reactions is a ferryl radical species called compound I. P450 compound I (P450-I) is significantly more reactive than CPO-I, which only cleaves activated C-H bonds. To provide insight into the differing reactivities of these intermediates, we examined CPO-I and P450-I with variable temperature Mössbauer and X-ray absorption spectroscopies. These measurements indicate that the Fe-S bond is significantly shorter in P450-I than in CPO-I. This difference in Fe-S bond lengths can be understood in terms of variations in hydrogen bonding patterns within the “cys-pocket” (a portion of the proximal helix that encircles the thiolate ligand). Weaker hydrogen bonding in P450-I results in a shorter Fe-S bond, which enables greater electron donation from the axial-thiolate ligand. This observation may in part explain P450's greater propensity for C-H bond activation.
To provide insight into the iron(IV)hydroxide pKa of histidine ligated heme proteins, we have probed the active site of myoglobin compound II over the pH range of 3.9–9.5, using EXAFS, Mössbauer, and resonance Raman spectroscopies. We find no indication of ferryl protonation over this pH range, allowing us to set an upper limit of 2.7 on the iron(IV)hydroxide pKa in myoglobin. Together with the recent determination of an iron(IV)hydroxide pKa ∼ 12 in the thiolate-ligated heme enzyme cytochrome P450, this result provides insight into Nature’s ability to tune catalytic function through its choice of axial ligand.
Strong electron-donation from the axial thiolate ligand of cytochrome P450 has been proposed to increase the reactivity of compound I with respect to C-H bond activation. However, it has proven difficult to test this hypothesis, and a direct link between reactivity and electron donation has yet to be established. To make this connection, we have prepared a selenolate-ligated cytochrome P450 compound I intermediate. This isoelectronic perturbation allows for direct comparisons with the wild-type enzyme. Selenium incorporation was achieved using a cysteine auxotrophic Escherichia coli strain. The intermediate was prepared with meta-chloroperbenzoic acid and characterized by UV-visible, Mössbauer and electron paramagnetic resonance spectroscopies. Measurements revealed increased asymmetry around the ferryl moiety, consistent with increased electron donation from the axial selenolate ligand. In line with this observation, we find that the selenolate-ligated compound I cleaves C-H bonds more rapidly than the wild-type intermediate.
High valent Fe–OH species are often invoked as key intermediates but have only been observed in Compound II of cytochrome P450s. To further address the properties of non-heme FeIV–OH complexes we demonstrate the reversible protonation of a synthetic FeIV–oxo species containing a tris-urea tripodal ligand. The same protonated FeIV–oxo species can be prepared via oxidation, suggesting a putative FeV–oxo species was initially generated. Computational, Mössbauer, XAS, and NRVS studies indicate that protonation of the FeIV–oxo complex most likely occur on the tripodal ligand, which undergoes a structural change that results in the formation of a new intramolecular hydrogen bond with the oxido ligand that aids in stabilizing the protonated adduct. We suggest that similar species for protonated high valent Fe–oxo species may occur in the active sites of proteins. This finding further argues for caution when assigning unverified high valent Fe–OH species to mechanisms.
Here, we report on the development of a genetic system for Marinobacter sp. strain CP1, previously isolated from the Biocathode MCL community and shown to oxidize iron and grow as a cathodic biofilm. Sequence analysis of the small and large subunits of the 16S rRNA gene of CP1, as well as comparison of select conserved proteins, indicate that it is most closely related to Marinobacter adhaerens HP15 and Marinobacter sp. ES.042. In silico DNA–DNA hybridization using the genome-to-genome distance calculator (GGDC) predicts CP1 to be a new species of Marinobacter described here as Marinobacter atlanticus. CP1 is competent for transformation with plasmid DNA using conjugation with Escherichia coli donor strain WM3064 and constitutive expression of green fluorescent protein (GFP) is stable in the absence of antibiotic selection. Targeted double deletion mutagenesis of homologs for the M. aquaeoli fatty acyl-CoA reductase (acrB) and fatty aldehyde reductase (farA) genes resulted in a loss of production of wax esters; however, single deletion mutants for either gene resulted in an increase in total wax esters recovered. Genetic tools presented here for CP1 will enable further exploration of wax ester synthesis for biotechnological applications, as well as furthering our efforts to understand the role of CP1 within the Biocathode MCL community.
The marine heterotroph, Marinobacter atlanticus strain CP1, was recently isolated from the electroautotrophic Biocathode MCL community, named for the three most abundant members: Marinobacter, an uncharacterized member of the Chromatiaceae, and Labrenzia. Biocathode MCL catalyzes the production of cathodic current coupled to carbon fixation through the activity of the uncharacterized Chromatiaceae, renamed as "Candidatus Tenderia electrophaga," but the contribution of M. atlanticus is currently unknown. Here, we report on the electrochemical characterization of pure culture M. atlanticus biofilms grown under aerobic conditions and supplemented with succinate as a carbon source at applied potentials ranging from 160 to 510 mV vs. SHE, and on three different electrode materials (graphite, carbon cloth, and indium tin oxide). M. atlanticus was found to produce either cathodic or anodic current that was an order of magnitude lower than that of the Biocathode MCL community depending on the oxygen concentration, applied potential, and electrode material. Cyclic voltammetry, differential pulse voltammetry (DPV), and square wave voltammetry (SWV) were performed to characterize putative redox mediators at the electrode surface; however no definitive redox peaks were observed. No effect on current was observed when genes encoding a putative rubredoxin (ACP86_RS07295), as well as a putative NADH:flavorubredoxin oxidoreductase (ACP86_RS07290), were deleted to evaluate their role in EET. The addition of either riboflavin or excess trace mineral solution increased anodic current by ca. an order of magnitude under the conditions in which Biocathode MCL is typically grown. These results indicate that M. atlanticus has a non-negligible ability to utilize electrodes as an electron acceptor, which can be enhanced by the presence of excess trace minerals already available in the growth medium. The ability of M. atlanticus to utilize trace minerals as electron shuttles with extracellular electron acceptors may have broader implications for its natural role in biogeochemical cycling.
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