Mechanism of Substrate Reduction by Nitrogenase

Nitrogen (N) is a chemical constituent for almost all biological molecules including proteins, DNA, RNA, lipids and is therefore vital for life. The ultimate source of nitrogen is the atmospheric dinitrogen (N2) but that only becomes bioavailable through a process of nitrogen fixation, the process that converts N2 to ammonia (NH3). The industrial Haber-Bosch process and biological nitrogen fixation account for the majority of nitrogen fixed every year. However, due to its high temperature, pressure and fossil fuel requirements, Haber-Bosch is an expensive process. Every year, approximately 3% of the global energy demand is used to manufacture ammonia through Haber-Bosch process. On the other hand, biological systems produce ammonia by reducing dinitrogen at ambient temperature and pressure using an anaerobic enzyme called nitrogenase. Research in understanding the mechanism of nitrogenase could eventually allow researchers to mimic the enzyme and fix nitrogen efficiently at standard temperature and pressure. In this research nitrogenase of Azotobacter vinelandii was studied to understand the mechanism of delivery of electrons/protons to the active site and how these accumulated reducing equivalents are used for substrates reduction. Through a series of studies, it has been demonstrated that the electrons and protons are added to the active site in a concerted manner which are then stored as bridging hydrides. The accumulated hydrides are used in four different mechanisms, namely reductive elimination, hydride protonolysis, migratory insertion and proton coupled electron transfer, to catalyze the reduction of varieties of unsaturated molecules. This fundamental understanding of molecular detail of nitrogenase catalysis could eventually help in development of more efficient, robust and selective catalysts

Nitrogenase bioelectrocatalysis: heterogeneous ammonia and hydrogen production by MoFe protein

notrogenase is the only enzyme known to catalyze the reduction of N2 to 2NH3. In vivo, the MoFe protein component of nitrogenase is exclusively reduced by the ATP-hydrolyzing Fe protein in a series of transient association/dissociation steps that are linked to the hyderolysis of two ATP for each electron transeferred. We report MoFe protein immobilized at an electrode surface, where cobaltocene (as an electron mediator that can be observed in real time at a carbon electrode) is used to reduce the MoFe protein (independent of the Fe protein and of ATP hydrolysis) and support the bioelectrocatalytic reduction of protons to dihydrogen, azide to ammonia, and nitrit to ammonia. Bulk bioelectrosynthetic N3 or NO2 reduction (50 mM) for 30 minutes yielded 70 +- 9 nmol NH3 and 234 +- 62 nmol NH3, with NO2 reduction operating at high faradaic efficiency

The Structural and Biochemical Basis of Apocarotenoid Processing by β-Carotene Oxygenase-2.

In mammals, carotenoids are converted by two carotenoid cleavage oxygenases into apocarotenoids, including vitamin A. Although knowledge about β-carotene oxygenase-1 (BCO1) and vitamin A metabolism has tremendously increased, the function of β-carotene oxygenase-2 (BCO2) remains less well-defined. We here studied the role of BCO2 in the metabolism of long chain β-apocarotenoids, which recently emerged as putative regulatory molecules in mammalian biology. We showed that recombinant murine BCO2 converted the alcohol, aldehyde, and carboxylic acid of a β-apocarotenoid substrate by oxidative cleavage at position C9,C10 into a β-ionone and a diapocarotenoid product. Chain length variation (C20 to C40) and ionone ring site modifications of the apocarotenoid substrate did not impede catalytic activity or alter the regioselectivity of the double bond cleavage by BCO2. Isotope labeling experiments revealed that the double bond cleavage of an apocarotenoid followed a dioxygenase reaction mechanism. Structural modeling and site directed mutagenesis identified amino acid residues in the substrate tunnel of BCO2 that are critical for apocarotenoid binding and catalytic processing. Mice deficient for BCO2 accumulated apocarotenoids in their livers, indicating that the enzyme engages in apocarotenoid metabolism. Together, our study provides novel structural and functional insights into BCO2 catalysis and establishes the enzyme as a key component of apocarotenoid homeostasis in mice

Evidence for distinct rate-limiting steps in the cleavage of alkenes by carotenoid cleavage dioxygenases

Carotenoid cleavage dioxygenases (CCDs) use a nonheme Fe(II) cofactor to split alkene bonds of carotenoid and stilbenoid substrates. The iron centers of CCDs are typically five-coordinate in their resting states, with solvent occupying an exchangeable site. The involvement of this iron-bound solvent in CCD catalysis has not been experimentally addressed, but computational studies suggest two possible roles. 1) Solvent dissociation provides a coordination site for O2, or 2) solvent remains bound to iron but changes its equilibrium position to allow O2 binding and potentially acts as a proton source. To test these predictions, we investigated isotope effects (H2O versus D2O) on two stilbenoid-cleaving CCDs, Novosphingobium aromaticivorans oxygenase 2 (NOV2) and Neurospora crassa carotenoid oxygenase 1 (CAO1), using piceatannol as a substrate. NOV2 exhibited an inverse isotope effect (k H/k D ∼ 0.6) in an air-saturated buffer, suggesting that solvent dissociates from iron during the catalytic cycle. By contrast, CAO1 displayed a normal isotope effect (k H/k D ∼ 1.7), suggesting proton transfer in the rate-limiting step. X-ray absorption spectroscopy on NOV2 and CAO1 indicated that the protonation states of the iron ligands are unchanged within pH 6.5-8.5 and that the Fe(II)-aquo bond is minimally altered by substrate binding. We pinpointed the origin of the differential kinetic behaviors of NOV2 and CAO1 to a single amino acid difference near the solvent-binding site of iron, and X-ray crystallography revealed that the substitution alters binding of diffusible ligands to the iron center. We conclude that solvent-iron dissociation and proton transfer are both associated with the CCD catalytic mechanism

Reductive Elimination of H2 Activates Nitrogenase to Reduce the N≡N Triple Bond: Characterization of the E4(4H) Janus Intermediate in Wild-Type Enzyme

We proposed a reductive elimination/oxidative addition (re/oa) mechanism for reduction of N2 to 2NH3 by nitrogenase, based on identification of a freeze-trapped intermediate of the α-70Val→IleMoFe protein as the Janus intermediate that stores four reducing equivalents on FeMo-co as two [Fe–H–Fe] bridging hydrides (denoted E4(4H)). The mechanism postulates that obligatory re of the hydrides as H2 drives reduction of N2 to a state (denoted E4(2N2H)) with a moiety at the diazene (HN═NH) reduction level bound to the catalytic FeMo-co. EPR/ENDOR/photophysical measurements on wild type (WT) MoFe protein now establish this mechanism. They show that a state freeze-trapped during N2 reduction by WT MoFe is the same Janus intermediate, thereby establishing the α-70Val→Ile intermediate as a reliable guide to mechanism. Monitoring the Janus state in WT MoFe during N2 reduction under mixed-isotope condition, H2O buffer/D2, and the converse, establishes that the bridging hydrides/deuterides do not exchange with solvent during enzymatic turnover, thereby solving longstanding puzzles. Relaxation of E4(2N2H) to the WT resting-state is shown to occur via oa of H2 and release of N2 to form Janus, followed by sequential release of two H2, demonstrating the kinetic reversibility of the re/oa equilibrium. Relative populations of E4(2N2H)/E4(4H) freeze-trapped during WT turnover furthermore show that the reversible re/oa equilibrium between [E4(4H) + N2] and [E4(2N2H) + H2] is ∼ thermoneutral (ΔreG0 ∼ −2 kcal/mol), whereas, by itself, hydrogenation of N2(g) is highly endergonic. These findings demonstrate that (i) re/oa accounts for the historical Key Constraintson mechanism, (ii) that Janus is central to N2 reduction by WT enzyme, which (iii) indeed occurs via the re/oa mechanism. Thus, emerges a picture of the central mechanistic steps by which nitrogenase carries out one of the most challenging chemical transformations in biology

Hydride Conformers of the Nitrogenase Femo-Cofactor Two-Electron Reduced State E\u3csub\u3e2\u3c/sub\u3e(2H), Assigned Using Cryogenic Intra Electron Paramagnetic Resonance Cavity Photolysis

Early studies in which nitrogenase was freeze-trapped during enzymatic turnover revealed the presence of high-spin (S = 3/2) electron paramagnetic resonance (EPR) signals from the active-site FeMo-cofactor (FeMo-co) in electron-reduced intermediates of the MoFe protein. Historically denoted as 1b and 1c, each of the signals is describable as a fictitious spin system, S′ = 1/2, with anisotropic g′ tensor, 1b with g′ = [4.21, 3.76, ?] and 1c with g′ = [4.69, ∼3.20, ?]. A clear discrepancy between the magnetic properties of 1b and 1c and the kinetic analysis of their appearance during pre-steady-state turnover left their identities in doubt, however. We subsequently associated 1b with the state having accumulated 2[e-/H+], denoted as E2(2H), and suggested that the reducing equivalents are stored on the catalytic FeMo-co cluster as an iron hydride, likely an [Fe-H-Fe] hydride bridge. Intra-EPR cavity photolysis (450 nm; temperature-independent from 4 to 12 K) of the E2(2H)/1b state now corroborates the identification of this state as storing two reducing equivalents as a hydride. Photolysis converts E2(2H)/1b to a state with the same EPR spectrum, and thus the same cofactor structure as pre-steady-state turnover 1c, but with a different active-site environment. Upon annealing of the photogenerated state at temperature T = 145 K, it relaxes back to E2(2H)/1b. This implies that the 1c signal comes from an E2(2H) hydride isomer of E2(2H)/1b that stores its two reducing equivalents either as a hydride bridge between a different pair of iron atoms or an Fe-H terminal hydride

The human mitochondrial enzyme BCO2 exhibits catalytic activity toward carotenoids and apocarotenoids.

The enzyme β-carotene oxygenase 2 (BCO2) converts carotenoids into more polar metabolites. Studies in mammals, fish, and birds revealed that BCO2 controls carotenoid homeostasis and is involved in the pathway for vitamin A production. However, it is controversial whether BCO2 function is conserved in humans, because of a 4-amino acid long insertion caused by a splice acceptor site polymorphism. We here show that human BCO2 splice variants, BCO2a and BCO2b, are expressed as pre-proteins with mitochondrial targeting sequence (MTS). The MTS of BCO2a directed a green fluorescent reporter protein to the mitochondria when expressed in ARPE-19 cells. Removal of the MTS increased solubility of BCO2a when expressed in Escherichia coli and rendered the recombinant protein enzymatically active. The expression of the enzymatically active recombinant human BCO2a was further improved by codon optimization and its fusion with maltose-binding protein. Introduction of the 4-amino acid insertion into mouse Bco2 did not impede the chimeric enzymes catalytic proficiency. We further showed that the chimeric BCO2 displayed broad substrate specificity and converted carotenoids into two ionones and a central C14-apocarotendial by oxidative cleavage reactions at C9,C10 and C9,C10. Thus, our study demonstrates that human BCO2 is a catalytically competent enzyme. Consequently, information on BCO2 becomes broadly applicable in human biology with important implications for the physiology of the eyes and other tissues

Nitrogenase bioelectrocatalysis: heterogeneous ammonia and hydrogen production by mofe protein

Nitrogenase is the only enzyme known to catalyze the reduction of N-2 to 2NH(3). In vivo, the MoFe protein component of nitrogenase is exclusively reduced by the ATP-hydrolyzing Fe protein in a series of transient association/dissociation steps that are linked to the hydrolysis of two ATP for each electron transferred. We report MoFe protein immobilized at an electrode surface, where cobaltocene (as an electron mediator that can be observed in real time at a carbon electrode) is used to reduce the MoFe protein (independent of the Fe protein and of ATP hydrolysis) and support the bioelectrocatalytic reduction of protons to dihydrogen, azide to ammonia, and nitrite to ammonia. Bulk bioelectrosynthetic N-3 or NO2 reduction (50 mM) for 30 minutes yielded 70 +/- 9 nmol NH3 and 234 +/- 62 nmol NH3, with NO2- reduction operating at high faradaic efficiency

Insights into the pathogenesis of dominant retinitis pigmentosa associated with a D477G mutation in RPE65.

RPE65 is the essential trans-cis isomerase of the classical retinoid (visual) cycle. Mutations in RPE65 give rise to severe retinal dystrophies, most of which are associated with loss of protein function and recessive inheritance. The only known exception is a c.1430G>A (D477G) mutation that gives rise to dominant retinitis pigmentosa with delayed onset and choroidal and macular involvement. Position 477 is distant from functionally critical regions of RPE65. Hence, the mechanism of D477G pathogenicity remains unclear, although protein misfolding and aggregation mechanisms have been suggested. We characterized a D477G knock-in mouse model which exhibited mild age-dependent changes in retinal structure and function. Immunoblot analysis of protein extracts from the eyes of these knock-in mice demonstrated the presence of ubiquitinated RPE65 and reduced RPE65 expression. We observed an accumulation of retinyl esters in the knock-in mice as well as a delay in rhodopsin regeneration kinetics and diminished electroretinography responses, indicative of RPE65 functional impairment induced by the D477G mutation in vivo. However, a cell line expressing D477G RPE65 revealed protein expression levels, cellular localization and retinoid isomerase activity comparable to cells expressing wild-type protein. Structural analysis of an RPE65 chimera suggested that the D477G mutation does not perturb protein folding or tertiary structure. Instead, the mutation generates an aggregation-prone surface that could induce cellular toxicity through abnormal complex formation as suggested by crystal packing analysis. These results indicate that a toxic gain-of-function induced by the D477G RPE65 substitution may play a role in the pathogenesis of this form of dominant retinitis pigmentosa