Acetyl-coenzyme A synthase: the case for a Nip0-based mechanism of catalysis

Small Molecule Activation at the acriPNP Pincer-Supported Nickel Sites

ConspectusNickel pincer systems have recently attracted much attention for applications in various organometallic reactions and catalysis involving small molecule activation. Their exploration is in part motivated by the presence of nickel in natural systems for efficient catalysis. Among such systems, the nickel-containing metalloenzyme carbon monoxide dehydrogenase (CODH) efficiently and reversibly converts CO2 to CO at its active site. The generated CO moves through a channel from the CODH active site and is transported to a dinuclear nickel site of acetyl-coenzyme A synthase (ACS), which catalyzes organometallic C-S and C-C bond forming reactions. An analogous C-S bond activation process is also mediated by the nickel containing enzyme methyl-coenzyme M reductase (MCR). The nickel centers in these systems feature sulfur- and nitrogen-rich environments, and in the particular case of lactate racemase, an organometallic nickel pincer motif revealing a Ni-C bond is observed. These bioinorganic systems inspired the development of several nickel pincer scaffolds not only to mimic enzyme active sites and their reactivity but also to further extend low-valent organonickel chemistry. In this Account, we detail our continuing efforts in the chemistry of nickel complexes supported by acridane-based PNP pincer ligands focusing on our long-standing interest in biomimetic small molecule activation. We have employed a series of diphosphinoamide pincer ligands to prepare various nickel(II/I/0) complexes and to study the conversion of C1 chemicals such as CO and CO2 to value-added products. In the transformation of C1 chemicals, the key C-O bond cleavage and C-E bond (E = C, N, O, or S, etc.) formation steps typically require overcoming high activation barriers. Interestingly, enzymatic systems overcome such difficulties for C1 conversion and operate efficiently under ambient conditions with the use of nickel organometallic chemistry. Furthermore, we have extended our efforts to the conversion of NOx anions to NO via the sequential deoxygenation by nickel mediated carbonylation, which was applied to catalytic C-N coupling to produce industrially important organonitrogen compound oximes as a strategy for NOx conversion and utilization (NCU). Notably, the rigidified acriPNP pincer backbone that enforces a planar geometry at nickel was found to be an important factor for diversifying organometallic transformations including (a) homolysis of various σ-bonds mediated by T-shaped nickel(I) metalloradical species, (b) C-H bond activation mediated by a nickel(0) dinitrogen species, (c) selective CO2 reactivity of nickel(0)-CO species, (d) C-C bond formation at low-valent nickel(I or 0)-CO sites with iodoalkanes, and (e) catalytic deoxygenation of NOx anions and subsequent C-N coupling of a nickel-NO species with alkyl halides for oxime production. Broadly, our results highlight the importance of molecular design and the rich chemistry of organonickel species for diverse small molecule transformations.

An alcove at the acetyl-CoA synthase nickel active site is required for productive substrate CO binding and anaerobic carbon fixation

One of the seven natural CO2 fixation pathways, the anaerobic Wood-Ljungdahl pathway (WLP) is unique in generating CO as a metabolic intermediate, operating through organometallic intermediates, and in conserving (versus utilizing) net ATP. The key enzyme in the WLP is acetyl-CoA synthase (ACS), which uses an active site [2Ni-4Fe-4S] cluster (A-cluster), a CO tunnel, and an organometallic (Ni-CO, Ni-methyl, and Ni-acetyl) reaction sequence to generate acetyl-CoA. Here, we reveal that an alcove, which interfaces the tunnel and the A-cluster, is essential for CO2 fixation and autotrophic growth by the WLP. In vitro spectroscopy, kinetics, binding, and in vivo growth experiments reveal that a Phe229A substitution at one wall of the alcove decreases CO affinity thirty-fold and abolishes autotrophic growth; however, a F229W substitution enhances CO binding 80-fold. Our results indicate that the structure of the alcove is exquisitely tuned to concentrate CO near the A-cluster; protect ACS from CO loss during catalysis, provide a haven for inhibitory CO, and stabilize the tetrahedral coordination at the Nip site where CO binds. The directing, concentrating, and protective effects of the alcove explain the inability of F209A to grow autotrophically. The alcove also could help explain current controversies over whether ACS binds CO and methyl through a random or ordered mechanism. Our work redefines what we historically refer to as the metallocenter "active site". The alcove is so crucial for enzymatic function that we propose it is part of the active site. The community should now look for such alcoves in all "gas handling" metalloenzymes.

Mixed Valence {Ni2+Ni1+} Clusters as Models of Acetyl Coenzyme A Synthase Intermediates

Acetyl coenzyme A synthase (ACS) catalyzes the formation and deconstruction of the key biological metabolite, acetyl coenzyme A (acetyl-CoA). The active site of ACS features a {NiNi} cluster bridged to a [Fe4S4]n+ cubane known as the A-cluster. The mechanism by which the A-cluster functions is debated, with few model complexes able to replicate the oxidation states, coordination features, or reactivity proposed in the catalytic cycle. In this work, we isolate the first bimetallic models of two hypothesized intermediates on the paramagnetic pathway of the ACS function. The heteroligated {Ni2+Ni1+} cluster, [K(12-crown-4)2][1], effectively replicates the coordination number and oxidation state of the proposed "Ared" state of the A-cluster. Addition of carbon monoxide to [1]- allows for isolation of a dinuclear {Ni2+Ni1+(CO)} complex, [K(12-crown-2)n][2] (n = 1-2), which bears similarity to the "ANiFeC" enzyme intermediate. Structural and electronic properties of each cluster are elucidated by X-ray diffraction, nuclear magnetic resonance, cyclic voltammetry, and UV/vis and electron paramagnetic resonance spectroscopies, which are supplemented by density functional theory (DFT) calculations. Calculations indicate that the pseudo-T-shaped geometry of the three-coordinate nickel in [1]- is more stable than the Y-conformation by 22 kcal mol-1, and that binding of CO to Ni1+ is barrierless and exergonic by 6 kcal mol-1. UV/vis absorption spectroscopy on [2]- in conjunction with time-dependent DFT calculations indicates that the square-planar nickel site is involved in electron transfer to the CO π*-orbital. Further, we demonstrate that [2]- promotes thioester synthesis in a reaction analogous to the production of acetyl coenzyme A by ACS.

Mechanism of Methyl Transfer Reaction between CH3Co(dmgBF2)2py and PPh3Ni(Triphos)

DFT calculations were performed for the methyl group transfer reaction between CH3Co (dmgBF2)py and PPh3Ni(Triphos). The reaction mechanism and its energetics were investigated. This reaction is relevant to the catalytic mechanism of the enzyme acetyl coenzyme A synthase. BP86 and PBE functionals and dispersion corrections were used. It was found that intermolecular interactions are very important for this reaction. The influence of the solvent on the reaction was studied.

Reactivity of low-valent nickel carbonyl species supported by acridane based PNP ligands towards iodoalkanes

Nickel monocarbonyl species with Ni(I) and Ni(0) have been synthesized and fully characterized by employing an acriPNP-Ph pincer ligand having a -C(Ph)2- bridge moiety to tether two aromatic rings. To see the effect of the bridge moiety, these complexes were structurally compared with the previously studied nickel complexes supported by PNP and acriPNP-Me ligands and methylation of the nickel carbonyl species was particularly investigated. Since a Ni(I)-CO species is known to be one of the key intermediates during the C-C coupling reaction to give an acetyl species, according to the paramagnetic mechanism of acetyl coenzyme A synthase (ACS), their reactivity toward MeI has been examined. Methylation of a nickel(I)-CO species reveals enhanced C-C coupling when both acriPNP-Me and acriPNP-Ph ligands were used. According to spin density analysis calculated by density functional theory, all Ni(I)-CO species reveal similar spin density at nickel and the carbon atom of CO. X-ray crystallographic data suggest that the corresponding selectivity may be related to the steric influence. For both (acriPNP-Ph)Ni-CO (2) and (acriPNP-Me)Ni-CO (2'), the nickel(I) site is sterically well protected, leading to selective interaction with a methyl radical to give a nickel acyl product. Steric influence was marginally observed when an anionic {(acriPNP-R)Ni-CO}- (R = Me or Ph) species reacted with MeI. The corresponding C-C coupled product was also observed from the methylation of nickel(0)-CO species.

Characterization of Methyl- and Acetyl-Ni Intermediates in Acetyl CoA Synthase Formed during Anaerobic CO2 and CO Fixation

The Wood-Ljungdahl Pathway is a unique biological mechanism of carbon dioxide and carbon monoxide fixation proposed to operate through nickel-based organometallic intermediates. The most unusual steps in this metabolic cycle involve a complex of two distinct nickel-iron-sulfur proteins: CO dehydrogenase and acetyl-CoA synthase (CODH/ACS). Here, we describe the nickel-methyl and nickel-acetyl intermediates in ACS completing the characterization of all its proposed organometallic intermediates. A single nickel site (Nip) within the A cluster of ACS undergoes major geometric and redox changes as it transits the planar Nip, tetrahedral Nip-CO and planar Nip-Me and Nip-Ac intermediates. We propose that the Nip intermediates equilibrate among different redox states, driven by an electrochemical-chemical (EC) coupling process, and that geometric changes in the A-cluster linked to large protein conformational changes control entry of CO and the methyl group.

The two-electron reduced A cluster in acetyl-CoA synthase: Preparation, characteristics and mechanistic implications

Acetyl-CoA synthase (ACS) is a central enzyme in the carbon and energy metabolism of certain anaerobic species of bacteria and archaea that catalyzes the direct synthesis and cleavage of the acetyl CC bond of acetyl-CoA by an unusual enzymatic mechanism of special interest for its use of organonickel intermediates. An Fe₄S₄ cluster associated with a proximal, reactive Ni_p and distal spectator Ni_d comprise the active site metal complex, known as the A cluster. Experimental and theoretical methods have uncovered much about the ACS mechanism, but have also opened new unanswered questions about the structure and reactivity of the A cluster in various intermediate forms. Here we report a method for large scale isolation of ACS with its A cluster in the acetylated state. Isolated acetyl-ACS and the two-electron reduced ACS, produced by acetyl-ACS reaction with CoA, were characterized by UV-visible and EPR spectroscopy. Reactivity with electron acceptors provided an assessment of the apparent E_m for two-electron reduction of the A cluster. The results help to distinguish between alternative electronic states of the reduced cluster, provide evidence for a role of the Fe/S cluster in catalysis, and offer an explanation of why one-electron reductive activation is observed for a reaction cycle involving 2-electron chemistry.

Structural Insights into Microbial One-Carbon Metabolic Enzymes Ni-Fe-S-Dependent Carbon Monoxide Dehydrogenases and Acetyl-CoA Synthases

Ni-Fe-S-dependent carbon monoxide dehydrogenases (CODHs) are enzymes that interconvert CO and CO₂ by using their catalytic Ni-Fe-S C-cluster and their Fe-S B- and D-clusters for electron transfer. CODHs are important in the microbiota of animals such as humans, ruminants, and termites because they can facilitate the use of CO and CO₂ as carbon sources and serve to maintain redox homeostasis. The bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is responsible for acetate production via the Wood-Ljungdahl pathway, where acetyl-CoA is assembled from two CO₂-derived one-carbon units. A Ni-Fe-S A-cluster is key to this chemistry. Whereas acetogens use the A- and C-clusters of CODH/ACS to produce acetate from CO₂, methanogens use A- and C-clusters of an acetyl-CoA decarbonylase/synthase complex (ACDS) to break down acetate en route to CO₂ and methane production. Here we review some of the recent advances in understanding the structure and mechanism of CODHs, CODH/ACSs, and ACDSs, their unusual metallocofactors, and their unique metabolic roles in the human gut and elsewhere.

Thioester synthesis by a designed nickel enzyme models prebiotic energy conversion

The formation of carbon-carbon bonds from prebiotic precursors such as carbon dioxide represents the foundation of all primordial life processes. In extant organisms, this reaction is carried out by the carbon monoxide dehydrogenase (CODH)/acetyl coenzyme A synthase (ACS) enzyme, which performs the cornerstone reaction in the ancient Wood-Ljungdahl metabolic pathway to synthesize the key biological metabolite, acetyl-CoA. Despite its significance, a fundamental understanding of this transformation is lacking, hampering efforts to harness analogous chemistry. To address these knowledge gaps, we have designed an artificial metalloenzyme within the azurin protein scaffold as a structural, functional, and mechanistic model of ACS. We demonstrate the intermediacy of the Ni^I species and requirement for ordered substrate binding in the bioorganometallic carbon-carbon bond-forming reaction from the one-carbon ACS substrates. The electronic and geometric structures of the nickel-acetyl intermediate have been characterized using time-resolved optical, electron paramagnetic resonance, and X-ray absorption spectroscopy in conjunction with quantum chemical calculations. Moreover, we demonstrate that the nickel-acetyl species is chemically competent for selective acyl transfer upon thiol addition to biosynthesize an activated thioester. Drawing an analogy to the native enzyme, a mechanism for thioester generation by this ACS model has been proposed. The fundamental insight into the enzymatic process provided by this rudimentary ACS model has implications for the evolution of primitive ACS-like proteins. Ultimately, these findings offer strategies for development of highly active catalysts for sustainable generation of liquid fuels from one-carbon substrates, with potential for broad applications across diverse fields ranging from energy storage to environmental remediation.

Functional Conversion of Acetyl-Coenzyme a Synthase to a Nickel Superoxide Dismutase via Rational Design of Coordination Microenvironment for the Nid-Site

The Ni_d site coordination microenvironment of a truncated acetyl-coenzyme A synthase has been designed systematically for functional conversion to a Ni-SOD-like enzyme. To this end, the first strategy is to introduce an axial histidine ligand, using mutations F598H, S594H and S594H-GP individually. The resulting three mutants obtained Ni-SOD-like activity successfully, although the catalytic activity was about 10-fold lower than in native Ni-SOD. The second strategy is to mimic the H-bond network in the second sphere coordination microenvironment of the native Ni-SOD. Two mutations based on F598H (EFG-F598H and YGP-F598H) were designed. The successful EFG-F598H exhibited ~3-fold Ni-SOD-like activity of F598H. These designed Ni-SOD-like metalloproteins were characterized by UV/Vis, EPR and Cyclic voltammetry while F598H was also characterized by X-ray protein crystallography. The pH titrations were performed to reveal the source of the two protons required for forming H₂O₂ in the SOD catalytic reaction. Based on all of the results, a proposed catalytic mechanism for the Ni-SOD-like metalloproteins is presented.

Theoretical Studies of Acetyl-CoA Synthase Catalytic Mechanism

DFT calculations were performed for the A-cluster from the enzyme Acetyl-CoA synthase (ACS). The acid constants (pKa), reduction potentials, and pH-dependent reduction potential for the A-cluster with different oxidation states and ligands were calculated. Good agreement of the reduction potentials, dependent on pH in the experiment, was obtained. On the basis of the calculations, a mechanism for the methylation reaction involving two–electron reduction and protonation on the proximal nickel atom of the reduced A-cluster is proposed.

Protein-based models offer mechanistic insight into complex nickel metalloenzymes

There are ten nickel enzymes found across biological systems, each with a distinct active site and reactivity that spans reductive, oxidative, and redox-neutral processes. We focus on the reductive enzymes, which catalyze reactions that are highly germane to the modern-day climate crisis: [NiFe] hydrogenase, carbon monoxide dehydrogenase, acetyl coenzyme A synthase, and methyl coenzyme M reductase. The current mechanistic understanding of each enzyme system is reviewed along with existing knowledge gaps, which are addressed through the development of protein-derived models, as described here. This opinion is intended to highlight the advantages of using robust protein scaffolds for modeling multiscale contributions to reactivity and inspire the development of novel artificial metalloenzymes for other small molecule transformations.

Thioester synthesis through geoelectrochemical CO2 fixation on Ni sulfides

A prevailing scenario of the origin of life postulates thioesters as key intermediates in protometabolism, but there is no experimental support for the prebiotic CO₂ fixation routes to thioesters. Here we demonstrate that, under a simulated geoelectrochemical condition in primordial ocean hydrothermal systems (-0.6 to -1.0 V versus the standard hydrogen electrode), nickel sulfide (NiS) gradually reduces to Ni⁰, while accumulating surface-bound carbon monoxide (CO) due to CO₂ electroreduction. The resultant partially reduced NiS realizes thioester (S-methyl thioacetate) formation from CO and methanethiol even at room temperature and neutral pH with the yield up to 35% based on CO. This thioester formation is not inhibited, or even improved, by 50:50 coprecipitation of NiS with FeS or CoS (the maximum yields; 27 or 56%, respectively). Such a simple thioester synthesis likely occurred in Hadean deep-sea vent environments, setting a stage for the autotrophic origin of life.

Ligand Field Inversion as a Mechanism to Gate Bioorganometallic Reactivity: Investigating a Biochemical Model of Acetyl CoA Synthase Using Spectroscopy and Computation

The biological global carbon cycle is largely regulated through microbial nickel enzymes, including carbon monoxide dehydrogenase (CODH), acetyl coenzyme A synthase (ACS), and methyl coenzyme M reductase (MCR). These systems are suggested to utilize organometallic intermediates during catalysis, though characterization of these species has remained challenging. We have established a mutant of nickel-substituted azurin as a scaffold upon which to develop protein-based models of enzymatic intermediates, including the organometallic states of ACS. In this work, we report the comprehensive investigation of the S = 1/2 Ni-CO and Ni-CH₃ states using pulsed EPR spectroscopy and computational techniques. While the Ni-CO state shows conventional metal-ligand interactions and a classical ligand field, the Ni-CH₃ hyperfine interactions between the methyl protons and the nickel indicate a closer distance than would be expected for an anionic methyl ligand. Structural analysis instead suggests a near-planar methyl ligand that can be best described as cationic. Consistent with this conclusion, the frontier molecular orbitals of the Ni-CH₃ species indicate a ligand-centered LUMO, with a d⁹ population on the metal center, rather than the d⁷ population expected for a typical metal-alkyl species generated by oxidative addition. Collectively, these data support the presence of an inverted ligand field configuration for the Ni-CH₃ Az species, in which the lowest unoccupied orbital is centered on the ligands rather than the more electropositive metal. These analyses provide the first evidence for an inverted ligand field within a biological system. The functional relevance of the electronic structures of both the Ni-CO and Ni-CH₃ species are discussed in the context of native ACS, and an inverted ligand field is proposed as a mechanism by which to gate reactivity both within ACS and in other thiolate-containing metalloenzymes.

Diverse Energy-Conserving Pathways in Clostridium difficile: Growth in the Absence of Amino Acid Stickland Acceptors and the Role of the Wood-Ljungdahl Pathway

Clostridium difficile is the leading cause of hospital-acquired antibiotic-associated diarrhea and is the only widespread human pathogen that contains a complete set of genes encoding the Wood-Ljungdahl pathway (WLP). In acetogenic bacteria, synthesis of acetate from 2 CO₂ molecules by the WLP functions as a terminal electron accepting pathway; however, C. difficile contains various other reductive pathways, including a heavy reliance on Stickland reactions, which questions the role of the WLP in this bacterium. In rich medium containing high levels of electron acceptor substrates, only trace levels of key WLP enzymes were found; therefore, conditions were developed to adapt C. difficile to grow in the absence of amino acid Stickland acceptors. Growth conditions were identified that produce the highest levels of WLP activity, determined by Western blot analyses of the central component acetyl coenzyme A synthase (AcsB) and assays of other WLP enzymes. Fermentation substrate and product analyses, enzyme assays of cell extracts, and characterization of a ΔacsB mutant demonstrated that the WLP functions to dispose of metabolically generated reducing equivalents. While WLP activity in C. difficile does not reach the levels seen in classical acetogens, coupling of the WLP to butyrate formation provides a highly efficient system for regeneration of NAD⁺ "acetobutyrogenesis," requiring only low flux through the pathways to support efficient ATP production from glucose oxidation. Additional insights redefine the amino acid requirements in C. difficile, explore the relationship of the WLP to toxin production, and provide a rationale for colocalization of genes involved in glycine synthesis and cleavage within the WLP operon.IMPORTANCE Clostridium difficile is an anaerobic, multidrug-resistant, toxin-producing pathogen with major health impacts worldwide. It is the only widespread pathogen harboring a complete set of Wood-Ljungdahl pathway (WLP) genes; however, the role of the WLP in C. difficile is poorly understood. In other anaerobic bacteria and archaea, the WLP can operate in one direction to convert CO₂ to acetic acid for biosynthesis or in either direction for energy conservation. Here, conditions are defined in which WLP levels in C. difficile increase markedly, functioning to support metabolism of carbohydrates. Amino acid nutritional requirements were better defined, with new insight into how the WLP and butyrate pathways act in concert, contributing significantly to energy metabolism by a mechanism that may have broad physiological significance within the group of nonclassical acetogens.

Nickel(ii)-methyl complexes adopting unusual seesaw geometries

Tris-carbene borate supported nickel methyl complexes adopt unusual seesaw geometries due to competing electronic and chelate effects.

A Biochemical Nickel(I) State Supports Nucleophilic Alkyl Addition: A Roadmap for Methyl Reactivity in Acetyl Coenzyme A Synthase

Nickel-containing enzymes such as methyl coenzyme M reductase (MCR) and carbon monoxide dehydrogenase/acetyl coenzyme A synthase (CODH/ACS) play a critical role in global energy conversion reactions, with significant contributions to carbon-centered processes. These enzymes are implied to cycle through a series of nickel-based organometallic intermediates during catalysis, though identification of these intermediates remains challenging. In this work, we have developed and characterized a nickel-containing metalloprotein that models the methyl-bound organometallic intermediates proposed in the native enzymes. Using a nickel(I)-substituted azurin mutant, we demonstrate that alkyl binding occurs via nucleophilic addition of methyl iodide as a methyl donor. The paramagnetic Ni^III-CH₃ species initially generated can be rapidly reduced to a high-spin Ni^II-CH₃ species in the presence of exogenous reducing agent, following a reaction sequence analogous to that proposed for ACS. These two distinct bioorganometallic species have been characterized by optical, EPR, XAS, and MCD spectroscopy, and the overall mechanism describing methyl reactivity with nickel azurin has been quantitatively modeled using global kinetic simulations. A comparison between the nickel azurin protein system and existing ACS model compounds is presented. Ni^III-CH₃ Az is only the second example of two-electron addition of methyl iodide to a Ni^I center to give an isolable species and the first to be formed in a biologically relevant system. These results highlight the divergent reactivity of nickel across the two intermediates, with implications for likely reaction mechanisms and catalytically relevant states in the native ACS enzyme.

A bioorganometallic model for acetyl coenzyme A synthase has been developed. This model protein is able to bind a cationic methyl group via direct addition to the nickel(I) center. The resultant nickel(III)-methyl species has been characterized via optical and electron paramagnetic resonance spectroscopy, and the reduced nickel(II)-methyl state has been characterized using magnetic circular dichroism and X-ray spectroscopy. Implications for further reactivity with CO are gleaned from electronic structure analysis of the nickel-methyl species.

Cobalt(ii) acyl intermediates in carbon-carbon bond formation and oxygenation

The organocobalt scorpionate compounds ToMCoR (ToM = tris(4,4-dimethyl-2-oxazolinyl)phenylborate; R = Bn, 1; CH2SiMe3, 2; Ph, 3; Et, 4; nBu, 5; Me, 6) react in carbonylation, oxidation, and carboxylation reactions via pathways that are distinctly influenced by the nature of the organometallic moiety. The compounds are prepared by reaction of ToMCoCl with the corresponding organolithium or organopotassium reagents. Compounds 1-6 were characterized by 8-line hyperfine coupling to cobalt in EPR spectra and solution phase magnetic measurements (μeff = 4-5μB) as containing a high-spin cobalt(ii) center. The UV-Vis spectra revealed an intense diagnostic band at ca. 700 nm (ε > 1000 M-1 cm-1) associated with the tetrahedral organocobalt(ii) center that was assigned to a d ← d transition on the basis of configuration interaction (CI) calculations. Complexes 1-6 react rapidly with CO to form equilibrating mixtures of the low spin organocobalt carbonyl ToMCo(R)CO, acyl ToMCoC([double bond, length as m-dash]O)R, and acyl carbonyl ToMCo{C([double bond, length as m-dash]O)R}CO. The 1H and 11B NMR spectra contained only one set of signals for the CO-treated solutions, whereas the solution-phase IR spectra contained up to two νCO and three νC([double bond, length as m-dash]O)R signals with intensities varying depending on the R group (R = Bn, 7; CH2SiMe3, 8; Ph, 9; Et, 10; nBu, 11; Me, 12). Single crystal X-ray diffraction of ToMCo{C([double bond, length as m-dash]O)Et}CO (10) supports its assignment as a square pyramidal cobalt(ii) acyl carbonyl complex. Upon evaporation of volatiles, solutions of 8-12 revert to the CO-free organocobalt starting materials 2-6, whereas attempts to isolate benzyl-derived 7 provide an unusual α-alkoxyketone species, characterized by single crystal X-ray diffraction. Despite the differences observed in the carbonylation of 1-6 as a result of varying the R group, compounds 7-12 all react rapidly with O2 through an oxygenation pathway to afford the corresponding carboxylate compounds ToMCoO2CR (R = Bn, 13; CH2SiMe3, 14; Ph, 15; Et, 16; nBu, 17; Me, 18). In contrast, the insertion of CO2 into the Co-C bond in 1-6 requires several days to weeks.

Evidence of mixotrophic carbon-capture by n-butanol-producer Clostridium beijerinckii

Recent efforts to combat increasing greenhouse gas emissions include their capture into advanced biofuels, such as butanol. Traditionally, biobutanol research has been centered solely on its generation from sugars. Our results show partial re-assimilation of CO₂ and H₂ by n-butanol-producer C. beijerinckii. This was detected as synchronous CO₂/H₂ oscillations by direct (real-time) monitoring of their fermentation gasses. Additional functional analysis demonstrated increased total carbon recovery above heterotrophic values associated to mixotrophic assimilation of synthesis gas (H₂, CO₂ and CO). This was further confirmed using ¹³C-Tracer experiments feeding ¹³CO₂ and measuring the resulting labeled products. Genome- and transcriptome-wide analysis revealed transcription of key C-1 capture and additional energy conservation genes, including partial Wood-Ljungdahl and complete reversed pyruvate ferredoxin oxidoreductase / pyruvate-formate-lyase-dependent (rPFOR/Pfl) pathways. Therefore, this report provides direct genetic and physiological evidences of mixotrophic inorganic carbon-capture by C. beijerinckii.

Rapid and ordered carbonylation and oxygenation of a cobalt(ii) methyl

The oxidative carbonylation of To^MCoMe (1; To^M = tris(4,4-dimethyl-2-oxazolinyl)phenylborate) involves its rapid, reversible reaction with CO to form To^MCo{C(O)Me}CO (2) followed by rapid reaction with O₂ yielding To^MCoOAc (3), in contrast to the slow direct carboxylation of To^MCoMe by CO₂.

Multielectron Chemistry within a Model Nickel Metalloprotein: Mechanistic Implications for Acetyl-CoA Synthase

The acetyl coenzyme A synthase (ACS) enzyme plays a central role in the metabolism of anaerobic bacteria and archaea, catalyzing the reversible synthesis of acetyl-CoA from CO and a methyl group through a series of nickel-based organometallic intermediates. Owing to the extreme complexity of the native enzyme systems, the mechanism by which this catalysis occurs remains poorly understood. In this work, we have developed a protein-based model for the Ni_P center of acetyl coenzyme A synthase using a nickel-substituted azurin protein (NiAz). NiAz is the first model nickel protein system capable of accessing three (Ni^I/Ni^II/Ni^III) distinct oxidation states within a physiological potential range in aqueous solution, a critical feature for achieving organometallic ACS activity, and binds CO and -CH₃ groups with biologically relevant affinity. Characterization of the Ni^I-CO species through spectroscopic and computational techniques reveals fundamentally similar features between the model NiAz system and the native ACS enzyme, highlighting the potential for related reactivity in this model protein. This work provides insight into the enzymatic process, with implications toward engineering biological catalysts for organometallic processes.

X-ray Absorption Spectroscopy Reveals an Organometallic Ni-C Bond in the CO-Treated Form of Acetyl-CoA Synthase

Acetyl-CoA synthase (ACS) is a key enzyme in the Wood-Ljungdahl pathway of anaerobic CO₂ fixation, which has long been proposed to operate by a novel mechanism involving a series of protein-bound organometallic (Ni-CO, methyl-Ni, and acetyl-Ni) intermediates. Here we report the first direct structural evidence of the proposed metal-carbon bond. We describe the preparation of the highly active metal-replete enzyme and near-quantitative generation of the kinetically competent carbonylated intermediate. This advance has allowed a combination of Ni and Fe K-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure experiments along with density functional theory calculations. The data reveal that CO binds to the proximal Ni of the six-metal metallocenter at the active site and undergoes dramatic structural and electronic perturbation in forming this organometallic Ni-CO intermediate. This direct identification of a Ni-carbon bond in the catalytically competent CO-bound form of the A cluster of ACS provides definitive experimental structural evidence supporting the proposed organometallic mechanism of anaerobic acetyl-CoA synthesis.

Ligand binding at the A-cluster in full-length or truncated acetyl-CoA synthase studied by X-ray absorption spectroscopy

Bacteria integrate CO₂ reduction and acetyl coenzyme-A (CoA) synthesis in the Wood-Ljungdal pathway. The acetyl-CoA synthase (ACS) active site is a [4Fe4S]-[NiNi] complex (A-cluster). The dinickel site structure (with proximal, p, and distal, d, ions) was studied by X-ray absorption spectroscopy in ACS variants comprising all three protein domains or only the C-terminal domain with the A-cluster. Both variants showed two square-planar Ni(II) sites and an OH^- bound at Ni(II)_p in oxidized enzyme and a H₂O at Ni(I)_p in reduced enzyme; a Ni(I)_p-CO species was induced by CO incubation and a Ni(II)-CH₃^- species with an additional water ligand by a methyl group donor. These findings render a direct effect of the N-terminal and middle domains on the A-cluster structure unlikely.

Reaction of a polydentate cysteine-based ligand and its nickel(ii) complex with electrophilic and nucleophilic methyl-transfer reagents - from S-methylation to acetyl coenzyme A synthase reactivity

The L-cysteine derived N2S2 ligand precursor H2L and its nickel(ii) complex L2Ni2 were investigated with respect to their behaviour in contact with electrophilic and nucleophilic methylation reagents (H2L = (N,N'-dimethyl-(2R,5R)-bis-(sulfanylmethyl)-piperazine). Treatment of deprotonated L(2-) with MeI led to the selective methylation of the thiolate groups thus generating a novel potential ligand, Me2L, which is neutral and contains two thioether donors. The coordinating properties of Me2L were demonstrated by the synthesis of a first nickel(ii) complex: reaction with NiBr2 led to a mononuclear complex 2 where all donor atoms coordinate to the nickel ion, which completes its octahedral coordination sphere by the two bromide ligands. If, however, the complex [LNi]2 (1) is treated with MeI only one thiolate function per ligand moiety is methylated, while the other one remains a thiolate. This leads to [MeLNi](+) complex metal fragments, which trimerize including a μ3-bridging iodide ion to give the compound 3 that was tested with regards to ACS reactivity. While it behaved inert towards CO, attempts to replace the bridging iodide ligand by methyl units in reactions with nucleophilic methylation reagents led to a product, which could not be identified but reacted with CO. Work-up showed that this protocol had converted the thiolate function of MeL(-) into a thioester function, which corresponds to an ACS-like reactivity.

Electrochemical, Spectroscopic, and Density Functional Theory Characterization of Redox Activity in Nickel-Substituted Azurin: A Model for Acetyl-CoA Synthase

Nickel-containing enzymes are key players in global hydrogen, carbon dioxide, and methane cycles. Many of these enzymes rely on Ni(I) oxidation states in critical catalytic intermediates. However, due to the highly reactive nature of these species, their isolation within metalloenzymes has often proved elusive. In this report, we describe and characterize a model biological Ni(I) species that has been generated within the electron transfer protein, azurin. Replacement of the native copper cofactor with nickel is shown to preserve the redox activity of the protein. The Ni(II/I) couple is observed at -590 mV versus NHE, with an interfacial electron transfer rate of 70 s(-1). Chemical reduction of Ni(II)Az generates a stable species with strong absorption features at 350 nm and a highly anisotropic, axial EPR signal with principal g-values of 2.56 and 2.10. Density functional theory calculations provide insight into the electronic and geometric structure of the Ni(I) species, suggesting a trigonal planar coordination environment. The predicted spectroscopic features of this low-coordinate nickel site are in good agreement with the experimental data. Molecular orbital analysis suggests potential for both metal-centered and ligand-centered reactivity, highlighting the covalency of the metal-thiolate bond. Characterization of a stable Ni(I) species within a model protein has implications for understanding the mechanisms of complex enzymes, including acetyl coenzyme A synthase, and developing scaffolds for unique reactivity.

Influence of key amino acid mutation on the active site structure and on folding in acetyl-CoA synthase: a theoretical perspective

Ad hoc quantum chemical modeling of the acetyl-CoA synthase local structure and folding allowed us to identify an unprecedented coordination mode of histidine sidechain to protein-embedded metal ions.

Nickel-dependent metalloenzymes

This review describes the functions, structures, and mechanisms of nine nickel-containing enzymes: glyoxalase I, acireductone dioxygenase, urease, superoxide dismutase, [NiFe]-hydrogenase, carbon monoxide dehydrogenase, acetyl-coenzyme A synthase/decarbonylase, methyl-coenzyme M reductase, and lactate racemase. These enzymes catalyze their various chemistries by using metallocenters of diverse structures, including mononuclear nickel, dinuclear nickel, nickel-iron heterodinuclear sites, more complex nickel-containing clusters, and nickel-tetrapyrroles. Selected other enzymes are active with nickel, but the physiological relevance of this metal specificity is unclear. Additional nickel-containing proteins of undefined function have been identified.

Transmethylation of a four-coordinate nickel(i) monocarbonyl species with methyl iodide

The reaction of a nickel(i) carbonyl species with CH₃I revealed the formation of (PNP)NiCOCH₃ which differs from its zerovalent congener.

Metal-metal bonds in biology

Nickel-containing carbon monoxide dehydrogenases, acetyl-CoA synthases, nickel-iron hydrogenases, and diron hydrogenases are distinct metalloenzymes yet they share a number of important characteristics. All are O(2)-sensitive, with active-sites composed of iron and/or nickel ions coordinated primarily by sulfur ligands. In each case, two metals are juxtaposed at the "heart" of the active site, within range of forming metal-metal bonds. These active-site clusters exhibit multielectron redox abilities and must be reductively activated for catalysis. Reduction potentials are milder than expected based on formal oxidation state changes. When reductively activated, each cluster attacks an electrophilic substrate via an oxidative addition reaction. This affords a two-electron-reduced substrate bound to one or both metals of an oxidized cluster. M-M bonds have been established in hydrogenases where they serve to initiate the oxidative addition of protons and perhaps stabilize active sites in multiple redox states. The same may be true of the CODH and ACS active sites-Ni-Fe and Ni-Ni bonds in these sites may play critical roles in catalysis, stabilizing low-valence states and initiating oxidative addition of CO(2) and methyl group cations, respectively. In this article, the structural and functional commonalities of these metalloenzyme active sites are described, and the case is made for the formation and use of metal-metal bonds in each enzyme mentioned. As a post-script, the importance of Fe-Fe bonds in the nitrogenase FeMoco active site is discussed.

The conversion of nickel-bound CO into an acetyl thioester: organometallic chemistry relevant to the acetyl coenzyme A synthase active site

When three become one: Within one nickel-based model system, the three reactants CO, MeI, and PhSH have been assembled to yield an acetyl thioester. The reactivity is of relevance for the functioning of the acetyl coenzyme A synthase active site and provides insights into possible binding sequences.

Metal centers in the anaerobic microbial metabolism of CO and CO2

Carbon dioxide and carbon monoxide are important components of the carbon cycle. Major research efforts are underway to develop better technologies to utilize the abundant greenhouse gas, CO(2), for harnessing 'green' energy and producing biofuels. One strategy is to convert CO(2) into CO, which has been valued for many years as a synthetic feedstock for major industrial processes. Living organisms are masters of CO(2) and CO chemistry and, here, we review the elegant ways that metalloenzymes catalyze reactions involving these simple compounds. After describing the chemical and physical properties of CO and CO(2), we shift focus to the enzymes and the metal clusters in their active sites that catalyze transformations of these two molecules. We cover how the metal centers on CO dehydrogenase catalyze the interconversion of CO and CO(2) and how pyruvate oxidoreductase, which contains thiamin pyrophosphate and multiple Fe(4)S(4) clusters, catalyzes the addition and elimination of CO(2) during intermediary metabolism. We also describe how the nickel center at the active site of acetyl-CoA synthase utilizes CO to generate the central metabolite, acetyl-CoA, as part of the Wood-Ljungdahl pathway, and how CO is channelled from the CO dehydrogenase to the acetyl-CoA synthase active site. We cover how the corrinoid iron-sulfur protein interacts with acetyl-CoA synthase. This protein uses vitamin B(12) and a Fe(4)S(4) cluster to catalyze a key methyltransferase reaction involving an organometallic methyl-Co(3+) intermediate. Studies of CO and CO(2) enzymology are of practical significance, and offer fundamental insights into important biochemical reactions involving metallocenters that act as nucleophiles to form organometallic intermediates and catalyze C-C and C-S bond formations.

Methods for analysis of acetyl-CoA synthase applications to bacterial and archaeal systems

The nickel- and iron-containing enzyme acetyl-CoA synthase (ACS) catalyzes de novo synthesis as well as overall cleavage of acetyl-CoA in acetogens, various other anaerobic bacteria, methanogens, and other archaea. The enzyme contains a unique active site metal cluster, designated the A cluster, that consists of a binuclear Ni-Ni center bridged to an [Fe(4)S(4)] cluster. In bacteria, ACS is tightly associated with CO dehydrogenase to form the bifunctional heterotetrameric enzyme CODH/ACS, whereas in archaea, ACS is a component of the large multienzyme complex acetyl-CoA decarbonylase/synthase (ACDS), which comprises five different subunits that make up the subcomponent proteins ACS, CODH, and a corrinoid enzyme. Characteristic properties of ACS are discussed, and key methods are described for analysis of the enzyme's multiple redox-dependent activities, including overall acetyl-CoA synthesis, acetyltransferase, and an isotopic exchange reaction between the carbonyl group of acetyl-CoA and CO. Systematic measurement of these activities, applied to different ACS protein forms, provides insight into the ACS catalytic mechanism and physiological functions in both CODH/ACS and ACDS systems.

Evidence that ferredoxin interfaces with an internal redox shuttle in Acetyl-CoA synthase during reductive activation and catalysis

Acetyl-CoA synthase (ACS), a subunit of the bifunctional CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex of Moorella thermoacetica requires reductive activation in order to catalyze acetyl-CoA synthesis and related partial reactions, including the CO/[1-(14)C]-acetyl-CoA exchange reaction. We show that the M. thermoacetica ferredoxin(II) (Fd-II), which harbors two [4Fe-4S] clusters and is an electron acceptor for CODH, serves as a redox activator of ACS. The level of activation depends on the oxidation states of both ACS and Fd-II, which strongly suggests that Fd-II acts as a reducing agent. By the use of controlled potential enzymology, the midpoint reduction potential for the catalytic one-electron redox-active species in the CO/acetyl-CoA exchange reaction is -511 mV, which is similar to the midpoint reduction potential that was earlier measured for other reactions involving ACS. Incubation of ACS with Fd-II and CO leads to the formation of the NiFeC species, which also supports the role of Fd-II as a reductant for ACS. In addition to being a reductant, Fd-II can accept electrons from acetylated ACS, as observed by the increased intensity of the EPR spectrum of reduced Fd-II, indicating that there is a stored electron within an "electron shuttle" in the acetyl-Ni(II) form of ACS. This "shuttle" is proposed to serve as a redox mediator during activation and at different steps of the ACS catalytic cycle.

S-S bond reactivity in metal-perthiocarboxylato compounds

While M-percarboxylato species are elusive intermediates, their sulfur containing analogues are known in some cases. The feasibility of isolation of M-perthioacetato compounds allowed, in this work, to obtain new insights into the pathways that follow the reactivity of M-E-ER (E = O, S) fragments. Herein we report on the isolation of two new M-perthioacetato compounds: trans-[Pt(CH(3)CS(2)S)(2)] () and [Ni(CH(3)CSS)(CH(3)CS(2)S)] (), which have been fully characterized, including X-ray structures. Reactivity of these compounds towards PPh(3) has been studied combining UV-vis monitorization and NMR measurements. Overall the accumulated data suggest that the evolution of the perthioacetato ligand in complexes and by reaction with PPh(3) consists of a complex multistep pathway in which the sulfur transfer is preceded by electron transfer. Cyclic voltammetry measurements indicate that the transference of two electrons from the phosphorus to the sulfur atom is not concerted, suggesting that the first step of the reaction with PPh(3) is the monoelectronic electron transfer followed by P-S bond formation. The results presented here show a novel pathway in the field of S-S bond reactivity processes relevant in biological, synthetic systems and in hydrocarbon desulfurization processes.

Dinuclear nickel complexes modeling the structure and function of the acetyl CoA synthase active site

A dinuclear nickel complex with methyl and thiolate ligands, Ni(dadt(Et))Ni(Me)(SDmp) (2), has been synthesized as a dinuclear Ni(d)-Ni(p)-site model of acetyl-CoA synthase (ACS) (dadt(Et) is N,N'-diethyl-3,7-diazanonane-1,9-dithiolate; Dmp is 2,6-dimesitylphenyl). Complex 2 was prepared via 2 methods: (i) ligand substitution of a dinuclear Ni(II)-Ni(II) cation complex [Ni(dadt(Et)) Ni(tmtu)2] (OTf)2 (1) with MeMgBr and KSDmp (tmtu is tetramethylthiourea), (ii) methyl transfer from methylcobaloxime Co(dmgBF2)2(Me)(Py) (5) to a Ni(II)-Ni(0) complex such as [Ni(dadt(Et))Ni(cod)] (3), generated in situ from Ni(dadt(Et)) and Ni(cod)(2), followed by addition of KSDmp (cod is 1,5-cyclooctadiene; dmgBF2 is difluoroboryl-dimethylglyoximate). Method ii models the formation of Nip-Me species proposed as a plausible intermediate in ACS catalysis. The reaction of 2 with excess CO affords the acetylthioester CH3C(O)SDmp (8) with concomitant formation of Ni(dadt(Et))Ni(CO)2 (9) and Ni(CO)4 plus Ni(dadt(Et)). When complex 2 is treated with 1 equiv of CO in the presence of excess 1,5-cyclooctadiene, the formation of 9 and Ni(CO)4 is considerably suppressed, and instead the dinuclear Ni(II)-Ni(0) complex is generated in situ, which further affords 2 upon successive treatment with Co(dmgBF2)2(Me)(Py) (5) and KSDmp. These results suggest that (i) ACS catalysis could include the Nid(II)-Nip(0) state as the active species, (ii) The Nid(II)-Nip(0) species could first react with methylcobalamin to afford Nid(II)-Nip(II)-Me, and (iii) CO insertion into the Nip-Me bond and the successive reductive elimination of acetyl-CoA occurs immediately when CoA is coordinated to the Nip site to form the active Nid(II)-Nip(0) species.