金属组学：Wood—Ljungdahl通路中的金属蛋白／金属酶

本文概述了厌氧微生物的Wood-Ljungdahl通路及通路中的一组金属蛋白／金属酶,主要介绍该通路的来源、过程及通路中的四种金属蛋白,金属酶：甲酸脱氢酶、钻铁硫蛋白、乙酰辅酶A合成酶和CO脱氢酶．甲酸脱氢酶催化CO2和甲酸的可逆氧化还原,是CO2转化为甲酸进而转化为甲基四氢叶酸的关键金属酶;钴铁硫蛋白是该通路中的甲基转换器,接受甲基四氢叶酸的甲基之后再传递给乙酰辅酶A合成酶;CO脱氢酶催化CO2与CO之间的可逆氧化还原;乙酰辅酶A合成酶通过浓缩甲基、CO和辅酶A而催化乙酰辅酶A的合成．本文重点对这四种金属蛋白／金属酶的结构、性质、功能及催化机理的研究进展进行了综述．     

Creating a Low‐Potential Redox Polymer for Efficient Electroenzymatic CO2 Reduction

Increasing greenhouse gas emissions have resulted in greater motivation to find novel carbon dioxide (CO₂) reduction technologies, where the reduction of CO₂ to valuable chemical commodities is desirable. Molybdenum‐dependent formate dehydrogenase (Mo‐FDH) from Escherichia coli is a metalloenzyme that is able to interconvert formate and CO₂. We describe a low‐potential redox polymer, synthesized by a facile method, that contains cobaltocene (grafted to poly(allylamine), Cc‐PAA) to simultaneously mediate electrons to Mo‐FDH and immobilize Mo‐FDH at the surface of a carbon electrode. The resulting bioelectrode reduces CO₂ to formate with a high Faradaic efficiency of 99±5 % at a mild applied potential of ?0.66 V vs. SHE.     

Structural and spectroscopic models of the A-cluster of acetyl coenzyme a synthase/carbon monoxide dehydrogenase: Nature's Monsanto acetic acid catalyst

Acetyl coenzyme A synthase/carbon monoxide dehydrogenase (ACS/CODH) is a bifunctional enzyme present in a number of anaerobic bacteria. The enzyme catalyzes two separate reactions namely, the reduction of atmospheric CO₂ to CO (CODH activity at the C-cluster) and the synthesis of acetyl coenzyme A (ACS activity at the A-cluster) from CO, CH₃ from a corrinoid iron-sulfur protein, and the thiol coenzyme A. The structure(s) of the A-cluster of ACS/CODH from Moorella thermoacetica revealed an unprecedented structure with three different metallic subunits linked to each other through bridging Cys-S residues comprising the active site. In these structure(s) a Fe₄S₄ cubane is bridged via Cys-S to a bimetallic metal cluster. This bimetallic cluster contains a four-coordinate Ni, Cu, or Zn as the proximal metal (to the Fe₄S₄ cluster; designated M_p), which in turn is bridged through two Cys-S residues to a terminal square planar Ni(II) (Ni_d, distal to Fe₄S₄) ligated by two deprotonated carboxamido nitrogens from the peptide backbone. It is now established that Ni is required at the M_p site for the ACS activity. Over the past several years modeling efforts by several groups have provided clues towards understanding the intrinsic properties of the unique site in ACS. To date most studies have focused on dinuclear compounds that model the M_p-Ni_d subsite. Synthesis of such models have revealed that the Ni_p sites (a) are readily removed when mixed with 1,10-phenanthroline (phen) and (b) can be reduced to the Ni(I) and/or Ni(0) oxidation state (deduced by EPR or electrochemical studies) and bind CO in terminal fashion with ν_co value similar to the enzyme. In contrast, the presence of Cu(I) centers at these M_p sites do not bind CO and are not removable with phen supporting a non-catalytic role for Cu(I) at the M_p site in the enzyme. The Ni_d site (coordinated by carboxamido-N/thiolato-S) in these models are very stable in the +2 oxidation state and not readily removed upon treatment with phen suggesting that the source of ‘labile Ni’ and the NiFeC signal arises from the presence of Ni at the M_p site in ACS. This review includes the results and implications of the modeling studies reported so far.     

EPR and infrared spectroscopic evidence that a kinetically competent paramagnetic intermediate is formed when acetyl-coenzyme A synthase reacts with CO

Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is a bifunctional enzyme which enables archaea and bacteria to grow autotrophically on CO and hydrogen/carbon dioxide using the Wood-Ljundahl pathway. CO produced from reduction of carbon dioxide by CODH is transferred to the active site of ACS through an intramolecular tunnel, where it combines with Coenzyme A and a methyl cation to produce acetyl-CoA. The active site of ACS contains a single [4Fe-4S] cluster bridged by a cysteine sulfur atom to a binuclear center. The binuclear center is composed of two Ni atoms bridged by two separate cysteine sulfurs. The Ni site attached to the [4Fe-4S] is referred to as proximal Ni, while the other Ni atom, which assumes a square-planar geometry, is referred to as the distal site. We report the characterization of the carbonylated form of highly active (0.67 spins/mol) heterologously expressed monomeric ACS from C. hydrogenoformans in E. coli by rapid-freeze quench EPR (RFQ-EPR) and stopped-flow infrared (SF-IR) spectroscopies. The reaction of ACS with CO produces a single metal-carbonyl species whose formation rate, measured by SF-IR, correlates with the rate of formation, measured by RFQ-EPR, of the paramagnetic state of the enzyme (NiFeC species). These results indicate that the NiFeC species is the predominant form observed in solution when ACS reacts with CO. The NiFeC species contains the proximal Ni in the +1 redox state and the [4Fe-4S] cluster in the 2+ state, thus there is no evidence for either a Ni(0) or a Ni(II) state in the active carbonylated form of the enzyme.     

Infrared Spectroscopy Elucidates the Inhibitor Binding Sites in a Metal-Dependent Formate Dehydrogenase

Biological carbon dioxide (CO₂) reduction is an important step by which organisms form valuable energy-richer molecules required for further metabolic processes. The Mo-dependent formate dehydrogenase (FDH) from Rhodobacter capsulatus catalyzes reversible formate oxidation to CO₂ at a bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor. To elucidate potential substrate binding sites relevant for the mechanism, we studied herein the interaction with the inhibitory molecules azide and cyanate, which are isoelectronic to CO₂ and charged as formate. We employed infrared (IR) spectroscopy in combination with density functional theory (DFT) and inhibition kinetics. One distinct inhibitory molecule was found to bind to either a non-competitive or a competitive binding site in the secondary coordination sphere of the active site. Site-directed mutagenesis of key amino acid residues in the vicinity of the bis-MGD cofactor revealed changes in both non-competitive and competitive binding, whereby the inhibitor is in case of the latter interaction presumably bound between the cofactor and the adjacent Arg587.     

Non‐natural Cofactor and Formate‐Driven Reductive Carboxylation of Pyruvate

A non‐natural cofactor and formate driven system for reductive carboxylation of pyruvate is presented. A formate dehydrogenase (FDH) mutant, FDH*, that favors a non‐natural redox cofactor, nicotinamide cytosine dinucleotide (NCD), for generation of a dedicated reducing equivalent at the expense of formate were acquired. By coupling FDH* and NCD‐dependent malic enzyme (ME*), the successful utilization of formate is demonstrated as both CO₂ source and electron donor for reductive carboxylation of pyruvate with a perfect stoichiometry between formate and malate. When ¹³C‐isotope‐labeled formate was used in in vitro trials, up to 53 % of malate had labeled carbon atom. Upon expression of FDH* and ME* in the model host E. coli, the engineered strain produced more malate in the presence of formate and NCD. This work provides an alternative and atom‐economic strategy for CO₂ fixation where formate is used in lieu of CO₂ and offers dedicated reducing power.     

Non-natural Cofactor and Formate-Driven Reductive Carboxylation of Pyruvate

A non-natural cofactor and formate driven system for reductive carboxylation of pyruvate is presented. A formate dehydrogenase (FDH) mutant, FDH*, that favors a non-natural redox cofactor, nicotinamide cytosine dinucleotide (NCD), for generation of a dedicated reducing equivalent at the expense of formate were acquired. By coupling FDH* and NCD-dependent malic enzyme (ME*), the successful utilization of formate is demonstrated as both CO₂ source and electron donor for reductive carboxylation of pyruvate with a perfect stoichiometry between formate and malate. When ¹³C-isotope-labeled formate was used in in vitro trials, up to 53 % of malate had labeled carbon atom. Upon expression of FDH* and ME* in the model host E. coli, the engineered strain produced more malate in the presence of formate and NCD. This work provides an alternative and atom-economic strategy for CO₂ fixation where formate is used in lieu of CO₂ and offers dedicated reducing power.     

Genetic construction of truncated and chimeric metalloproteins derived from the alpha subunit of acetyl-CoA synthase from Clostridium thermoaceticum

In this study, a genetics-based method is used to truncate acetyl-coenzyme A synthase from Clostridium thermoaceticum (ACS), an alpha(2)beta(2) tetrameric 310 kDa bifunctional enzyme. ACS catalyzes the reversible reduction of CO(2) to CO and the synthesis of acetyl-CoA from CO (or CO(2) in the presence of low-potential reductants), CoA, and a methyl group bound to a corrinoid-iron sulfur protein (CoFeSP). ACS contains seven metal-sulfur clusters of four different types called A, B, C, and D. The B, C, and D clusters are located in the 72 kDa beta subunit, while the A-cluster, a Ni-X-Fe(4)S(4) cluster that serves as the active site for acetyl-CoA synthase activity, is located in the 82 kDa alpha subunit. The extent to which the essential properties of the cluster, including catalytic, redox, spectroscopic, and substrate-binding properties, were retained as ACS was progressively truncated was determined. Acetyl-CoA synthase catalytic activity remained when the entire beta subunit was removed, as long as CO, rather than CO(2) and a low-potential reductant, was used as a substrate. Truncating an approximately 30 kDa region from the N-terminus of the alpha subunit yielded a 49 kDa protein that lacked catalytic activity but exhibited A-cluster-like spectroscopic, redox, and CO-binding properties. Further truncation afforded a 23 kDa protein that lacked recognizable A-cluster properties except for UV-vis spectra typical of [Fe(4)S(4)](2+) clusters. Two chimeric proteins were constructed by fusing the gene encoding a ferredoxin from Chromatium vinosum to genes encoding the 49 and 82 kDa fragments of the alpha subunit. The chimeric proteins exhibited EPR signals that were not the simple sum of the signals from the separate proteins, suggesting magnetic interactions between clusters. This study highlights the potential for using genetics to simplify the study of complex multicentered metalloenzymes and to generate new complex metalloenzymes with interesting properties.     

Kinetics of CO insertion and acetyl group transfer steps, and a model of the acetyl-CoA synthase catalytic mechanism

Acetyl-CoA synthase/carbon monoxide dehydrogenase is a Ni-Fe-S-containing enzyme that catalyzes the synthesis of acetyl-CoA from CO, CoA, and a methyl group. The methyl group is transferred onto the enzyme from a corrinoid-iron-sulfur protein (CoFeSP). The kinetics of two steps within the catalytic mechanism were studied using the stopped-flow method, including the insertion of CO into a putative Ni(2+)-CH(3) bond and the transfer of the resulting acetyl group to CoA. Neither step had been studied previously. Reactions were monitored indirectly, starting with the methylated intermediate form of the enzyme. Resulting traces were analyzed by constructing a simple kinetic model describing the catalytic mechanism under reducing conditions. Besides methyl group transfer, CO insertion, and acetyl group transfer, fitting to experimental traces required the inclusion of an inhibitory step in which CO reversibly bound to the form of the enzyme obtained immediately after product release. Global simulation of the reported datasets afforded a consistent set of kinetic parameters. The equilibrium constant for the overall synthesis of acetyl-CoA was estimated and compared to the product of the individual equilibrium constants. Simulations obtained with the model duplicated the essential behavior of the enzyme, in terms of the variation of activity with [CO], and the time-dependent decay of the NiFeC EPR signal upon reaction with CoFeSP. Under standard assay conditions, the model suggests that the vast majority of active enzyme molecules in a population should be in the methylated form, suggesting that the subsequent catalytic step, namely CO insertion, is rate limiting. This conclusion is further supported by a sensitivity analysis showing that the rate is most sensitively affected by a change in the rate coefficient associated with the CO insertion step.     

Structures and energetics of models for the active site of acetyl-coenzyme a synthase: role of distal and proximal metals in catalysis

Acetyl-coenzyme A (CoA) synthase/carbon monoxide dehydrogenase (ACS/CODH) is a bifunctional enzyme that generates CO from carbon dioxide in the C-cluster of the beta subunit and synthesizes acetyl-CoA from carbon monoxide (CO), CoA, and CH3+ at the active site of the A-cluster in the alpha subunit. On the basis of density functional calculations, we predict that methylation of Nip occurs first, and CO then adds to the NipII-CH3 species to form the intermediate, NipII(CO)(CH3), in which Nip deligates one of its SNid bonds. The CO-insertion/CH3-migration occurs on one metal, the proximal Ni, forming the trigonal planar NipII-acetyl intermediate. The thiolate can bind to NipII and reductively eliminate the thioester. Our calculations disfavor the unprecedented bimetallic CO-insertion/CH3-migration. Ni in the proximal site produces a better catalyst than does Cu.     

Interfacing Formate Dehydrogenase with Metal Oxides for the Reversible Electrocatalysis and Solar‐Driven Reduction of Carbon Dioxide

The integration of enzymes with synthetic materials allows efficient electrocatalysis and production of solar fuels. Here, we couple formate dehydrogenase ( FDH ) from Desulfovibrio vulgaris Hildenborough (DvH) to metal oxides for catalytic CO₂ reduction and report an in‐depth study of the resulting enzyme–material interface. Protein film voltammetry (PFV) demonstrates the stable binding of FDH on metal‐oxide electrodes and reveals the reversible and selective reduction of CO₂ to formate. Quartz crystal microbalance (QCM) and attenuated total reflection infrared (ATR‐IR) spectroscopy confirm a high binding affinity for FDH to the TiO₂ surface. Adsorption of FDH on dye‐sensitized TiO₂ allows for visible‐light‐driven CO₂ reduction to formate in the absence of a soluble redox mediator with a turnover frequency (TOF) of 11±1 s^?1. The strong coupling of the enzyme to the semiconductor gives rise to a new benchmark in the selective photoreduction of aqueous CO₂ to formate.     

Binding of CO to structural models of the bimetallic subunit at the A-cluster of acetyl coenzyme A synthase/CO dehydrogenase

Trinuclear Ni-Cu-Ni and Ni-Ni-Ni complexes derived from an Ni(ii)-dicarboxamido-dithiolato metallosynthon exhibit redox behavior and CO binding properties similar to those of the A-cluster in acetyl coenzyme A synthase/CO dehydrogenase (ACS/CODH).     

Investigation of main group promoted carbon dioxide reduction

The reduction of carbon dioxide (CO₂) is of interest to the chemical industry, as many synthetic materials can be derived from CO₂. To help determine the reagents needed for the functionalization of carbon dioxide this experimental and computational study describes the reduction of CO₂ to formate and CO with hydride, electron, and proton sources in the presence of sterically bulky Lewis acids and bases. The insertion of carbon dioxide into a main group hydride, generating a main group formate, was computed to be more thermodynamically favorable for more hydridic (reducing) main group hydrides. A ten kcal/mol increase in hydricity (more reducing) of a main group hydride resulted in a 35% increase in the main group hydride's ability to insert CO₂ into the main group hydride bond. The resulting main group formate exhibited a hydricity (reducing ability) about 10% less than the respective main group hydride prior to CO₂ insertion. Coordination of a second identical Lewis acid to a main group formate complex further reduced the hydricity by about another 20%. The addition of electrons to the CO₂ adduct of ^tBu₃P and B(C₆F₅)₃ resulted in converting the sequestered CO₂ molecule to CO. Reduction of the CO₂ adduct of ^tBu₃P and B(C₆F₅)₃ with both electrons and protons resulted in only proton reduction.     

Influence of Composition of Nickel-Iron Nanoparticles for Abiotic CO2 Conversion to Early Prebiotic Organics

Abiotic synthesis of formate and short hydrocarbons takes place in serpentinizing vents where some members of vent microbial communities live on abiotic formate as their main carbon source. To better understand the catalytic properties of Ni−Fe minerals that naturally exist in hydrothermal vents, we have investigated the ability of synthetic Ni−Fe based nanoparticular solids to catalyze the H₂-dependent reduction of CO₂, the first step required for the beginning of pre-biotic chemistry. Mono and bimetallic Ni−Fe nanoparticles with varied Ni-to-Fe ratios transform CO₂ and H₂ into intermediates and products of the acetyl-coenzyme A pathway—formate, acetate, and pyruvate—in mM range under mild hydrothermal conditions. Furthermore, Ni−Fe catalysts converted CO₂ to similar products without molecular H₂ by using water as a hydrogen source. Both CO₂ chemisorption analysis and post-reaction characterization of materials indicate that Ni and Fe metals play complementary roles for CO₂ fixation.     

Photoreduction of carbon dioxide by hydrogen and methane

Zirconium oxide is active for photoreduction of gaseous carbon dioxide to carbon monoxide with hydrogen. A stable surface species arises under the photoreduction of CO₂ on zirconium oxide, and it is identified as surface formate by infrared spectroscopy. Adsorbed CO₂ is converted to formate by photoreaction with hydrogen. The surface formate is a true reaction intermediate since CO is formed by the photoreaction of formate and CO₂; surface formate works as a reductant of carbon dioxide to yield carbon monoxide. The dependence on the wavelength of irradiation light shows that a bulk ZrO₂ is not a photoactive species. When ZrO₂ adsorbs CO₂ a new band appears in photoluminescence excitation spectrum. The photoactive species in the reaction that CO₂+H₂ yields HCOO⁻ is presumably formed by the adsorption of CO₂ on ZrO₂ surface. Hydrogen molecules play a role to supply an atomic hydrogen. Therefore, methane molecules can also be used as a reductant of carbon dioxide.     

Effect of Zn on acetyl coenzyme a synthase: evidence for a conformational change in the alpha subunit during catalysis

Acetyl coenzyme A synthase (ACS) is an alpha2beta2 tetramer in which the active-site A-cluster, located in the alpha subunits, consists of an Fe4S4 cubane bridged to a {Nip Nid} binuclear site. The alpha subunits exist in two conformations. In the open conformation, Nip is surface-exposed, while the proximal metal is buried in the closed conformation. Nip is labile and can be replaced by Cu. In this study, the effects of Zn are reported. ACS in which Zn replaced Nip was inactive and did not exhibit the so-called NiFeC EPR signal nor the ability to accept a methyl group from the corrinoid-iron-sulfur protein (CoFeSP). Once Zn-bound, it could not be replaced by subsequently adding Ni. The Zn-bound A-cluster cannot be reduced and bound with CO or become methylated, probably because Zn (like Cu) is insufficiently nucleophilic for these functions. Unexpectedly, Zn replaced Nip only while ACS was engaged in catalysis. Under these conditions, replacement occurred with kapp approximately 0.6 min-1. Replacement was blocked by including EDTA in the assay mix. Zn appears to replace Nip when ACS is in an intermediate state (or states) of catalysis but this(these) state(s) must not be present when ACS is reduced in CO alone, or in the presence of CoA, CoFeSP, or reduced methyl viologen. Nip appears susceptible to Zn-attack when the alpha subunit is in the open conformation and protected from attack when it is in the closed conformation. This is the first evidence that the structurally-characterized conformations of the alpha subunit change during catalysis, indicating a mechanistic role for this conformational change.     

Stopped-Flow Kinetics of Methyl Group Transfer between the Corrinoid-Iron-Sulfur Protein and Acetyl-Coenzyme A Synthase from Clostridium thermoaceticum

Kinetics of methyl group transfer between the Ni-Fe-S-containing acetyl-CoA synthase (ACS) and the corrinoid protein (CoFeSP) from Clostridium thermoaceticum were investigated using the stopped-flow method at 390 nm. Rates of the reaction CH(3)-Co(3+)FeSP + ACS(red) <==> Co(1+)FeSP + CH(3)-ACS(ox) in both forward and reverse directions were determined using various protein and reductant concentrations. Ti(3+)citrate, dithionite, and CO were used to reductively activate ACS (forming ACS(red)). The simplest mechanism that adequately fit the data involved formation of a [CH(3)-Co(3+)FeSP]:[ACS(red)] complex, methyl group transfer (forming [Co(1+)FeSP]:[CH(3)-ACS(ox)]), product dissociation (forming Co(1+)FeSP + CH(3)-ACS(ox)), and CO binding yielding a nonproductive enzyme state (ACS(red) + CO <==> ACS(red)-CO). Best-fit rate constants were obtained. CO inhibited methyl group transfer by binding ACS(red) in accordance with K(D) = 180 +/- 90 microM. Fits were unimproved when >1 CO was assumed to bind. Ti(3+)citrate and dithionite inhibited the reverse methyl group transfer reaction, probably by reducing the D-site of CH(3)-ACS(ox). This redox site is oxidized by 2e(-) when the methyl cation is transferred from CH(3)-Co(3+)FeSP to ACS(red), and is reduced during the reverse reaction. Best-fit K(D) values for pre- and post-methyl-transfer complexes were 0.12 +/- 0.06 and 0.3 +/- 0.2 microM, respectively. Intracomplex methyl group transfer was reversible with K(eq) = 2.3 +/- 0.9 (k(f)/k(r) = 6.9 s(-1)/3.0 s(-1)). The nucleophilicity of the [Ni(2+)D(red)] unit appears comparable to that of Co(1+) cobalamins. Reduction of the D-site may cause the Ni(2+) of the A-cluster to behave like the Ni of an organometallic Ni(0) complex.     

A simple assay for formate dehydrogenase activity by gas chromatography-mass spectrometry.

A new method using GC-MS was devised for the convenient measurement of formate dehydrogenase (FDH) activity in crude tissue samples. FDH activity was detected by measuring headspace 13CO2, which was enzymically converted from [13C]formic acid. This method proved to be sensitive and simple for the estimation of FDH activity without complicated pretreatment.     

Direct synthesis of dimethyl carbonate from methanol and carbon dioxide using heteropolyoxometalates: the effects of cation and addenda atoms

The direct synthesis of dimethyl carbonate (DMC) from methanol and carbon dioxide over a series of Keggin-type heteropolyoxometalates has been investigated. The effects of the cations and the addenda atoms of the heteropolyoxometalate on the conversion and the product selectivities were investigated. The results showed that Co_1.5PW₁₂O₄₀ was the best catalyst of the series. The effect of reaction temperature and CO₂ pressure on the direct synthesis of DMC demonstrated that lower temperatures and higher pressures are favorable for the synthesis of DMC. Higher temperatures favor the formation of dimethoxymethane (DMM) and methyl formate (MF).     

Back Cover: Bio-Inspired Bimetallic Cooperativity Through a Hydrogen Bonding Spacer in CO2 Reduction (Angew. Chem. Int. Ed. 8/2023)

At the core of carbon monoxide dehydrogenase (CODH) active site two metal ions together with hydrogen bonding scheme from amino acids orchestrate the interconversion between CO₂ and CO. We have designed a molecular catalyst implementing a bimetallic iron complex with an embarked second coordination sphere with multi-point hydrogen-bonding interactions. We found that, when immobilized on carbon paper electrode, the dinuclear catalyst enhances up to four fold the heterogeneous CO₂ reduction to CO in water with an improved selectivity and stability compared to the mononuclear analogue. Interestingly, quasi-identical catalytic performances are obtained when one of the two iron centers was replaced by a redox inactive Zn metal, questioning the cooperative action of the two metals. Snapshots of X-ray structures indicate that the two metalloporphyrin units tethered by a urea group is a good compromise between rigidity and flexibility to accommodate CO₂ capture, activation, and reduction.