The hydrogenase activity of the molybdenum/copper-containing carbon monoxide dehydrogenase of Oligotropha carboxidovorans

CO Oxidation Mechanism of Silver-Substituted Mo/Cu CO-Dehydrogenase - Analogies and Differences to the Native Enzyme

The aerobic oxidation of carbon monoxide to carbon dioxide is catalysed by the Mo/Cu-containing CO-dehydrogenase enzyme in the soil bacterium Oligotropha carboxidovorans, enabling the organism to grow on the small gas molecule as carbon and energy source. It was shown experimentally that silver can be substituted for copper in the active site of Mo/Cu CODH to yield a functional enzyme. In this study, we employed QM/MM calculations to investigate whether the reaction mechanism of the silver-substituted enzyme is similar to that of the native enzyme. Our results suggest that the Ag-substituted enzyme can oxidize CO and release CO2 following the same reaction steps as the native enzyme, with a computed rate-limiting step of 10.4 kcal/mol, consistent with experimental findings. Surprisingly, lower activation energies for C-O bond formation have been found in the presence of silver. Furthermore, comparison of rate constants for reduction of copper- and silver-containing enzymes suggests a discrepancy in the transition state stabilization upon silver substitution. We also evaluated the effects that differences in the water-active site interaction may exert on the overall energy profile of catalysis. Finally, the formation of a thiocarbonate intermediate along the catalytic pathway was found to be energetically unfavorable for the Ag-substituted enzyme. This finding aligns with the hypothesis proposed for the wild-type form, suggesting that the creation of such species may not be necessary for the enzymatic catalysis of CO oxidation.

Molybdenum-Copper Antagonism In Metalloenzymes And Anti-Copper Therapy

The connection between 3d (Cu) and 4d (Mo) via the "Mo-S-Cu" unit is called Mo-Cu antagonism. Biology offers case studies of such interactions in metalloproteins such as Mo/Cu-CO Dehydrogenases (Mo/Cu-CODH), and Mo/Cu Orange Protein (Mo/Cu-ORP). The CODH significantly maintains the CO level in the atmosphere below the toxic level by converting it to non-toxic CO2 for respiring organisms. Several models were synthesized to understand the structure-function relationship of these native enzymes. However, this interaction was first observed in ruminants, and they convert molybdate (MoO4 2- ) into tetrathiomolybdate (MoS4 2- ; TTM), reacting with cellular Cu to yield biological unavailable Mo/S/Cu cluster, then developing Cu-deficiency diseases. These findings inspire the use of TTM as a Cu-sequester drug, especially for treating Cu-dependent human diseases such as Wilson diseases (WD) and cancer. It is well known that a balanced Cu homeostasis is essential for a wide range of biological processes, but negative consequence leads to cell toxicity. Therefore, this review aims to connect the Mo-Cu antagonism in metalloproteins and anti-copper therapy.

Studies Relevant to the Functional Model of Mo-Cu CODH: In Situ Reactions of Cu(I)-L Complexes with Mo(VI) and Synthesis of Stable Structurally Characterized Heterotetranuclear MoVI2CuI2 Complex

In this study, we report the synthesis, characterization, and reactions of Cu(I) complexes of the general form Cu(L)(LigH₂) (LigH₂ = xanthene-based heterodinucleating ligand (E)-3-(((5-(bis(pyridin-2-ylmethyl)amino)-2,7-di-tert-butyl-9,9-dimethyl-9H-xanthen-4-yl)imino)methyl)benzene-1,2-diol); L = PMe₃, PPh₃, CN(2,6-Me₂C₆H₃)). New complexes [Cu(PMe₃)(LigH₂)] and [CuCN(2,6-Me₂C₆H₃)(LigH₂)] were synthesized by treating [Cu(LigH₂)](PF₆) with trimethylphosphine and 2,6-dimethylphenyl isocyanide, respectively. These complexes were characterized by multinuclear NMR spectroscopy, IR spectroscopy, high-resolution mass spectrometry (HRMS), and X-ray crystallography. In contrast, attempted reactions of [Cu(LigH₂)](PF₆) with cyanide or styrene failed to produce isolable crystalline products. Next, the reactivity of these and previously synthesized Cu(I) phosphine and isocyanide complexes with molybdate was interrogated. IR (for isocyanide) and ³¹P NMR (for PPh₃/PMe₃) spectroscopy demonstrates the lack of oxidation reactivity. We also describe herein the first example of a structurally characterized multinuclear complex combining both Mo(VI) and Cu(I) metal ions within the same system. The heterobimetallic tetranuclear complex [Cu₂Mo₂O₄(μ₂-O)(Lig)₂]·HOSiPh₃ was obtained by the reaction of the silylated Mo(VI) precursor (Et₄N)(MoO₃(OSiPh₃)) with LigH₂, followed by the addition of [Cu(NCMe)₄](PF₆). This complex was characterized by NMR spectroscopy, high-resolution mass spectrometry, and X-ray crystallography.

Spectroscopic Studies of Mononuclear Molybdenum Enzyme Centers

A concise review is provided of the contributions that various spectroscopic methods have made to our understanding of the physical and electronic structures of mononuclear molybdenum enzymes. Contributions to our understanding of the structure and function of each of the major families of these enzymes is considered, providing a perspective on how spectroscopy has impacted the field.

Tungsten Enzyme Using Hydrogen as an Electron Donor to Reduce Carboxylic Acids and NAD. ACS Catal 2022;12:8707-8717. [PMID: 35874620 PMCID: PMC9295118 DOI: 10.1021/acscatal.2c02147]

Tungsten-dependent aldehyde oxidoreductases (AORs) catalyze the oxidation of aldehydes to acids and are the only known enzymes reducing non-activated acids using electron donors with low redox potentials. We report here that AOR from Aromatoleum aromaticum (AOR_Aa) catalyzes the reduction of organic acids not only with low-potential Eu(II) or Ti(III) complexes but also with H₂ as an electron donor. Additionally, AOR_Aa catalyzes the H₂-dependent reduction of NAD⁺ or benzyl viologen. The rate of H₂-dependent NAD⁺ reduction equals to 10% of that of aldehyde oxidation, representing the highest H₂ turnover rate observed among the Mo/W enzymes. As AOR_Aa simultaneously catalyzes the reduction of acids and NAD⁺, we designed a cascade reaction utilizing a NAD(P)H-dependent alcohol dehydrogenase to reduce organic acids to the corresponding alcohols with H₂ as the only reductant. The newly discovered W-hydrogenase side activity of AOR_Aa may find applications in either NADH recycling or conversion of carboxylic acids to more useful biochemicals.

Application of EPR and related methods to molybdenum-containing enzymes

A description is provided of the contributions made to our understanding of molybdenum-containing enzymes through the application of electron paramagnetic resonance spectroscopy and related methods, by way of illustrating how these can be applied to better understand enzyme structure and function. An emphasis is placed on the use of EPR to identify both the coordination environment of the molybdenum coordination sphere as well as the structures of paramagnetic intermediates observed transiently in the course of reaction that have led to the elucidation of reaction mechanism.

Can water act as a nucleophile in CO oxidation catalysed by Mo/Cu CO-dehydrogenase? Answers from theory

The aerobic CO dehydrogenase from Oligotropha carboxidovorans is an environmentally crucial bacterial enzyme for maintenance of subtoxic concentration of CO in the lower atmosphere, as it allows for the oxidation of CO to CO₂ which takes place at its Mo−Cu heterobimetallic active site. Despite extensive experimental and theoretical efforts, significant uncertainties still concern the reaction mechanism for the CO oxidation. In this work, we used the hybrid quantum mechanical/molecular mechanical approach to evaluate whether a water molecule present in the active site might act as a nucleophile upon formation of the new C−O bond, a hypothesis recently suggested in the literature. Our study shows that activation of H₂O can be favoured by the presence of the Mo=O_eq group. However, overall our results suggest that mechanisms other than the nucleophilic attack by Mo=O_eq to the activated carbon of the CO substrate are not likely to constitute reactive channels for the oxidation of CO by the enzyme.

Exploiting Aerobic Carboxydotrophic Bacteria for Industrial Biotechnology

Aerobic carboxydotrophic bacteria are a group of microorganisms which possess the unique trait to oxidize carbon monoxide (CO) as sole energy source with molecular oxygen (O₂) to produce carbon dioxide (CO₂) which subsequently is used for biomass formation via the Calvin-Benson-Bassham cycle. Moreover, most carboxydotrophs are also able to oxidize hydrogen (H₂) with hydrogenases to drive the reduction of carbon dioxide in the absence of CO. As several abundant industrial off-gases contain significant amounts of CO, CO₂, H₂ as well as O₂, these bacteria come into focus for industrial application to produce chemicals and fuels from such gases in gas fermentation approaches. Since the group of carboxydotrophic bacteria is rather unknown and not very well investigated, we will provide an overview about their lifestyle and the underlying metabolic characteristics, introduce promising members for industrial application, and give an overview of available genetic engineering tools. We will point to limitations and discuss challenges, which have to be overcome to apply metabolic engineering approaches and to utilize aerobic carboxydotrophs in the industrial environment.

QM/MM study of the binding of H2 to MoCu CO dehydrogenase: development and applications of improved H2 van der Waals parameters

The MoCu CO dehydrogenase enzyme not only transforms CO into CO₂ but it can also oxidise H₂. Even if its hydrogenase activity has been known for decades, a debate is ongoing on the most plausible mode for the binding of H₂ to the enzyme active site and the hydrogen oxidation mechanism. In the present work, we provide a new perspective on the MoCu-CODH hydrogenase activity by improving the in silico description of the enzyme. Energy refinement—by means of the BigQM approach—was performed on the intermediates involved in the dihydrogen oxidation catalysis reported in our previously published work (Rovaletti, et al. “Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase.” Inorganics 7 (2019) 135). A suboptimal description of the H₂–HN(backbone) interaction was observed when the van der Waals parameters described in previous literature for H₂ were employed. Therefore, a new set of van der Waals parameters is developed here in order to better describe the hydrogen–backbone interaction. They give rise to improved binding modes of H₂ in the active site of MoCu CO dehydrogenase. Implications of the resulting outcomes for a better understanding of hydrogen oxidation catalysis mechanisms are proposed and discussed.

Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase

The Mo/Cu-dependent CO dehydrogenase from O. carboxydovorans is an enzyme that is able to catalyse CO oxidation to CO 2 ; moreover, it also expresses hydrogenase activity, as it is able to oxidize H 2 . Here, we have studied the dihydrogen oxidation catalysis by this enzyme using QM/MM calculations. Our results indicate that the equatorial oxo ligand of Mo is the best suited base for catalysis. Moreover, extraction of the first proton from H 2 by means of this basic centre leads to the formation of a Mo–OH–Cu I H hydride that allows for the stabilization of the copper hydride, otherwise known to be very unstable. In light of our results, two mechanisms for the hydrogenase activity of the enzyme are proposed. The first reactive channel depends on protonation of the sulphur atom of a Cu-bound cysteine residues, which appears to favour the binding and activation of the substrate. The second reactive channel involves a frustrated Lewis pair, formed by the equatorial oxo group bound to Mo and by the copper centre. In this case, no binding of the hydrogen molecule to the Cu center is observed but once H 2 enters into the active site, it can be split following a low-energy path.

The Challenging in silico Description of Carbon Monoxide Oxidation as Catalyzed by Molybdenum-Copper CO Dehydrogenase

Carbon monoxide (CO) is a highly toxic gas to many living organisms. However, some microorganisms are able to use this molecule as the sole source of carbon and energy. Soil bacteria such as the aerobic Oligotropha carboxidovorans are responsible for the annual removal of about 2x108 tons of CO from the atmosphere. Detoxification through oxidation of CO to CO2 is enabled by the MoCu-dependent CO-dehydrogenase enzyme (MoCu-CODH) which-differently from other enzyme classes with similar function-retains its catalytic activity in the presence of atmospheric O2. In the last few years, targeted advancements have been described in the field of bioengineering and biomimetics, which is functional for future technological exploitation of the catalytic properties of MoCu-CODH and for the reproduction of its reactivity in synthetic complexes. Notably, a growing interest for the quantum chemical investigation of this enzyme has recently also emerged. This mini-review compiles the current knowledge of the MoCu-CODH catalytic cycle, with a specific focus on the outcomes of theoretical studies on this enzyme class. Rather controversial aspects from different theoretical studies will be highlighted, thus illustrating the challenges posed by this system as far as the application of density functional theory and hybrid quantum-classical methods are concerned.

Carbon Monoxide Dehydrogenases

Carbon monoxide dehydrogenases (CODHs) catalyze the reversible oxidation of CO with water to CO₂, two electrons, and two protons. Two classes of CODHs exist, having evolved from different scaffolds featuring active sites built from different transition metals. The basic properties of both classes are described in this overview chapter.

Something special about CO-dependent CO2 fixation

Carbon dioxide enters metabolism via six known CO₂ fixation pathways, of which only one is linear, exergonic in the direction of CO₂‐assimilation, and present in both bacterial and archaeal anaerobes – the Wood‐Ljungdahl (WL) or reductive acetyl‐CoA pathway. Carbon monoxide (CO) plays a central role in the WL pathway as an energy rich intermediate. Here, we scan the major biochemical reaction databases for reactions involving CO and CO₂. We identified 415 reactions corresponding to enzyme commission (EC) numbers involving CO₂, which are non‐randomly distributed across different biochemical pathways. Their taxonomic distribution, reversibility under physiological conditions, cofactors and prosthetic groups are summarized. In contrast to CO₂, only 15 reaction classes involving CO were detected. Closer inspection reveals that CO interfaces with metabolism and the carbon cycle at only two enzymes: anaerobic carbon monoxide dehydrogenase (CODH), a Ni‐ and Fe‐containing enzyme that generates CO for CO₂ fixation in the WL pathway, and aerobic CODH, a Mo‐ and Cu‐containing enzyme that oxidizes environmental CO as an electron source. The CO‐dependent reaction of the WL pathway involves carbonyl insertion into a methyl carbon‐nickel at the Ni‐Fe‐S A‐cluster of acetyl‐CoA synthase (ACS). It appears that no alternative mechanisms to the CO‐dependent reaction of ACS have evolved in nearly 4 billion years, indicating an ancient and mechanistically essential role for CO at the onset of metabolism.

Models for aerobic carbon monoxide dehydrogenase: synthesis, characterization and reactivity of paramagnetic MoVO(μ-S)CuI complexes

Complexes exhibiting the Mo^VO(μ-S)Cu^I cores, EPR properties, electronic structures and biomimetic reactions of aerobic Mo/Cu-containing carbon monoxide dehydrogenases are reported.

Reaction of [CoCp₂][Tp^iPrMoOS(OAr)] [Cp = η⁵-cyclopentadienyl; Tp^iPr = hydrotris(3-isopropylpyrazol-1-yl)borate; OAr = phenolate or derivative thereof] with [Cu(NCMe)(Me₃tcn)]BF₄ (Me₃tcn = 1,4,7-trimethyl-1,4,7-triazacyclononane) in MeCN at –30 °C results in the formation of red-brown/black, paramagnetic, μ-sulfido-Mo(v)/Cu(i) complexes, Tp^iPrMoO(OAr)(μ-S)Cu(Me₃tcn). The complexes possess the MoO(μ-S)Cu core found in aerobic carbon monoxide dehydrogenases (CODHs) and exhibit X-band EPR spectra closely related to those of semi-reduced CODH, with g_iso ∼ 1.937, hyperfine coupling to ^95,97Mo (a_iso = 39–42 × 10^–4 cm^–1) and strong superhyperfine coupling to ^63,65Cu (a_iso = 34–63 × 10^–4 cm^–1). Anisotropic spectra exhibit monoclinic symmetry with g₁ ∼ 1.996, g₂ ∼ 1.944 and g₃ ∼ 1.882, and nearly isotropic A_Cu values (75–90 × 10^–4 cm^–1). The X-ray structures of four derivatives (Ar = Ph, C₆H₄^tBu-2, C₆H₄^sBu-2, C₆H₄Ph-4) are reported and discussed along with that of the Ar = C₆H₃^tBu₂-3,5 derivative (communicated in C. Gourlay, D. J. Nielsen, J. M. White, S. Z. Knottenbelt, M. L. Kirk and C. G. Young, J. Am. Chem. Soc., 2006, 128, 2164). The complexes exhibit distorted octahedral oxo-Mo(v) and distorted tetrahedral Cu(i) centres bridged by a single bent μ-sulfido ligand, with Mo–S and Cu–S distances and Mo–S–Cu angles in the ranges 2.262–2.300 Å, 2.111–2.134 Å and 115.87–134.27°, respectively. The 2 t-butyl derivative adopts a unique phenolate conformation with O Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> Mo–O–Cα and O Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> Mo–S–Cu torsion angles of 92.7 and 21.1°, respectively, very different from those of the other structurally characterized derivatives (31–47 and 33–45°, respectively) and exhibits a relatively short Mo···Cu distance [3.752(2) Å vs. 3.806(7)–4.040(2) Å]. As well, the a_Cu value of this complex (34.3 × 10^–4 cm^–1) is much lower than the values observed for other members of the series (55–63 × 10^–4 cm^–1), supporting the hypothesis that the electronic structure of the MoO(μ-S)Cu core unit and the degree of intermetallic communication are strongly dependent on the geometry of the MoO(OR)(μ-S)Cu unit. The complexes participate in an electrochemically reversible Mo(vi)/Mo(v) redox couple and react with cyanide undergoing decupration and desulfurization reactions of the type observed for CODH.

CODH-IV: A High-Efficiency CO-Scavenging CO Dehydrogenase with Resistance to O2

CO dehydrogenases (CODHs) catalyse the reversible conversion between CO and CO₂ . Genomic analysis indicated that the metabolic functions of CODHs vary. The genome of Carboxydothermus hydrogenoformans encodes five CODHs (CODH-I-V), of which CODH-IV is found in a gene cluster near a peroxide-reducing enzyme. Our kinetic and crystallographic experiments reveal that CODH-IV differs from other CODHs in several characteristic properties: it has a very high affinity for CO, oxidizes CO at diffusion-limited rate over a wide range of temperatures, and is more tolerant to oxygen than CODH-II. Thus, our observations support the idea that CODH-IV is a CO scavenger in defence against oxidative stress and highlight that CODHs are more diverse in terms of reactivity than expected.

A theoretical study on the reactivity of the Mo/Cu-containing carbon monoxide dehydrogenase with dihydrogen

The Mo/Cu-dependent CO dehydrogenase from Oligotropha carboxidovorans is an enzyme that is able to catalyze CO oxidation to CO2; moreover, it can also oxidize H2, thus eliciting a characteristic EPR signal. Interestingly, the Ag-substituted enzyme form proved unable to catalyze H2 oxidation. In the present contribution, we characterized the reactivity of the enzyme with H2 by quantum-chemical calculations. It was found that dihydrogen binding to the wild-type enzyme requires significant structural rearrangements of the active site Theoretical EPR spectra for plausible H2-bound models of the partially reduced, paramagnetic active site are also presented and compared with the experimental counterpart. Finally, density functional theory modeling shows that Ag substitution impairs H2 binding at the active site.

Electronic structure contributions to reactivity in xanthine oxidase family enzymes

We review the xanthine oxidase (XO) family of pyranopterin molybdenum enzymes with a specific emphasis on electronic structure contributions to reactivity. In addition to xanthine and aldehyde oxidoreductases, which catalyze the two-electron oxidation of aromatic heterocycles and aldehyde substrates, this mini-review highlights recent work on the closely related carbon monoxide dehydrogenase (CODH) that catalyzes the oxidation of CO using a unique Mo-Cu heterobimetallic active site. A primary focus of this mini-review relates to how spectroscopy and computational methods have been used to develop an understanding of critical relationships between geometric structure, electronic structure, and catalytic function.

Orbital contributions to CO oxidation in Mo-Cu carbon monoxide dehydrogenase

A molecular orbital analysis provides new insight into the mechanism of Mo/Cu carbon monoxide dehydrogenase, and reveals electronic structure contributions to reactivity that are remarkably similar to the structurally related molybdenum hydroxylases. A calculated reaction barrier of ~12 kcal mol(-1) is in excellent agreement with experiment.