Reaction mechanism of formate dehydrogenase studied by computational methods

An allosteric redox switch involved in oxygen protection in a CO2 reductase

Metal-dependent formate dehydrogenases reduce CO2 with high efficiency and selectivity, but are usually very oxygen sensitive. An exception is Desulfovibrio vulgaris W/Sec-FdhAB, which can be handled aerobically, but the basis for this oxygen tolerance was unknown. Here we show that FdhAB activity is controlled by a redox switch based on an allosteric disulfide bond. When this bond is closed, the enzyme is in an oxygen-tolerant resting state presenting almost no catalytic activity and very low formate affinity. Opening this bond triggers large conformational changes that propagate to the active site, resulting in high activity and high formate affinity, but also higher oxygen sensitivity. We present the structure of activated FdhAB and show that activity loss is associated with partial loss of the metal sulfido ligand. The redox switch mechanism is reversible in vivo and prevents enzyme reduction by physiological formate levels, conferring a fitness advantage during O2 exposure.

Transcriptional Reprogramming of Candida tropicalis in Response to Isoespintanol Treatment

Candida tropicalis, an opportunistic pathogen, ranks among the primary culprits of invasive candidiasis, a condition notorious for its resistance to conventional antifungal drugs. The urgency to combat these drug-resistant infections has spurred the quest for novel therapeutic compounds, with a particular focus on those of natural origin. In this study, we set out to evaluate the impact of isoespintanol (ISO), a monoterpene derived from Oxandra xylopioides, on the transcriptome of C. tropicalis. Leveraging transcriptomics, our research aimed to unravel the intricate transcriptional changes induced by ISO within this pathogen. Our differential gene expression analysis unveiled 186 differentially expressed genes (DEGs) in response to ISO, with a striking 85% of these genes experiencing upregulation. These findings shed light on the multifaceted nature of ISO's influence on C. tropicalis, spanning a spectrum of physiological, structural, and metabolic adaptations. The upregulated DEGs predominantly pertained to crucial processes, including ergosterol biosynthesis, protein folding, response to DNA damage, cell wall integrity, mitochondrial activity modulation, and cellular responses to organic compounds. Simultaneously, 27 genes were observed to be repressed, affecting functions such as cytoplasmic translation, DNA damage checkpoints, membrane proteins, and metabolic pathways like trans-methylation, trans-sulfuration, and trans-propylamine. These results underscore the complexity of ISO's antifungal mechanism, suggesting that it targets multiple vital pathways within C. tropicalis. Such complexity potentially reduces the likelihood of the pathogen developing rapid resistance to ISO, making it an attractive candidate for further exploration as a therapeutic agent. In conclusion, our study provides a comprehensive overview of the transcriptional responses of C. tropicalis to ISO exposure. The identified molecular targets and pathways offer promising avenues for future research and the development of innovative antifungal therapies to combat infections caused by this pathogenic yeast.

Structure and function relationship of formate dehydrogenases: an overview of recent progress

Formate dehydrogenases (FDHs) catalyze the two-electron oxidation of formate to carbon dioxide. FDHs can be divided into several groups depending on their subunit composition and active-site metal ions. Metal-dependent (Mo- or W-containing) FDHs from prokaryotic organisms belong to the superfamily of molybdenum enzymes and are members of the dimethylsulfoxide reductase family. In this short review, recent progress in the structural analysis of FDHs together with their potential biotechnological applications are summarized.

Biological and Catalytic Properties of Selenoproteins

Selenocysteine is a catalytic residue at the active site of all selenoenzymes in bacteria and mammals, and it is incorporated into the polypeptide backbone by a co-translational process that relies on the recoding of a UGA termination codon into a serine/selenocysteine codon. The best-characterized selenoproteins from mammalian species and bacteria are discussed with emphasis on their biological function and catalytic mechanisms. A total of 25 genes coding for selenoproteins have been identified in the genome of mammals. Unlike the selenoenzymes of anaerobic bacteria, most mammalian selenoenzymes work as antioxidants and as redox regulators of cell metabolism and functions. Selenoprotein P contains several selenocysteine residues and serves as a selenocysteine reservoir for other selenoproteins in mammals. Although extensively studied, glutathione peroxidases are incompletely understood in terms of local and time-dependent distribution, and regulatory functions. Selenoenzymes take advantage of the nucleophilic reactivity of the selenolate form of selenocysteine. It is used with peroxides and their by-products such as disulfides and sulfoxides, but also with iodine in iodinated phenolic substrates. This results in the formation of Se-X bonds (X = O, S, N, or I) from which a selenenylsulfide intermediate is invariably produced. The initial selenolate group is then recycled by thiol addition. In bacterial glycine reductase and D-proline reductase, an unusual catalytic rupture of selenium-carbon bonds is observed. The exchange of selenium for sulfur in selenoproteins, and information obtained from model reactions, suggest that a generic advantage of selenium compared with sulfur relies on faster kinetics and better reversibility of its oxidation reactions.

Electrochemical Kinetics Support a Second Coordination Sphere Mechanism in Metal-Based Formate Dehydrogenase

Metal-based formate dehydrogenases are molybdenum or tungsten-dependent enzymes that catalyze the interconversion between formate and CO₂ . According to the current consensus, the metal ion of the catalytic center in its active form is coordinated by 6 S (or 5 S and 1 Se) atoms, leaving no free coordination sites to which formate could bind to the metal. Some authors have proposed that one of the active site ligands decoordinates during turnover to allow formate binding. Another proposal is that the oxidation of formate takes place in the second coordination sphere of the metal. Here, we have used electrochemical steady-state kinetics to elucidate the order of the steps in the catalytic cycle of two formate dehydrogenases. Our results strongly support the "second coordination sphere" hypothesis.

Tracking W-Formate Dehydrogenase Structural Changes During Catalysis and Enzyme Reoxidation

Metal-dependent formate dehydrogenases (Fdh) catalyze the reversible conversion of CO₂ to formate, with unrivalled efficiency and selectivity. However, the key catalytic aspects of these enzymes remain unknown, preventing us from fully benefiting from their capabilities in terms of biotechnological applications. Here, we report a time-resolved characterization by X-ray crystallography of the Desulfovibrio vulgaris Hildenborough SeCys/W-Fdh during formate oxidation. The results allowed us to model five different intermediate structures and to chronologically map the changes occurring during enzyme reduction. Formate molecules were assigned for the first time to populate the catalytic pocket of a Fdh. Finally, the redox reversibility of DvFdhAB in crystals was confirmed by reduction and reoxidation structural studies.

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.

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Gases like H₂, N₂, CO₂, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N₂, CO₂, and CO and the production of H₂ require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N₂ fixation by nitrogenase and H₂ production by hydrogenase as well as CO₂ and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.

Spectroscopic and Structural Characterization of Reduced Desulfovibrio vulgaris Hildenborough W-FdhAB Reveals Stable Metal Coordination during Catalysis

Metal-dependent formate dehydrogenases are important enzymes due to their activity of CO₂ reduction to formate. The tungsten-containing FdhAB formate dehydrogenase from Desulfovibrio vulgaris Hildenborough is a good example displaying high activity, simple composition, and a notable structural and catalytic robustness. Here, we report the first spectroscopic redox characterization of FdhAB metal centers by EPR. Titration with dithionite or formate leads to reduction of three [4Fe-4S]¹⁺ clusters, and full reduction requires Ti(III)-citrate. The redox potentials of the four [4Fe-4S]¹⁺ centers range between -250 and -530 mV. Two distinct W^V signals were detected, W_D^V and W_F^V, which differ in only the g₂-value. This difference can be explained by small variations in the twist angle of the two pyranopterins, as determined through DFT calculations of model compounds. The redox potential of W^VI/V was determined to be -370 mV when reduced by dithionite and -340 mV when reduced by formate. The crystal structure of dithionite-reduced FdhAB was determined at high resolution (1.5 Å), revealing the same structural alterations as reported for the formate-reduced structure. These results corroborate a stable six-ligand W coordination in the catalytic intermediate W^V state of FdhAB.

Membrane-anchored HDCR nanowires drive hydrogen-powered CO2 fixation

Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive¹. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO₂ fixation-hydrogen-dependent CO₂ reductase (HDCR)^2,3-which directly converts H₂ and CO₂ into formic acid. HDCR reduces CO₂ with a higher activity than any other known biological or chemical catalyst^4,5, and it has therefore gained considerable interest in two areas of global relevance: hydrogen storage and combating climate change by capturing atmospheric CO₂. However, the mechanistic basis of the high catalytic turnover rate of HDCR has remained unknown. Here we use cryo-electron microscopy to reveal the structure of a short HDCR filament from the acetogenic bacterium Thermoanaerobacter kivui. The minimum repeating unit is a hexamer that consists of a formate dehydrogenase (FdhF) and two hydrogenases (HydA2) bound around a central core of hydrogenase Fe-S subunits, one HycB3 and two HycB4. These small bacterial polyferredoxin-like proteins oligomerize through their C-terminal helices to form the backbone of the filament. By combining structure-directed mutagenesis with enzymatic analysis, we show that filamentation and rapid electron transfer through the filament enhance the activity of HDCR. To investigate the structure of HDCR in situ, we imaged T. kivui cells with cryo-electron tomography and found that HDCR filaments bundle into large ring-shaped superstructures attached to the plasma membrane. This supramolecular organization may further enhance the stability and connectivity of HDCR to form a specialized metabolic subcompartment within the cell.

Influence of the Greater Protein Environment on the Electrostatic Potential in Metalloenzyme Active Sites: The Case of Formate Dehydrogenase

The Mo/W-containing metalloenzyme formate dehydrogenase (FDH) is an efficient and selective natural catalyst that reversibly converts CO₂ to formate under ambient conditions. In this study, we investigate the impact of the greater protein environment on the electrostatic potential (ESP) of the active site. To model the enzyme environment, we used a combination of classical molecular dynamics and multiscale quantum-mechanical (QM)/molecular-mechanical (MM) simulations. We leverage charge shift analysis to systematically construct QM regions and analyze the electronic environment of the active site by evaluating the degree of charge transfer between the core active site and the protein environment. The contribution of the terminal chalcogen ligand to the ESP of the metal center is substantial and dependent on the chalcogen identity, with similar, less negative ESPs for Se and S terminal chalcogens in comparison to O regardless of whether the metal is Mo or W. The orientation of the side chains and conformations of the cofactor also affect the ESP, highlighting the importance of sampling dynamic fluctuations in the protein. Overall, our observations suggest that the terminal chalcogen ligand identity plays an important role in the enzymatic activity of FDH, suggesting opportunities for a rational bioinspired catalyst design.

Molecular Catalysts with Diphosphine Ligands Containing Pendant Amines

Pendant amines play an invaluable role in chemical reactivity, especially for molecular catalysts based on earth-abundant metals. As inspired by [FeFe]-hydrogenases, which contain a pendant amine positioned for cooperative bifunctionality, synthetic catalysts have been developed to emulate this multifunctionality through incorporation of a pendant amine in the second coordination sphere. Cyclic diphosphine ligands containing two amines serve as the basis for a class of catalysts that have been extensively studied and used to demonstrate the impact of a pendant base. These 1,5-diaza-3,7-diphosphacyclooctanes, now often referred to as "P₂N₂" ligands, have profound effects on the reactivity of many catalysts. The resulting [Ni(P^R₂N^R'₂)₂]²⁺ complexes are electrocatalysts for both the oxidation and production of H₂. Achieving the optimal benefit of the pendant amine requires that it has suitable basicity and is properly positioned relative to the metal center. In addition to the catalytic efficacy demonstrated with [Ni(P^R₂N^R'₂)₂]²⁺ complexes for the oxidation and production of H₂, catalysts with diphosphine ligands containing pendant amines have also been demonstrated for several metals for many different reactions, both in solution and immobilized on surfaces. The impact of pendant amines in catalyst design continues to expand.

Energetics for CO2 Reduction by Molybdenum-Containing Formate Dehydrogenase

The level of carbon dioxide in the atmosphere has increased in a dangerous way during the past century. Methods to decrease this level are therefore of high interest at present. Inspiration to do so in an efficient way could come from biological systems. Molybdenum-containing formate dehydrogenase (Mo-FDH) is one of the most interesting enzymes in this respect. For example, the reduction potential required is not very low. The normal reaction catalyzed by Mo-FDH is actually the opposite one of oxidizing formate to CO₂. However, recent electrochemical studies have shown that the reaction can be reversed by a moderate lowering of the reduction potential. The goal of the present study has been to study the full mechanism of Mo-FDH, particularly in the most interesting direction of reducing CO₂, which has not been done before. The methods used are the same as those that have been shown to give excellent results for redox enzymes in all cases they have been tested. The results obtained for Mo-FDH are also in excellent agreement with the experimental results.

Enzymes for Efficient CO2 Conversion

The accumulation of carbon dioxide in the atmosphere as a result of human activities has caused a number of adverse circumstances in the world. For this reason, the proposed solutions lie within the aim of reducing carbon dioxide emissions have been quite valuable. However, as the human activity continues to increase on this planet, the possibility of reducing carbon dioxide emissions decreases with the use of conventional methods. The emergence of compounds than can be used in different fields by converting the released carbon dioxide into different chemicals will construct a fundamental solution to the problem. Although electro-catalysis or photolithography methods have emerged for this purpose, they have not been able to achieve successful results. Alternatively, another proposed solution are enzyme based systems. Among the enzyme-based systems, pyruvate decarboxylase, carbonic anhydrase and dehydrogenases have been the most studied enzymes. Pyruvate dehydrogenase and carbonic anhydrase have either been an expensive method or were incapable of producing the desired result due to the reaction cascade they catalyze. However, the studies reporting the production of industrial chemicals from carbon dioxide using dehydrogenases and in particular, the formate dehydrogenase enzyme, have been remarkable. Moreover, reported studies have shown the existence of more active and stable enzymes, especially the dehydrogenase family that can be identified from the biome. In addition to this, their redesign through protein engineering can have an immense contribution to the increased use of enzyme-based methods in CO₂ reduction, resulting in an enormous expansion of the industrial capacity.

The complete catalytic mechanism of xanthine oxidase: a computational study

In this article, quantum mechanical/molecular mechanical (QM/MM) methods were used to study the full catalytic mechanism of xanthine oxidase (XO).

Reaction mechanism of lysyl oxidase-like 2 (LOXL2) studied by computational methods

Lysyl oxidase-like 2 (LOXL2) is a copper-dependent amine oxidase that catalyzes the oxidative deamination of the ε-amino group of lysines/hydroxylysines on substrate proteins (collagen and elastin) to form aldehyde groups. The generated aldehyde groups are of significance in crosslinking with the adjacent aldehyde or ε-amino group on proteins in extracellular matrix. In this paper, we have studied the reaction mechanism of LOXL2 by means of quantum mechanics (QM) and combined QM and molecular mechanics (QM/MM) methods. This study is divided into two parts, i.e. the biosynthesis of lysine tyrosylquinone (LTQ) cofactor and oxidative deamination of ε-amino group of lysine by LTQ. For the former part, the reaction is driven by a large exothermicity of about 284 kJ/mol. Dopaquinone radical (DPQr) is suggested to be an intermediate state in this reaction. In addition, His652 residue is predicted to serve as proton acceptor. The rate-determining step for the biosynthesis of LTQ is found to be hydrogen-atom abstraction from the benzene ring on substrate by Cu²⁺-hydroxide, which is a proton-coupled electron transfer (PCET) process with an energy barrier of 84 kJ/mol. For the latter part, the reaction is exothermic by about 145 kJ/mol, and the copper ion is proposed to play a role of redox catalyst in the last step to generate the product of aldehyde. However, the copper ion might not be indispensable for the latter part, which is consistent with the previous study.

Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview

Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.

Direct electrochemical reduction of carbon dioxide by a molybdenum-containing formate dehydrogenase

Formate dehydrogenase enzymes catalyse the reversible two-electron oxidation of formate to carbon dioxide. The class of metal-dependent formate dehydrogenases comprises prokaryotic enzymes holding redox-active centres and a catalytic site, containing either molybdenum or tungsten ion, that mediates the formate/carbon dioxide interconversion. The carbon dioxide reduction is of a particular interest, since it may be a route for its atmospheric mitigation with the simultaneous production of added-value products, as formate-derived compounds. Recently, the periplasmic formate dehydrogenase from Desulfovibrio desulfuricans, a molybdenum-containing enzyme, was proven to be an efficient enzyme for the CO₂ reduction to formate. In this work, the immobilized formate dehydrogenase isolated from Desulfovibrio desulfuricans direct electrochemical behaviour was attained in the presence and absence of substrates and the formal potentials associated with the catalytic centre transitions were determined in non-turnover conditions. The enzyme catalytic activity towards carbon dioxide reduction was observed using direct electrochemical methods.

Reactivity of a biomimetic W(iv) bis-dithiolene complex with CO2 leading to formate production and structural rearrangement

A mononuclear W(iv) bis-dithiolene complex reduces CO₂ to formate while generating a dinuclear W(v) complex.