Implications of a Carboxylate-Bound C-Cluster Structure of Carbon Monoxide Dehydrogenase

The Moon-Forming Impact and the Autotrophic Origin of Life

The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.

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.

Sulfide and transition metals - A partnership for life

Sulfide and transition metals often came together in Biology. The variety of possible structural combinations enabled living organisms to evolve an array of highly versatile metal-sulfide centers to fulfill different physiological roles. The ubiquitous iron‑sulfur centers, with their structural, redox, and functional diversity, are certainly the best-known partners, but other metal-sulfide centers, involving copper, nickel, molybdenum or tungsten, are equally crucial for Life. This review provides a concise overview of the exclusive sulfide properties as a metal ligand, with emphasis on the structural aspects and biosynthesis. Sulfide as catalyst and as a substrate is discussed. Different enzymes are considered, including xanthine oxidase, formate dehydrogenases, nitrogenases and carbon monoxide dehydrogenases. The sulfide effect on the activity and function of iron‑sulfur, heme and zinc proteins is also addressed.

First-Principles Calculations on Ni,Fe-Containing Carbon Monoxide Dehydrogenases Reveal Key Stereoelectronic Features for Binding and Release of CO2 to/from the C-Cluster

In view of the depletion of fossil fuel reserves and climatic effects of greenhouse gas emissions, Ni,Fe-containing carbon monoxide dehydrogenase (Ni-CODH) enzymes have attracted increasing interest in recent years for their capability to selectively catalyze the reversible reduction of CO₂ to CO (CO₂ + 2H⁺ + 2e^– CO + H₂O). The possibility of converting the greenhouse gas CO₂ into useful materials that can be used as synthetic building blocks or, remarkably, as carbon fuels makes Ni-CODH a very promising target for reverse-engineering studies. In this context, in order to provide insights into the chemical principles underlying the biological catalysis of CO₂ activation and reduction, quantum mechanics calculations have been carried out in the framework of density functional theory (DFT) on different-sized models of the Ni-CODH active site. With the aim of uncovering which stereoelectronic properties of the active site (known as the C-cluster) are crucial for the efficient binding and release of CO₂, different coordination modes of CO₂ to different forms and redox states of the C-cluster have been investigated. The results obtained from this study highlight the key role of the protein environment in tuning the reactivity and the geometry of the C-cluster. In particular, the protonation state of His93 is found to be crucial for promoting the binding or the dissociation of CO₂. The oxidation state of the C-cluster is also shown to be critical. CO₂ binds to C_red2 according to a dissociative mechanism (i.e., CO₂ binds to the C-cluster after the release of possible ligands from Fe_u) when His93 is doubly protonated. CO₂ can also bind noncatalytically to C_red1 according to an associative mechanism (i.e., CO₂ binding is preceded by the binding of H₂O to Fe_u). Conversely, CO₂ dissociates when His93 is singly protonated and the C-cluster is oxidized at least to the C_int redox state.

Density functional theory was used to investigate Ni,Fe-containing carbon monoxide dehydrogenase enzymes. Different coordination modes of the substrate CO₂ to several forms and redox states of the C-cluster—the enzyme active site—were considered. The obtained results highlight the key role of the protein environment in tuning the reactivity and the geometry of the C-cluster. This helps to uncover which stereoelectronic properties of the active site are crucial for the efficient binding and release of CO₂.

The two CO-dehydrogenases of Thermococcus sp. AM4

Ni-containing CO-dehydrogenases (CODHs) allow some microorganisms to couple ATP synthesis to CO oxidation, or to use either CO or CO₂ as a source of carbon. The recent detailed characterizations of some of them have evidenced a great diversity in terms of catalytic properties and resistance to O₂. In an effort to increase the number of available CODHs, we have heterologously produced in Desulfovibrio fructosovorans, purified and characterized the two CooS-type CODHs (CooS1 and CooS2) from the hyperthermophilic archaeon Thermococcus sp. AM4 (Tc). We have also crystallized CooS2, which is coupled in vivo to a hydrogenase. CooS1 and CooS2 are homodimers, and harbour five metalloclusters: two [Ni4Fe-4S] C clusters, two [4Fe-4S] B clusters and one interfacial [4Fe-4S] D cluster. We show that both are dependent on a maturase, CooC1 or CooC2, which is interchangeable. The homologous protein CooC3 does not allow Ni insertion in either CooS. The two CODHs from Tc have similar properties: they can both oxidize and produce CO. The Michaelis constants (K_m) are in the microM range for CO and in the mM range (CODH 1) or above (CODH 2) for CO₂. Product inhibition is observed only for CO₂ reduction, consistent with CO₂ binding being much weaker than CO binding. The two enzymes are rather O₂ sensitive (similarly to CODH II from Carboxydothermus hydrogenoformans), and react more slowly with O₂ than any other CODH for which these data are available.

A dual-responsive colorimetric probe for the detection of Cu2+ and Ni2+ species in real water samples and human serum

The monitoring of heavy transition metals has increasingly attracted great attention because they pollute the environment and have unique physiological functions. Chemosensors are useful tools for monitoring heavy transition metals due to their simple visualization, excellent sensitivity and high selectivity. Herein, we have developed a novel chemosensor for the detection of water-soluble Cu2+ and Ni2+ species with different mechanisms, and low detection limits of 2.1 nM for Cu2+ and 1.2 nM for Ni2+ were obtained. The colorimetric probe CPH has been applied to qualitative and quantitative detection of Cu2+ and Ni2+ species in real samples.

Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase

The C-cluster of the enzyme carbon monoxide dehydrogenase (CODH) is a structurally distinctive Ni-Fe-S cluster employed to catalyze the reduction of CO₂ to CO as part of the Wood-Ljungdahl carbon fixation pathway. Using X-ray crystallography, we have observed unprecedented conformational dynamics in the C-cluster of the CODH from Desulfovibrio vulgaris, providing the first view of an oxidized state of the cluster. Combined with supporting spectroscopic data, our structures reveal that this novel, oxidized cluster arrangement plays a role in avoiding irreversible oxidative degradation at the C-cluster. Furthermore, mutagenesis of a conserved cysteine residue that binds the C-cluster in the oxidized state but not in the reduced state suggests that the oxidized conformation could be important for proper cluster assembly, in particular Ni incorporation. Together, these results lay a foundation for future investigations of C-cluster activation and assembly, and contribute to an emerging paradigm of metallocluster plasticity.

Investigations by Protein Film Electrochemistry of Alternative Reactions of Nickel-Containing Carbon Monoxide Dehydrogenase

Protein film electrochemistry has been used to investigate reactions of highly active nickel-containing carbon monoxide dehydrogenases (CODHs). When attached to a pyrolytic graphite electrode, these enzymes behave as reversible electrocatalysts, displaying CO2 reduction or CO oxidation at minimal overpotential. The O2 sensitivity of CODH is suppressed by adding cyanide, a reversible inhibitor of CO oxidation, or by raising the electrode potential. Reduction of N2O, isoelectronic with CO2, is catalyzed by CODH, but the reaction is sluggish, despite a large overpotential, and results in inactivation. Production of H2 and formate under highly reducing conditions is consistent with calculations predicting that a nickel-hydrido species might be formed, but the very low rates suggest that such a species is not on the main catalytic pathway.

Investigations of the efficient electrocatalytic interconversions of carbon dioxide and carbon monoxide by nickel-containing carbon monoxide dehydrogenases

Carbon monoxide dehydrogenases (CODH) play an important role in utilizing carbon monoxide (CO) or carbon dioxide (CO2) in the metabolism of some microorganisms. Two distinctly different types of CODH are distinguished by the elements constituting the active site. A Mo-Cu containing CODH is found in some aerobic organisms, whereas a Ni-Fe containing CODH (henceforth simply Ni-CODH) is found in some anaerobes. Two members of the simplest class (IV) of Ni-CODH behave as efficient, reversible electrocatalysts of CO2/CO interconversion when adsorbed on a graphite electrode. Their intense electroactivity sets an important benchmark for the standard of performance at which synthetic molecular and material electrocatalysts comprised of suitably attired abundant first-row transition elements must be able to operate. Investigations of CODHs by protein film electrochemistry (PFE) reveal how the enzymes respond to the variable electrode potential that can drive CO2/CO interconversion in each direction, and identify the potential thresholds at which different small molecules, both substrates and inhibitors, enter or leave the catalytic cycle. Experiments carried out on a much larger (Class III) enzyme CODH/ACS, in which CODH is complexed tightly with acetyl-CoA synthase, show that some of these characteristics are retained, albeit with much slower rates of interfacial electron transfer, attributable to the difficulty in making good electronic contact at the electrode. The PFE results complement and clarify investigations made using spectroscopic investigations.

Investigations of two bidirectional carbon monoxide dehydrogenases from Carboxydothermus hydrogenoformans by protein film electrochemistry

Carbon monoxide dehydrogenases (CODHs) catalyse the reversible conversion between CO and CO2 . Several small molecules or ions are inhibitors and probes for different oxidation states of the unusual [Ni-4 Fe-4 S] cluster that forms the active site. The actions of these small probes on two enzymes-CODH ICh and CODH IICh -produced by Carboxydothermus hydrogenoformans have been studied by protein film voltammetry to compare their behaviour and to establish general characteristics. Whereas CODH ICh is, so far, the better studied of the two isozymes in terms of its electrocatalytic properties, it is CODH IICh that has been characterised by X-ray crystallography. The two isozymes, which share 58.3% sequence identity and 73.9% sequence similarity, show similar patterns of behaviour with regard to selective inhibition of CO2 reduction by CO (product) and cyanate, potent and selective inhibition of CO oxidation by cyanide, and the action of sulfide, which promotes oxidative inactivation of the enzyme. For both isozymes, rates of binding of substrate analogues CN(-) (for CO) and NCO(-) (for CO2 ) are orders of magnitude lower than turnover, a feature that is clearly revealed through hysteresis of cyclic voltammetry. Inhibition by CN(-) and CO is much stronger for CODH IICh than for CODH ICh, a property that has relevance for applying these enzymes as model catalysts in solar-driven CO2 reduction.

A unified electrocatalytic description of the action of inhibitors of nickel carbon monoxide dehydrogenase

Several small molecules and ions, notably carbon monoxide, cyanide, cyanate, and hydrogen sulfide, are potent inhibitors of Ni-containing carbon monoxide dehydrogenases (Ni-CODH) that catalyze very rapid, efficient redox interconversions of CO(2) and CO. Protein film electrochemistry, which probes the dependence of steady-state catalytic rate over a wide potential range, reveals how these inhibitors target particular oxidation levels of Ni-CODH relating to intermediates (C(ox), C(red1), and C(red2)) that have been established for the active site. The following properties are thus established: (1) CO suppresses CO(2) reduction (CO is a product inhibitor), but its binding affinity decreases as the potential becomes more negative. (2) Cyanide totally inhibits CO oxidation, but its effect on CO(2) reduction is limited to a narrow potential region (between -0.5 and -0.6 V), below which CO(2) reduction activity is restored. (3) Cyanate is a strong inhibitor of CO(2) reduction but inhibits CO oxidation only within a narrow potential range just above the CO(2)/CO thermodynamic potential--EPR spectra confirm that cyanate binds selectively to C(red2). (4) Hydrogen sulfide (H(2)S/HS(-)) inhibits CO oxidation but not CO(2) reduction--the complex on/off characteristics are consistent with it binding at the same oxidation level as C(ox) and forming a modified version of this inactive state rather than reacting directly with C(red1). The results provide a new perspective on the properties of different catalytic intermediates of Ni-CODH--uniting and clarifying many previous investigations.

Carbon monoxide dehydrogenase reaction mechanism: a likely case of abnormal CO2 insertion to a Ni-H(-) bond

Ni-containing carbon monoxide dehydrogenases (CODH), present in many anaerobic microorganisms, catalyze the reversible oxidation of CO to CO(2) at the so-called C-cluster. This atypical active site is composed of a [NiFe(3)S(4)] cluster and a single unusual iron ion called ferrous component II or Fe(u) that is bridged to the cluster via one sulfide ion. After additional refinement of recently published high-resolution structures of COOH(x)-, OH(x)-, and CN-bound CODH from Carboxydothermus hydrogenoformans (Jeoung and Dobbek Science 2007, 318, 1461-1464; J. Am. Chem. Soc. 2009, 131, 9922-9923), we have used computational methods on the predominant resulting structures to investigate the spectroscopically well-characterized catalytic intermediates, C(red1) and the two-electron more-reduced C(red2). Several models were geometry-optimized for both states using hybrid quantum mechanical/molecular mechanical potentials. The comparison of calculated Mössbauer parameters of these active site models with experimental data allows us to propose that the C(red1) state has a Fe(u)-Ni(2+) bridging hydroxide ligand and the C(red2) state has a hydride terminally bound to Ni(2+). Using our combined structural and theoretical data, we put forward a revised version of an earlier proposal for the catalytic cycle of Ni-containing CODH (Volbeda and Fontecilla-Camps Dalton Trans. 2005, 21, 3443-3450) that agrees with available spectroscopic and structural data. This mechanism involves an abnormal CO(2) insertion into the Ni(2+)-H(-) bond.

A turn-on fluorescent sensor for detecting nickel in living cells

We present the synthesis and properties of Nickelsensor-1 (NS1), a new water-soluble, turn-on fluorescent sensor that is capable of selectively responding to Ni(2+) in aqueous solution and in living cells. NS1 combines a BODIPY chromophore and a mixed N/O/S receptor to provide good selectivity for Ni(2+) over a range of biologically abundant metal ions in aqueous solution. In addition to these characteristics, confocal microscopy experiments further show that NS1 can be delivered into living cells and report changes in intracellular Ni(2+) levels in a respiratory cell model.

Crystal structure of the ATP-dependent maturation factor of Ni,Fe-containing carbon monoxide dehydrogenases

CooC proteins are ATPases involved in the incorporation of nickel into the complex active site ([Ni-4Fe-4S]) cluster of Ni,Fe-dependent carbon monoxide dehydrogenases. The genome of the carboxydotrophic bacterium Carboxydothermus hydrogenoformans encodes five carbon monoxide dehydrogenases and three CooC-type proteins, of which CooC1 was shown to be a nickel-binding ATPase. We determined the crystal structure of CooC1 in four different states: empty, ADP-bound, Zn(2+)/ADP-bound, and Zn(2+)-bound. The structure of CooC1 consists of two spatially separated functional modules: an ATPase module containing the deviant Walker A motif and a metal-binding module that confers the specific function of CooC1. The ATPase module is homologous to other members of the MinD family and, in analogy to the dimeric structure of ATP-bound Soj, is likely responsible for the ATP-dependent dimerization of CooC1. Its core topology classifies CooC1 as a member of the MinD family of SIMIBI (signal recognition particle, MinD and BioD)-class NTPases. The crystal structure of Zn(2+)-bound CooC1 reveals a conserved C-X-C motif as the metal-binding site responsible for metal-induced dimerization. The competitive binding of Ni(2+) and Zn(2+) to CooC1 in solution confirms that the conserved C-X-C motif is also responsible for the interaction with Ni(2+). A comparison of the different CooC1 structures determined suggests a mutual dependence of metal-binding site and nucleotide-binding site.

Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites

Biomimetic inorganic chemistry has as its primary goal the synthesis of molecules that approach or achieve the structures, oxidation states, and electronic and reactivity features of native metal-containing sites of variant nuclearity. Comparison of properties of accurate analogues and these sites ideally provides insight into the influence of protein structure and environment on intrinsic properties as represented by the analogue. For polynuclear sites in particular, the goal provides a formidable challenge for, with the exception of iron-sulfur clusters, all such site structures have never been achieved and few have even been closely approximated by chemical synthesis. This account describes the current status of the synthetic analogue approach as applied to the mononuclear sites in certain molybdoenzymes and the polynuclear sites in hydrogenases, nitrogenase, and carbon monoxide dehydrogenases.

Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation

Conceptually, the simplest way to synthesize an organic molecule is to construct it one carbon at a time. The Wood-Ljungdahl pathway of CO(2) fixation involves this type of stepwise process. The biochemical events that underlie the condensation of two one-carbon units to form the two-carbon compound, acetate, have intrigued chemists, biochemists, and microbiologists for many decades. We begin this review with a description of the biology of acetogenesis. Then, we provide a short history of the important discoveries that have led to the identification of the key components and steps of this usual mechanism of CO and CO(2) fixation. In this historical perspective, we have included reflections that hopefully will sketch the landscape of the controversies, hypotheses, and opinions that led to the key experiments and discoveries. We then describe the properties of the genes and enzymes involved in the pathway and conclude with a section describing some major questions that remain unanswered.