Acetylene Hydratase Research Articles

Towards Structural‐Functional Mimics of Acetylene Hydratase: Reversible Activation of Acetylene using a Biomimetic Tungsten Complex

AbstractThe synthesis and characterization of a biomimetic system that can reversibly bind acetylene (ethyne) is reported. The system has been designed to mimic catalytic intermediates of the tungstoenzyme acetylene hydratase. The thiophenyloxazoline ligand S‐Phoz (2‐(4′,4′‐dimethyloxazolin‐2′‐yl)thiophenolate) is used to generate a bioinspired donor environment around the W center, facilitating the stabilization of W–acetylene adducts. The featured complexes [W(C2H2)(CO)(S‐Phoz)2] (2) and [WO(C2H2)(S‐Phoz)2] (3) are extremely rare from a synthetic and structural point of view as very little is known about W–C2H2 adducts. Upon exposure to visible light, 3 can release C2H2 from its coordination sphere to yield the 14‐electron species [WO(S‐Phoz)2] (4). Under light‐exclusion 4 re‐activates C2H2 making this the first fully characterized system for the reversible activation of acetylene.

Assessment of DFT methods for computing activation energies of Mo/W-mediated reactions.

Using high level ab initio coupled cluster calculations as reference, the performances of 15 commonly used density functionals (DFs) on activation energy calculations for typical Mo/W-mediated reactions have been systematically assessed for the first time in this work. The selected representative Mo/W-mediated reactions cover a wide range from enzymatic reactions to organometallic reactions, which include Mo-catalyzed aldehyde oxidation (aldehyde oxidoreductase), Mo-catalyzed dimethyl sulfoxide (DMSO) reduction (DMSO reductase), W-catalyzed acetylene hydration (acetylene hydratase), Mo/W-mediated olefin metathesis, Mo/W-mediated olefin epoxidation, W-mediated alkyne metathesis, and W-mediated C-H bond activation. Covering both Mo- and W-mediated reactions, four DFs of B2GP-PLYP, M06, B2-PLYP, and B3LYP are uniformly recommended with and without DFT empirical dispersion correction. Among these four DFs, B3LYP is notably improved in performance by DFT empirical dispersion correction. In addition to the absolute value of calculation error, if the trend of DFT results is also a consideration, B2GP-PLYP, B2-PLYP, and M06 keep better performance than other functionals tested and constitute our final recommendation of DFs for both Mo- and W-mediated reactions.

Living on acetylene. A primordial energy source.

The tungsten iron-sulfur enzyme acetylene hydratase catalyzes the conversion of acetylene to acetaldehyde by addition of one water molecule to the C-C triple bond. For a member of the dimethylsulfoxide (DMSO) reductase family this is a rather unique reaction, since it does not involve a net electron transfer. The acetylene hydratase from the strictly anaerobic bacterium Pelobacter acetylenicus is so far the only known and characterized acetylene hydratase. With a crystal structure solved at 1.26 Å resolution and several amino acids around the active site exchanged by site-directed mutagenesis, many key features have been explored to understand the function of this novel tungsten enzyme. However, the exact reaction mechanism remains unsolved. Trapped in the reduced W(IV) state, the active site consists of an octahedrally coordinated tungsten ion with a tightly bound water molecule. An aspartate residue in close proximity, forming a short hydrogen bond to the water molecule, was shown to be essential for enzyme activity. The arrangement is completed by a small hydrophobic pocket at the end of an access funnel that is distinct from all other enzymes of the DMSO reductase family.

Convergence in the QM‐only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase

We report systematic quantum mechanics-only (QM-only) and QM/molecular mechanics (MM) calculations on an enzyme-catalyzed reaction to assess the convergence behavior of QM-only and QM/MM energies with respect to the size of the chosen QM region. The QM and MM parts are described by density functional theory (typically B3LYP/def2-SVP) and the CHARMM force field, respectively. Extending our previous work on acetylene hydratase with QM regions up to 157 atoms (Liao and Thiel, J. Chem. Theory Comput. 2012, 8, 3793), we performed QM/MM geometry optimizations with a QM region M4 composed of 408 atoms, as well as further QM/MM single-point calculations with even larger QM regions up to 657 atoms. A charge deletion analysis was conducted for the previously used QM/MM model (M3a, with a QM region of 157 atoms) to identify all MM residues with strong electrostatic contributions to the reaction energetics (typically more than 2 kcal/mol), which were then included in M4. QM/MM calculations with this large QM region M4 lead to the same overall mechanism as the previous QM/MM calculations with M3a, but there are some variations in the relative energies of the stationary points, with a mean absolute deviation (MAD) of 2.7 kcal/mol. The energies of the two relevant transition states are close to each other at all levels applied (typically within 2 kcal/mol), with the first (second) one being rate-limiting in the QM/MM calculations with M3a (M4). QM-only gas-phase calculations give a very similar energy profile for QM region M4 (MAD of 1.7 kcal/mol), contrary to the situation for M3a where we had previously found significant discrepancies between the QM-only and QM/MM results (MAD of 7.9 kcal/mol). Extension of the QM region beyond M4 up to M7 (657 atoms) leads to only rather small variations in the relative energies from single-point QM-only and QM/MM calculations (MAD typically about 1-2 kcal/mol). In the case of acetylene hydratase, a model with 408 QM atoms thus seems sufficient to achieve convergence in the computed relative energies to within 1-2 kcal/mol.

On the Effect of Varying Constraints in the Quantum Mechanics Only Modeling of Enzymatic Reactions: The Case of Acetylene Hydratase

Quantum mechanics only (QM-only) studies of enzymatic reactions employ a coordinate-locking scheme, in which certain key atoms at the periphery of the chosen cluster model are fixed to their crystal structure positions. We report a case study on acetylene hydratase to assess the uncertainties introduced by this scheme. Random displacements of 0.1, 0.15, and 0.2 Å were applied at the ten terminal atoms fixed in the chosen 116-atom cluster model to generate sets of ten distorted structures for each given displacement. The relevant stationary points were reoptimized under these modified constraints to determine the variations of the computed energies and geometries induced by the displacements of the fixed atoms. Displacements of 0.1 Å cause a relatively minor perturbation that can be accommodated during geometry optimization, resulting in rather small changes in key bond distances and relative energies (typically of the order of 0.01 Å and 1 kcal/mol), whereas displacements of 0.2 Å lead to larger fluctuations (typically twice as high) and may sometimes even cause convergence to different local minima during geometry optimization. A literature survey indicates that protein crystal structures with a resolution higher than 2.0 Å are normally associated with a coordinate error of less than 0.1 Å for the backbone atoms. Judging from the present results for acetylene hydratase, such uncertainties seem tolerable in the design of QM-only models with more than 100 atoms, which are flexible enough to adapt during geometry optimization and thus keep the associate uncertainties in the computed energies and bond distances at tolerable levels (around 1 kcal/mol and 0.01 Å, respectively). On the other hand, crystal structures with significantly lower resolution should be used with great caution when setting up QM-only models because the resulting uncertainties in the computational results may become larger than acceptable. The present conclusions are mostly based on systematic DFT(B3LYP) calculations with a medium-size basis set. Test calculations on selected structures confirm that similar results are obtained for larger basis sets, different functionals (ωB97X, BMK, M06), and upon including solvation and zero-point corrections, even though the fluctuations in the computed relative energies become somewhat larger in some cases.

Comparison of QM-Only and QM/MM Models for the Mechanism of Tungsten-Dependent Acetylene Hydratase.

We report a comparison of QM-only and QM/MM approaches for the modeling of enzymatic reactions. For this purpose, we present a QM/MM case study on the formation of vinyl alcohol in the catalytic cycle of tungsten-dependent acetylene hydratase. Three different QM regions ranging from 32 to 157 atoms are designed for the reinvestigation of the previously suggested one-water attack mechanism. The QM/MM calculations with the minimal QM region M1 (32 atoms) yield a two-step reaction profile, with an initial nucleophilic attack followed by the protonation of the formed vinyl anion intermediate, as previously proposed on the basis of QM-only calculations on cluster model M2 (116 atoms); however, the overall QM/MM barrier with M1 is much too high, mainly due to an overestimate of the QM/MM electrostatic repulsions. QM/MM calculations with QM region M2 (116 atoms) fail to reproduce the published QM-only results, giving a one-step profile with a very high barrier. This is traced back to the strong electrostatic influence of the two neighboring diphosphate groups that were neglected in the QM-only work but are present at the QM/MM level. These diphosphate groups and other electrostatically important nearby residues are included in QM region M3 (157 atoms). QM/MM calculations with M3 recover the two-step mechanism and yield a reasonable overall barrier of 16.7 kcal/mol at the B3LYP/MM level. They thus lead to a similar overall mechanistic scenario as the previous QM-only calculations, but there are also some important variations. Most notably, the initial nucleophilic attack becomes rate limiting at the QM/MM level. A modified two-water attack mechanism is also considered but is found to be less favorable than the previously proposed one-water attack mechanism. Detailed residue interaction analyses and comparisons between QM/MM results with electronic and mechanical embedding and QM-only results without and with continuum solvation show that the protein environment plays a key role in determining the mechanistic preferences in acetylene hydratase. The combined use of QM-only and QM/MM methods provides a powerful approach for the modeling of enzyme catalysis.

A Biogeochemical and Genetic Survey of Acetylene Fermentation by Environmental Samples and Bacterial Isolates

Anoxic samples (sediment and groundwater) from 13 chemically diverse field sites were assayed for their ability to consume acetylene (C2H2). Over incubation periods ranging from ∼ 10 to 80 days, selected samples from 7 of the 13 tested sites displayed significant C2H2 removal. No significant formation of ethylene was noted in these incubations; therefore, C2H2 consumption could be attributed to acetylene hydratase (AH) rather than nitrogenase activity. This putative AH (PAH) activity was observed in only 21% of the total of assayed samples, while amplification of AH genes from extracted DNA using degenerate primers derived from Pelobacter acetylenicus occurred in even fewer (9.8%) samples. Acetylene-fermenting bacteria were isolated as a pure culture from the sediments of a tidal mudflat in San Francisco Bay (SFB93) and as an enrichment culture from freshwater Searsville Lake (SV7). Comparison of 16S rDNA clone libraries revealed that SFB93 was closely related to P. carbolinicus, while SV7 consisted of several unrelated bacteria. AH gene was amplified from SFB93 but not SV7. The inability of the primers to generate amplicons in the SV7 enrichment, as well as from several of the environmental samples that displayed PAH activity, implied that either the primers were too highly constrained in their specificity or that there was a different type of AH gene in these environmental samples than occurs in P. acetylenicus. The significance of this work with regard to the search for life in the outer Solar System, where C2H2 is abundant, is discussed.

Discovery of acetylene hydratase activity of the iron–sulphur protein IspH

The final step of the methylerythritol phosphate isoprenoid biosynthesis pathway is catalysed by the iron-sulphur enzyme IspH, producing the universal precursors of terpenes: isopentenyl diphosphate and dimethylallyl diphosphate. Here we report an unforeseen reaction discovered during the investigation of the interaction of IspH with acetylene inhibitors by X-ray crystallography, Mößbauer, and nuclear magnetic resonance spectroscopy. In addition to its role as a 2H(+)/2e(-) reductase, IspH can hydrate acetylenes to aldehydes and ketones via anti-Markovnikov/Markovnikov addition. The reactions only occur with the oxidised protein and proceed via η(1)-O-enolate intermediates. One of these is characterized crystallographically and contains a C4 ligand oxygen bound to the unique, fourth iron in the 4Fe-4S cluster: this intermediate subsequently hydrolyzes to produce an aldehyde product. This unexpected side to IspH reactivity is of interest in the context of the mechanism of action of other acetylene hydratases, as well as in the design of antiinfectives targeting IspH.

Theoretical Study of the Chemoselectivity of Tungsten-Dependent Acetylene Hydratase

The tungsten-dependent enzyme acetylene hydratase catalyzes the hydration of acetylene to acetaldehyde. Very recently, we proposed a reaction mechanism for this enzyme based on density functional c ...

Theoretical investigation of the first-shell mechanism of acetylene hydration catalyzed by a biomimetic tungsten complex

The reaction mechanism of the hydration of acetylene to acetaldehyde catalyzed by [W(IV)O(mnt)(2)](2-) (where mnt(2-) is 1,2-dicyanoethylenedithiolate) is studied using density functional theory. Both the uncatalyzed and the catalyzed reaction are considered to find out the origin of the catalysis. Three different models are investigated, in which an aquo, a hydroxo, or an oxo coordinates to the tungsten center. A first-shell mechanism is suggested, similarly to recent calculations on tungsten-dependent acetylene hydratase. The acetylene substrate first coordinates to the tungsten center in an η(2) fashion. Then, the tungsten-bound hydroxide activates a water molecule to perform a nucleophilic attack on the acetylene, resulting in the formation of a vinyl anion and a tungsten-bound water molecule. This is followed by proton transfer from the tungsten-bound water molecule to the newly formed vinyl anion intermediate. Tungsten is directly involved in the reaction by binding and activating acetylene and providing electrostatic stabilization to the transition states and intermediates. Three other mechanisms are also considered, but the associated energetic barriers were found to be very high, ruling out those possibilities.

Exploring the Active Site of the Tungsten, Iron-Sulfur Enzyme Acetylene Hydratase

The soluble tungsten, iron-sulfur enzyme acetylene hydratase (AH) from mesophilic Pelobacter acetylenicus is a member of the dimethyl sulfoxide (DMSO) reductase family. It stands out from its class as it catalyzes a nonredox reaction, the addition of H₂O to acetylene (H-C≡C-H) to form acetaldehyde (CH₃CHO). Caught in its active W(IV) state, the high-resolution three-dimensional structure of AH offers an excellent starting point to tackle its unique chemistry and to identify catalytic amino acid residues within the active site cavity: Asp13 close to W(IV) coordinated to two molybdopterin-guanosine-dinucleotide ligands, Lys48 which couples the [4Fe-4S] cluster to the W site, and Ile142 as part of a hydrophobic ring at the end of the substrate access channel designed to accommodate the substrate acetylene. A protocol was developed to express AH in Escherichia coli and to produce active-site variants which were characterized with regard to activity and occupancy of the tungsten and iron-sulfur centers. By this means, fusion of the N-terminal chaperone binding site of the E. coli nitrate reductase NarG to the AH gene improved the yield and activity of AH and its variants significantly. Results from site-directed mutagenesis of three key residues, Asp13, Lys48, and Ile142, document their important role in catalysis of this unusual tungsten enzyme.

Mechanism of tungsten-dependent acetylene hydratase from quantum chemical calculations

Acetylene hydratase is a tungsten-dependent enzyme that catalyzes the nonredox hydration of acetylene to acetaldehyde. Density functional theory calculations are used to elucidate the reaction mechanism of this enzyme with a large model of the active site devised on the basis of the native X-ray crystal structure. Based on the calculations, we propose a new mechanism in which the acetylene substrate first displaces the W-coordinated water molecule, and then undergoes a nucleophilic attack by the water molecule assisted by an ionized Asp13 residue at the active site. This is followed by proton transfer from Asp13 to the newly formed vinyl anion intermediate. In the subsequent isomerization, Asp13 shuttles a proton from the hydroxyl group of the vinyl alcohol to the α-carbon. Asp13 is thus a key player in the mechanism, but also W is directly involved in the reaction by binding and activating acetylene and providing electrostatic stabilization to the transition states and intermediates. Several other mechanisms are also considered but the energetic barriers are found to be very high, ruling out these possibilities.

A DFT study of the possible role of vinylidene and carbene intermediates in the mechanism of the enzyme acetylene hydratase

The mode of action of the tungstoprotein, acetylene hydratase, is unresolved at present.We have carried out density functional theory (DFT) calculations to investigate two proposed mechanisms, and also propose a new mechanism based on our calculations. We find that the previously proposed single step mechanisms which involve the attack of a water molecule, catalysed by Asp13, have barriers greater than 40 kcal mol(-1). We propose a new mechanism which involves two tungsten complexes, a vinylidene and a carbene, as stable intermediates. We calculate the potential energy surfaces for their formation, and for the decomposition of the carbene complex to yield acetaldehyde. All the barriers along the pathway are less than 30 kcal mol(-1), except for the barrier to carbene formation which is 34 kcal mol(-1).

Theoretical Studies of Models of the Active Site of the Tungstoenzyme Acetylene Hydratase

Models of the tungstoenzyme acetylene hydratase (AH), which catalyzes the addition of water to acetylene through a nonredox process, are examined using density-functional theory (DFT). The relative energy of acetylene adduct formation was calculated for several tungsten- and molydbenum-oxo dithiocarbamates (dtc) and dithiolates (dtl). Stronger coordination of acetylene to tungsten and dtc complexes is consistent with experimental Keq values and attributed to the larger W 5d orbitals and the overall negative charge of the dithiolate complexes. The recently solved AH X-ray crystal structure suggests the presence of a water molecule bonded to the metal and the possibility that catalysis occurs via a non-organometallic intermediate. Models of the truncated active site are used to analyze this claim by determining the relative energies of acetylene versus water coordination. Complexation of acetylene is favored over water by 12 kcal/mol with the aquo complex formation endergonic by 7 kcal/mol (ΔG). These resul...

Tungsten, the Surprisingly Positively Acting Heavy Metal Element for Prokaryotes

The history and changing function of tungsten as the heaviest element in biological systems is given. It starts from an inhibitory element/anion, especially for the iron molybdenum-cofactor (FeMoCo)-containing enzyme nitrogenase involved in dinitrogen fixation, as well as for the many "metal binding pterin" (MPT)-, also known as tricyclic pyranopterin- containing classic molybdoenzymes, such as the sulfite oxidase and the xanthine dehydrogenase family of enzymes. They are generally involved in the transformation of a variety of carbon-, nitrogen- and sulfur-containing compounds. But tungstate can serve as a potential positively acting element for some enzymes of the dimethyl sulfoxide (DMSO) reductase family, especially for CO(2)-reducing formate dehydrogenases (FDHs), formylmethanofuran dehydrogenases and acetylene hydratase (catalyzing only an addition of water, but no redox reaction). Tungsten even becomes an essential element for nearly all enzymes of the aldehyde oxidoreductase (AOR) family. Due to the close chemical and physical similarities between molybdate and tungstate, the latter was thought to be only unselectively cotransported or cometabolized with other tetrahedral anions, such as molybdate and also sulfate. However, it has now become clear that it can also be very selectively transported compared to molybdate into some prokaryotic cells by two very selective ABC-type of transporters that contain a binding protein TupA or WtpA. Both proteins exhibit an extremely high affinity for tungstate (K(D) < 1 nM) and can even discriminate between tungstate and molybdate. By that process, tungsten finally becomes selectively incorporated into the few enzymes noted above.

Acetylene as Fast Food: Implications for Development of Life on Anoxic Primordial Earth and in the Outer Solar System

Acetylene occurs, by photolysis of methane, in the atmospheres of jovian planets and Titan. In contrast, acetylene is only a trace component of Earth's current atmosphere. Nonetheless, a methane-rich atmosphere has been hypothesized for early Earth; this atmosphere would also have been rich in acetylene. This poses a paradox, because acetylene is a potent inhibitor of many key anaerobic microbial processes, including methanogenesis, anaerobic methane oxidation, nitrogen fixation, and hydrogen oxidation. Fermentation of acetylene was discovered approximately 25 years ago, and Pelobacter acetylenicus was shown to grow on acetylene by virtue of acetylene hydratase, which results in the formation of acetaldehyde. Acetaldehyde subsequently dismutates to ethanol and acetate (plus some hydrogen). However, acetylene hydratase is specific for acetylene and does not react with any analogous compounds. We hypothesize that microbes with acetylene hydratase played a key role in the evolution of Earth's early biosphere by exploiting an available source of carbon from the atmosphere and in so doing formed protective niches that allowed for other microbial processes to flourish. Furthermore, the presence of acetylene in the atmosphere of a planet or planetoid could possibly represent evidence for an extraterrestrial anaerobic ecosystem.

Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase

The tungsten-iron-sulfur enzyme acetylene hydratase stands out from its class because it catalyzes a nonredox reaction, the hydration of acetylene to acetaldehyde. Sequence comparisons group the protein into the dimethyl sulfoxide reductase family, and it contains a bis-molybdopterin guanine dinucleotide-ligated tungsten atom and a cubane-type [4Fe:4S] cluster. The crystal structure of acetylene hydratase at 1.26 A now shows that the tungsten center binds a water molecule that is activated by an adjacent aspartate residue, enabling it to attack acetylene bound in a distinct, hydrophobic pocket. This mechanism requires a strong shift of pK(a) of the aspartate, caused by a nearby low-potential [4Fe:4S] cluster. To access this previously unrecognized W-Asp active site, the protein evolved a new substrate channel distant from where it is found in other molybdenum and tungsten enzymes.

Novel bacterial molybdenum and tungsten enzymes: three-dimensional structure, spectroscopy, and reaction mechanism

The molybdenum enzymes 4-hydroxybenzoyl-CoA reductase and pyrogallol-phloroglucinol transhydroxylase and the tungsten enzyme acetylene hydratase catalyze reductive dehydroxylation reactions, i.e., transhydroxylation between phenolic residues and the addition of water to a triple bond. Such activities are unusual for this class of enzymes, which carry either a mononuclear Mo or W center. Crystallization and subsequent structural analysis by high-resolution X-ray crystallography has helped to resolve the reaction centers of these enzymes to a degree that allows us to understand the interaction of the enzyme and the respective substrate(s) in detail, and to develop a concept for the respective reaction mechanism, at least in two cases.

Crystallization and preliminary X-ray analysis of the tungsten-dependent acetylene hydratase from Pelobacter acetylenicus.

Acetylene hydratase is a tungsten-containing hydroxylase that converts acetylene to acetaldehyde in a unique reaction that requires a strong reductant. The subsequent disproportionation of acetaldehyde yields acetate and ethanol. Crystals of the tungsten/iron-sulfur protein acetylene hydratase from Pelobacter acetylenicus strain WoAcy 1 (DSM 3246) were grown by the vapour-diffusion method in an N2/H2 atmosphere using polyethylene glycol as precipitant. Growth of crystals suitable for X-ray analysis strictly depended on the presence of Ti(III) citrate or dithionite as reducing agents.

Acetylene hydratase of Pelobacter acetylenicus. Molecular and spectroscopic properties of the tungsten iron-sulfur enzyme.

Acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. Expression of the enzyme was increased 10-fold by feeding a 50-L batch culture continuously with 104 Pa acetylene at pH 6.8-7.0. Acetylene hydratase was purified to homogeneity by a three-step procedure in either the absence or presence of dioxygen. The enzyme was a monomer with a molecular mass of 73 kDa (SDS/PAGE) or 83 kDa (matrix-assisted laser-desorption ionization MS) and contained 0.5 +/- 0.1 W (inductively coupled plasma/MS) and 1.3 +/- 0.1 molybdopterin-guanine dinucleotide per mol. Selenium was absent. EPR spectra (enzyme as isolated, under air) showed a signal typical of a [3Fe-4S] cluster with gav = 2.01, at 10 K. In enzyme prepared under N2/H2, this signal was absent and reaction with dithionite led to a rhombic signal with gz = 2.048, gy = 1.939 and gx = 1.920 indicative of a low-potential ferredoxin-type [4Fe-4S] cluster. Upon oxidation with hexacyanoferrate(III), a new signal appeared with gx = 2.007, gy = 2.019 and gz = 2.048 (gav = 2.022), which disappeared after further oxidation. The signal was still visible at 150 K and was tentatively assigned to a W(V) center. The iron-sulfur center of acetylene hydratase (prepared under N2/H2) gave a midpoint redox potential of -410 +/- 20 mV in a spectrophotometric titration with dithionite. Enzyme activity depended on the redox potential of the solution, with 50% of maximum activity at -340 +/- 20 mV. The presence of a pterin-guanine dinucleotide cofactor differentiates acetylene hydratase from the aldehyde ferredoxin oxidoreductase-type enzymes which have a pterin mononucleotide cofactor.