Acetylene hydratase: a non-redox enzyme with tungsten and iron-sulfur centers at the active site

Active Site Characterization of a Campylobacter jejuni Nitrate Reductase Variant Provides Insight into the Enzyme Mechanism

Mo K-edge X-ray absorption spectroscopy (XAS) is used to probe the structure of wild-type Campylobacter jejuni nitrate reductase NapA and the C176A variant. The results of extended X-ray absorption fine structure (EXAFS) experiments on wt NapA support an oxidized Mo(VI) hexacoordinate active site coordinated by a single terminal oxo donor, four sulfur atoms from two separate pyranopterin dithiolene ligands, and an additional S atom from a conserved cysteine amino acid residue. We found no evidence of a terminal sulfido ligand in wt NapA. EXAFS analysis shows the C176A active site to be a 6-coordinate structure, and this is supported by EPR studies on C176A and small molecule analogs of Mo(V) enzyme forms. The SCys is replaced by a hydroxide or water ligand in C176A, and we find no evidence of a coordinated sulfhydryl (SH) ligand. Kinetic studies show that this variant has completely lost its catalytic activity toward nitrate. Taken together, the results support a critical role for the conserved C176 in catalysis and an oxygen atom transfer mechanism for the catalytic reduction of nitrate to nitrite that does not employ a terminal sulfido ligand in the catalytic cycle.

Vinyl-pyrazole as a biomimetic acetaldehyde surrogate

Inspired by the enzyme acetylene hydratase, we investigated the reactivity of acetylene with tungsten(II) pyrazole complexes. Our research revealed that the complex [WBr2(pz-NHCCH3)(CO)3] (pz = 3,5-dimethyl-pyrazolate) facilitates the stochiometric reaction between pzH and acetylene to give N-vinyl-pz. This vinyl compound readily hydrolyzes to acetaldehyde, mirroring the product of acetylene hydration in the enzymatic process. The formation of the vinyl compound likely involves a reactive intermediate complex where acetylene acts as a two-electron donor, in contrast to isolable acetylene complexes that are inert to nucleophilic attack by water. Results suggest an alternative mechanism for the enzyme, including vinylation of a neighboring amino acid by acetylene in the active site prior to hydration.

Nucleophiles Target the Tungsten Center Over Acetylene in Biomimetic Models

Inspired by the first shell mechanism proposed for the tungstoenzyme acetylene hydratase, the electrophilic reactivity of tungsten-acetylene complexes [W(CO)(C2H2)(6-MePyS)2] (1) and [WO(C2H2)(6-MePyS)2] (2) was investigated. The biological nucleophile water/hydroxide and tert-butyl isocyanide were employed. Our findings consistently show that, regardless of the nucleophile used, both tungsten centers W(II) and W(IV), respectively, are the preferred targets over the coordinated acetylene. Treatment of 2 with aqueous NaOH led to protonation of coordinated acetylene to ethylene, pointing toward the Brønsted basic character of the coordinated alkyne instead of the anticipated electrophilic behavior. In cases involving isocyanides as nucleophiles, the attack on the W(II) center of 1 took place first, whereas the W(IV) complex 2 remained unchanged. These experiments indicate that the direct nucleophilic attack of W-coordinated acetylene by water, as some computational studies of acetylene hydratase propose, is unlikely to occur.

Advancing Our Understanding of Pyranopterin-Dithiolene Contributions to Moco Enzyme Catalysis

The pyranopterin dithiolene ligand is remarkable in terms of its geometric and electronic structure and is uniquely found in mononuclear molybdenum and tungsten enzymes. The pyranopterin dithiolene is found coordinated to the metal ion, deeply buried within the protein, and non-covalently attached to the protein via an extensive hydrogen bonding network that is enzyme-specific. However, the function of pyranopterin dithiolene in enzymatic catalysis has been difficult to determine. This focused account aims to provide an overview of what has been learned from the study of pyranopterin dithiolene model complexes of molybdenum and how these results relate to the enzyme systems. This work begins with a summary of what is known about the pyranopterin dithiolene ligand in the enzymes. We then introduce the development of inorganic small molecule complexes that model aspects of a coordinated pyranopterin dithiolene and discuss the results of detailed physical studies of the models by electronic absorption, resonance Raman, X-ray absorption and NMR spectroscopies, cyclic voltammetry, X-ray crystallography, and chemical reactivity.

Dioxygen Activation by a Bioinspired Tungsten(IV) Complex

An increasing number of discovered tungstoenzymes raises interest in the biomimetic chemistry of tungsten complexes in oxidation states +IV, +V, and +VI. Bioinspired (sulfur-rich) tungsten(VI) dioxido complexes are relatively prevalent in literature. Still, their energetically demanding reduction directly correlates with a small number of known tungsten(IV) oxido complexes, whose chemistry is not well explored. In this paper, a reduction of the [WO₂(6-MePyS)₂] (6-MePyS = 6-methylpyridine-2-thiolate) complex with PMe₃ to a phosphine-stabilized tungsten(IV) oxido complex [WO(6-MePyS)₂(PMe₃)₂] is described. This tungsten(IV) complex partially releases one PMe₃ ligand in solution, creating a vacant coordination site capable of activating dioxygen to form [WO₂(6-MePyS)₂] and OPMe₃. Therefore, [WO₂(6-MePyS)₂] can be used as a catalyst for the aerobic oxidation of PMe₃, rendering this complex a rare example of a tungsten system utilizing dioxygen in homogeneous catalysis. Additionally, the investigation of the reactivity of the tungsten(IV) oxido complex with acetylene, substrate of a tungstoenzyme acetylene hydratase (AH), revealed the formation of the tungsten(IV) acetylene adduct. Although this adduct was previously reported as an oxidation product of the tungsten(II) acetylene carbonyl complex, here it is obtained via substitution at the sulfur-rich tungsten(IV) center, mimicking the initial step of the first shell mechanism for AH as suggested by computational studies.

The elements of life: A biocentric tour of the periodic table

Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.

Emerging Chemical Diversity and Potential Applications of Enzymes in the DMSO Reductase Superfamily

Molybdenum- and tungsten-dependent proteins catalyze essential processes in living organisms and biogeochemical cycles. Among these enzymes, members of the dimethyl sulfoxide (DMSO) reductase superfamily are considered the most diverse, facilitating a wide range of chemical transformations that can be categorized as oxygen atom installation, removal, and transfer. Importantly, DMSO reductase enzymes provide high efficiency and excellent selectivity while operating under mild conditions without conventional oxidants such as oxygen or peroxides. Despite the potential utility of these enzymes as biocatalysts, such applications have not been fully explored. In addition, the vast majority of DMSO reductase enzymes still remain uncharacterized. In this review, we describe the reactivities, proposed mechanisms, and potential synthetic applications of selected enzymes in the DMSO reductase superfamily. We also highlight emerging opportunities to discover new chemical activity and current challenges in studying and engineering proteins in the DMSO reductase superfamily. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Complete Genome Sequence of Rhodococcus opacus Strain MoAcy1 (DSM 44186), an Aerobic Acetylenotroph Isolated from Soil

We report the genome of Rhodococcus opacus strain MoAcy1 (DSM 44186), an aerobic soil isolate capable of using acetylene as its primary carbon and energy source (acetylenotrophy). The genome is composed of a single circular chromosome of ∼8 Mbp and two closed plasmids, with a G+C content of 67.3%.

Got acetylene: a personal research retrospective

In research, sometimes sheer happenstance and serendipity make for an unexpected discovery. Once revealed and if interesting enough, such a finding and its follow-up investigations can lead to advances by others that leave its originators 'scooped' and mulling about what next to do with their unpublished data, specifically what journals could it still be published in and be perceived as original. This is what occurred with us nearly 40 years ago with regard to our follow-up observations of acetylene fermentation and led us to concoct a 'cock-and-bull' story. We hypothesized about a plausible role for acetylene metabolism in the primordial biogeochemistry of Earth and the possibility of acetylene serving as a key life-sustaining substrate for alien microbes dwelling in the orbs of the outer solar system. With the passage of time, advances were made in whole-genome sequencing coupled with major in silico progress in bioinformatics. In parallel came the results of explorations of the outer solar system (i.e. the Cassini mission to Saturn and its moons). It now appears that these somewhat harebrained ideas of ours, arisen at first out of a sense of desperation, actually ring true in fact, and particularly well in song: 'Tell a tale of cock and bull, Of convincing detail full Tale tremendous, Heav'n defend us! What a tale of cock and bull!' From 'The Yeoman of the Guard' by Gilbert & Sullivan.

Synthesis and Reactivity of a Bioinspired Molybdenum(IV) Acetylene Complex

The isolation of a molybdenum(IV) acetylene (C₂H₂) complex containing two bioinspired 6-methylpyridine-2-thiolate ligands is reported. The synthesis can be performed either by oxidation of a molybdenum(II) C₂H₂ complex or by substitution of a coordinated PMe₃ by C₂H₂ on a molybdenum(IV) center. Both C₂H₂ complexes were characterized by spectroscopic means as well as by single-crystal X-ray diffraction. Furthermore, the reactivity of the coordinated C₂H₂ was investigated with regard to acetylene hydratase, one of two enzymes that accept C₂H₂ as a substrate. While the reaction with water resulted in the vinylation of the pyridine-2-thiolate ligands, an intermolecular nucleophilic attack on the coordinated C₂H₂ with the soft nucleophile PMe₃ was observed to give a cationic ethenyl complex. A comparison with the tungsten analogues revealed less tightly bound C₂H₂ in the molybdenum variant, which, however, shows a higher reactivity toward nucleophiles.

Syntrophotalea acetylenivorans sp. nov., a diazotrophic, acetylenotrophic anaerobe isolated from intertidal sediments

A Gram-stain-negative, strictly anaerobic, non-motile, rod-shaped bacterium, designated SFB93^T, was isolated from the intertidal sediments of South San Francisco Bay, located near Palo Alto, CA, USA. SFB93^T was capable of acetylenotrophic and diazotrophic growth, grew at 22-37 °C, pH 6.3-8.5 and in the presence of 10-45 g l^-1 NaCl. Phylogenetic analyses based on 16S rRNA gene sequencing showed that SFB93^T represented a member of the genus Syntrophotalea with highest 16S rRNA gene sequence similarities to Syntrophotalea acetylenica DSM 3246^T (96.6 %), Syntrophotalea carbinolica DSM 2380^T (96.5 %), and Syntrophotalea venetiana DSM 2394^T (96.7 %). Genome sequencing revealed a genome size of 3.22 Mbp and a DNA G+C content of 53.4 %. SFB93^T had low genome-wide average nucleotide identity (81-87.5 %) and <70 % digital DNA-DNA hybridization value with other members of the genus Syntrophotalea. The phylogenetic position of SFB93^T within the family Syntrophotaleaceae and as a novel member of the genus Syntrophotalea was confirmed via phylogenetic reconstruction based on concatenated alignments of 92 bacterial core genes. On the basis of the results of phenotypic, genotypic and phylogenetic analyses, a novel species, Syntrophotalea acetylenivorans sp. nov., is proposed, with SFB93^T (=DSM 106009^T=JCM 33327^T=ATCC TSD-118^T) as the type strain.

Acetylene-Fueled Trichloroethene Reductive Dechlorination in a Groundwater Enrichment Culture

In aquifers, acetylene (C2H2) is a product of abiotic degradation of trichloroethene (TCE) catalyzed by in situ minerals. C2H2 can, in turn, inhibit multiple microbial processes including TCE dechlorination and metabolisms that commonly support dechlorination, in addition to supporting the growth of acetylenotrophic microorganisms. Previously, C2H2 was shown to support TCE reductive dechlorination in synthetic, laboratory-constructed cocultures containing the acetylenotroph Pelobacter sp. strain SFB93 and Dehalococcoides mccartyi strain 195 or strain BAV1. In this study, we demonstrate TCE and perchloroethene (PCE) reductive dechlorination by a microbial community enriched from contaminated groundwater and amended with C2H2 as the sole electron donor and organic carbon source. The metagenome of the stable, enriched community was analyzed to elucidate putative community functions. A novel anaerobic acetylenotroph in the phylum Actinobacteria was identified using metagenomic analysis. These results demonstrate that the coupling of acetylenotrophy and reductive dechlorination can occur in the environment with native bacteria and broaden our understanding of biotransformation at contaminated sites containing both TCE and C2H2IMPORTANCE Understanding the complex metabolisms of microbial communities in contaminated groundwaters is a challenge. PCE and TCE are among the most common groundwater contaminants in the United States that, when exposed to certain minerals, exhibit a unique abiotic degradation pathway in which C2H2 is a product. C2H2 can act as both an inhibitor of TCE dechlorination and of supporting metabolisms and an energy source for acetylenotrophic bacteria. Here, we combine laboratory microcosm studies with computational approaches to enrich and characterize an environmental microbial community that couples two uncommon metabolisms, demonstrating unique metabolic interactions only yet reported in synthetic, laboratory-constructed settings. Using this comprehensive approach, we have identified the first reported anaerobic acetylenotroph in the phylum Actinobacteria, demonstrating the yet-undescribed diversity of this metabolism that is widely considered to be uncommon.

Soft Scorpionate Hydridotris(2-mercapto-1-methylimidazolyl) borate) Tungsten-Oxido and -Sulfido Complexes as Acetylene Hydratase Models

A series of WIV alkyne complexes with the sulfur-rich ligand hydridotris(2-mercapto-1-methylimidazolyl) borate) (TmMe ) are presented as bio-inspired models to elucidate the mechanism of the tungstoenzyme acetylene hydratase (AH). The mono- and/or bis-alkyne precursors were reacted with NaTmMe and the resulting complexes [W(CO)(C2 R2 )(TmMe )Br] (R=H 1, Me 2) oxidized to the target [WE(C2 R2 )(TmMe )Br] (E=O, R=H 4, Me 5; E=S, R=H 6, Me 7) using pyridine-N-oxide and methylthiirane. Halide abstraction with TlOTf in MeCN gave the cationic complexes [WE(C2 R2 )(MeCN)(TmMe )](OTf) (E=CO, R=H 10, Me 11; E=O, R=H 12, Me 13; E=S, R=H 14, Me 15). Without MeCN, dinuclear complexes [W2 O(μ-O)(C2 Me2 )2 (TmMe )2 ](OTf)2 (8) and [W2 (μ-S)2 (C2 Me2 )(TmMe )2 ](OTf)2 (9) could be isolated showing distinct differences between the oxido and sulfido system with the latter exhibiting only one molecule of C2 Me2 . This provides evidence that a fine balance of the softness at W is important for acetylene coordination. Upon dissolving complex 8 in acetonitrile complex 13 is reconstituted in contrast to 9. All complexes exhibit the desired stability toward water and the observed effective coordination of the scorpionate ligand avoids decomposition to disulfide, an often-occurring reaction in sulfur ligand chemistry. Hence, the data presented here point toward a mechanism with a direct coordination of acetylene in the active site and provide the basis for further model chemistry for acetylene hydratase.

Bioinspired Tungsten Complexes Employing a Thioether Scorpionate Ligand

The synthesis and characterization of a series of novel tungsten complexes employing the bioinspired, sulfur-rich scorpionate ligand [PhTt] (phenyltris((methylthio)methyl)borate) are reported. Starting from the previously published tungsten precursor [WBr₂(CO)₃(NCMe)₂], a salt metathesis reaction with 1 equiv of Cs[PhTt] led to the desired complex [WBr(CO)₃(PhTt)] (1), making it the first tungsten complex employing a poly(thioether)borate ligand. Surprisingly, the reaction of [WBr₂(CO)₃(NCMe)₂] with an excess of the ligand gave complex [W(CO)₂(η²-CH₂SMe)(PhTt)] (2) with a bidentate (methylthio)methanide ligand as the major product. Thereby, phenyldi((methylthio)methyl)borane is formed, which was isolated and characterized by NMR spectroscopy. The bromido ligand in [WBr(CO)₃(PhTt)] was further substituted by the S,N-bidentate methimazole in order to make the first coordination sphere more sulfur-rich forming [W(CO)₂(mt)(PhTt)] (3). Alkyne tungsten complexes employing the sulfur-rich scorpionate ligand were accessible by reaction of [WBr₂(CO)(C₂R₂)₂(NCMe)] (R = Me, Ph) with Cs[PhTt] forming [WBr(CO)(C₂R₂)₂(PhTt- S, S')] (R = Me 4, Ph 5), with the potentially tridentate ligand coordinated only via two sulfur atoms. In the case of 4, the higher flexibility of the bidentate coordination leads to the formation of two isomers with respect to the six-membered ring formed by the tungsten center and the two coordinated sulfur atoms of the ligand. All complexes 1-5 were characterized by single-crystal X-ray diffraction analysis.

Activation and Photoinduced Release of Alkynes on a Biomimetic Tungsten Center: The Photochemical Behavior of the W-S-Phoz System

The synthesis and structural determination of four tungsten alkyne complexes coordinated by the bio-inspired S,N-donor ligand 2-(4',4'-dimethyloxazoline-2'-yl)thiophenolate (S-Phoz) is presented. A previously established protocol that involved the reaction of the respective alkyne with the bis-carbonyl precursor [W(CO)2 (S-Phoz)2 ] was used for the complexes [W(CO)(C2 R2 )(S-Phoz)2 ] (R=H, 1 a; Me, 1 b; Ph, 1 c). Oxidation with pyridine-N-oxide gave the corresponding W-oxo species [WO(C2 R2 )(S-Phoz)2 ] (R=H, 2 a; Me, 2 b; Ph, 2 c). All W-oxo-alkyne complexes (2 a, b, c) were found to be capable of alkyne release upon light irradiation to afford five-coordinate [WO(S-Phoz)2 ] (3). The photoinduced release of the alkyne ligand was studied in detail by in situ 1 H NMR measurements, which revealed correlation of the photodissociation rate constant (2 b>2 a>2 c) with the elongation of the alkyne C≡C bond in the molecular structures. Oxidation of [WO(S-Phoz)2 ] (3) with pyridine-N-oxide yielded [WO2 (S-Phoz)2 ] (4), which shows highly fluxional behavior in solution. Variable-temperature 1 H NMR spectroscopy revealed three isomeric forms with respect to the ligand arrangement versus each other. Furthermore, compound 4 rearranges to tetranuclear oxo compound [W4 O4 (μ-O)6 (S-Phoz)4 ] (5) and dinuclear [{WO(μ-O)(S-Phoz)}2 ] (6) over time. The latter two were identified by single-crystal X-ray diffraction analyses.

Acetylenotrophy: a hidden but ubiquitous microbial metabolism?

Acetylene (IUPAC name: ethyne) is a colorless, gaseous hydrocarbon, composed of two triple bonded carbon atoms attached to hydrogens (C2H2). When microbiologists and biogeochemists think of acetylene, they immediately think of its use as an inhibitory compound of certain microbial processes and a tracer for nitrogen fixation. However, what is less widely known is that anaerobic and aerobic microorganisms can degrade acetylene, using it as a sole carbon and energy source and providing the basis of a microbial food web. Here, we review what is known about acetylene degrading organisms and introduce the term 'acetylenotrophs' to refer to the microorganisms that carry out this metabolic pathway. In addition, we review the known environmental sources of acetylene and postulate the presence of an hidden acetylene cycle. The abundance of bacteria capable of using acetylene and other alkynes as an energy and carbon source suggests that there are energy cycles present in the environment that are driven by acetylene and alkyne production and consumption that are isolated from atmospheric exchange. Acetylenotrophs may have developed to leverage the relatively high concentrations of acetylene in the pre-Cambrian atmosphere, evolving later to survive in specialized niches where acetylene and other alkynes were produced.

ATP-dependent substrate reduction at an [Fe8S9] double-cubane cluster

Chemically demanding reductive conversions in biology, such as the reduction of dinitrogen to ammonia or the Birch-type reduction of aromatic compounds, depend on Fe/S-cluster-containing ATPases. These reductions are typically catalyzed by two-component systems, in which an Fe/S-cluster-containing ATPase energizes an electron to reduce a metal site on the acceptor protein that drives the reductive reaction. Here, we show a two-component system featuring a double-cubane [Fe₈S₉]-cluster [{Fe₄S₄(SCys)₃}₂(μ₂-S)]. The double-cubane-cluster-containing enzyme is capable of reducing small molecules, such as acetylene (C₂H₂), azide (N₃^-), and hydrazine (N₂H₄). We thus present a class of metalloenzymes akin in fold, metal clusters, and reactivity to nitrogenases.

Is the tungsten(IV) complex (NEt4)2[WO(mnt)2] a functional analogue of acetylene hydratase?

The tungsten(IV) complex (Et₄N)₂[W(O)(mnt)₂] (1; mnt = maleonitriledithiolate) was proposed (Sarkar et al., J. Am. Chem. Soc.1997, 119, 4315) to be a functional analogue of the active center of the enzyme acetylene hydratase from Pelobacter acetylenicus, which hydrates acetylene (ethyne; 2) to acetaldehyde (ethanal; 3). In the absence of a satisfactory mechanistic proposal for the hydration reaction, we considered the possibility of a metal–vinylidene type activation mode, as it is well established for ruthenium-based alkyne hydration catalysts with anti-Markovnikov regioselectivity. To validate the hypothesis, the regioselectivity of tungsten-catalyzed alkyne hydration of a terminal, higher alkyne had to be determined. However, complex 1 was not a competent catalyst for the hydration of 1-octyne under the conditions tested. Furthermore, we could not observe the earlier reported hydration activity of complex 1 towards acetylene. A critical assessment of, and a possible explanation for the earlier reported results are offered. The title question is answered with "no".

Detection of Diazotrophy in the Acetylene-Fermenting Anaerobe Pelobacter sp. Strain SFB93

Acetylene (C₂H₂) is a trace constituent of the present Earth's oxidizing atmosphere, reflecting a mixture of terrestrial and marine emissions from anthropogenic, biomass-burning, and unidentified biogenic sources. Fermentation of acetylene was serendipitously discovered during C₂H₂ block assays of N₂O reductase, and Pelobacter acetylenicus was shown to grow on C₂H₂ via acetylene hydratase (AH). AH is a W-containing, catabolic, low-redox-potential enzyme that, unlike nitrogenase (N₂ase), is specific for acetylene. Acetylene fermentation is a rare metabolic process that is well characterized only in P. acetylenicus DSM3246 and DSM3247 and Pelobacter sp. strain SFB93. To better understand the genetic controls for AH activity, we sequenced the genomes of the three acetylene-fermenting Pelobacter strains. Genome assembly and annotation produced three novel genomes containing gene sequences for AH, with two copies being present in SFB93. In addition, gene sequences for all five compulsory genes for iron-molybdenum N₂ase were also present in the three genomes, indicating the cooccurrence of two acetylene transformation pathways. Nitrogen fixation growth assays showed that DSM3426 could ferment acetylene in the absence of ammonium, but no ethylene was produced. However, SFB93 degraded acetylene and, in the absence of ammonium, produced ethylene, indicating an active N₂ase. Diazotrophic growth was observed under N₂ but not in experimental controls incubated under argon. SFB93 exhibits acetylene fermentation and nitrogen fixation, the only known biochemical mechanisms for acetylene transformation. Our results indicate complex interactions between N₂ase and AH and suggest novel evolutionary pathways for these relic enzymes from early Earth to modern days.IMPORTANCE Here we show that a single Pelobacter strain can grow via acetylene fermentation and carry out nitrogen fixation, using the only two enzymes known to transform acetylene. These findings provide new insights into acetylene transformations and adaptations for nutrient (C and N) and energy acquisition by microorganisms. Enhanced understanding of acetylene transformations (i.e., extent, occurrence, and rates) in modern environments is important for the use of acetylene as a potential biomarker for extraterrestrial life and for degradation of anthropogenic contaminants.