The exchange activities of [Fe] hydrogenase (iron-sulfur-cluster-free hydrogenase) from methanogenic archaea in comparison with the exchange activities of [FeFe] and [NiFe] hydrogenases.
Ontology highlight
ABSTRACT:
SUBMITTER: Vogt S
PROVIDER: S-EPMC2757585 | biostudies-other | 2008 Jan
REPOSITORIES: biostudies-other
Similar Datasets
Project description:The study of hydrogenase enzymes (H2ases) is necessary because of their importance to a future hydrogen energy economy. These enzymes come in three distinct classes: [NiFe] H2ases, which have a propensity toward H2 oxidation; [FeFe] H2ases, which have a propensity toward H2 evolution; and [Fe] H2ases, which catalyze H- transfer. Modeling these enzymes has so far treated them as different species, which is understandable given the different cores and ligand sets of the natural molecules. Here, we demonstrate, using x-ray analysis and nuclear magnetic resonance, infrared, Mössbauer spectroscopies, and electrochemical measurement, that the catalytic properties of all three enzymes can be mimicked with only three isomers of the same NiFe complex.
| S-EPMC7286669 | biostudies-literature
Project description:New mixed-valence iron-nickel dithiolates are described that exhibit structures similar to those of mixed-valence diiron dithiolates. The interaction of tricarbonyl salt [(dppe)Ni(pdt)Fe(CO)(3)]BF(4) ([1]BF(4), where dppe = Ph(2)PCH(2)CH(2)PPh(2) and pdt(2-) = -SCH(2)CH(2)CH(2)S-) with P-donor ligands (L) afforded the substituted derivatives [(dppe)Ni(pdt)Fe(CO)(2)L]BF(4) incorporating L = PHCy(2) ([1a]BF(4)), PPh(NEt(2))(2) ([1b]BF(4)), P(NMe(2))(3) ([1c]BF(4)), P(i-Pr)(3) ([1d]BF(4)), and PCy(3) ([1e]BF(4)). The related precursor [(dcpe)Ni(pdt)Fe(CO)(3)]BF(4) ([2]BF(4), where dcpe = Cy(2)PCH(2)CH(2)PCy(2)) gave the more electron-rich family of compounds [(dcpe)Ni(pdt)Fe(CO)(2)L]BF(4) for L = PPh(2)(2-pyridyl) ([2a]BF(4)), PPh(3) ([2b]BF(4)), and PCy(3) ([2c]BF(4)). For bulky and strongly basic monophosphorus ligands, the salts feature distorted coordination geometries at iron: crystallographic analyses of [1e]BF(4) and [2c]BF(4) showed that they adopt "rotated" Fe(I) centers, in which PCy(3) occupies a basal site and one CO ligand partially bridges the Ni and Fe centers. Like the undistorted mixed-valence derivatives, members of the new class of complexes are described as Ni(II)Fe(I) (S = ½) systems according to electron paramagnetic resonance spectroscopy, although with attenuated (31)P hyperfine interactions. Density functional theory calculations using the BP86, B3LYP, and PBE0 exchange-correlation functionals agree with the structural and spectroscopic data, suggesting that the spin for [1e](+) is mostly localized in a Fe(I)-centered d(z(2)) orbital, orthogonal to the Fe-P bond. The PCy(3) complexes, rare examples of species featuring "rotated" Fe centers, both structurally and spectroscopically incorporate features from homobimetallic mixed-valence diiron dithiolates. Also, when the NiS(2)Fe core of the [NiFe]-hydrogenase active site is reproduced, the "hybrid models" incorporate key features of the two major classes of hydrogenase. Furthermore, cyclic voltammetry experiments suggest that the highly basic phosphine ligands enable a second oxidation corresponding to the couple [(dxpe)Ni(pdt)Fe(CO)(2)L](+/2+). The resulting unsaturated 32e(-) dications represent the closest approach to modeling the highly electrophilic Ni-SI(a) state. In the case of L = PPh(2) (2-pyridyl), chelation of this ligand accompanies the second oxidation.
| S-EPMC3432505 | biostudies-literature
Project description:BackgroundFeFe-hydrogenases are the most active class of H2-producing enzymes known in nature and may have important applications in clean H2 energy production. Many potential uses are currently complicated by a crucial weakness: the active sites of all known FeFe-hydrogenases are irreversibly inactivated by O2.ResultsWe have developed a synthetic metabolic pathway in E. coli that links FeFe-hydrogenase activity to the production of the essential amino acid cysteine. Our design includes a complementary host strain whose endogenous redox pool is insulated from the synthetic metabolic pathway. Host viability on a selective medium requires hydrogenase expression, and moderate O2 levels eliminate growth. This pathway forms the basis for a genetic selection for O2 tolerance. Genetically selected hydrogenases did not show improved stability in O2 and in many cases had lost H2 production activity. The isolated mutations cluster significantly on charged surface residues, suggesting the evolution of binding surfaces that may accelerate hydrogenase electron transfer.ConclusionsRational design can optimize a fully heterologous three-component pathway to provide an essential metabolic flux while remaining insulated from the endogenous redox pool. We have developed a number of convenient in vivo assays to aid in the engineering of synthetic H2 metabolism. Our results also indicate a H2-independent redox activity in three different FeFe-hydrogenases, with implications for the future directed evolution of H2-activating catalysts.
| S-EPMC3130634 | biostudies-literature
Project description:Methanogenic archaea have long been implicated in microbially influenced corrosion (MIC) of oil and gas infrastructure, yet a first understanding of the underlying molecular mechanisms has only recently emerged. We surveyed pipeline-associated microbiomes from geographically distinct oil field facilities and found methanogens to account for 0.2 to 9.3% of the 16S rRNA gene sequencing reads. Neither the type nor the abundance of the detected methanogens was correlated with the perceived severity of MIC in these pipelines. Using fluids from one pipeline, MIC was reproduced in the laboratory, both under stagnant conditions and in customized corrosion reactors simulating pipeline flow. High corrosion rates (up to 2.43 mm Fe0 · yr-1) with macroscopic, localized corrosion features were attributed to lithotrophic, mesophilic microbial activity. Other laboratory tests with the same waters yielded negligible corrosion rates (<0.08 mm Fe0 · yr-1). Recently, a novel [NiFe] hydrogenase from Methanococcus maripaludis strain OS7 was demonstrated to accelerate corrosion. We developed a specific quantitative PCR (qPCR) assay and detected the gene encoding the large subunit of this hydrogenase (labeled micH) in corrosive (>0.15 mm Fe0 · yr-1) biofilms. The micH gene, on the other hand, was absent in noncorrosive biofilms, despite an abundance of methanogens. Reconstruction of a nearly complete Methanococcus maripaludis genome from a highly corrosive mixed biofilm revealed micH and associated genes in nearly identical genetic configuration to that in strain OS7, thereby supporting our hypothesis that the encoded molecular mechanism contributed to corrosion. Lastly, the proposed MIC biomarker was detected in multiple oil fields, indicating a geographically widespread involvement of this [NiFe] hydrogenase in MIC.IMPORTANCE Microorganisms can deteriorate built environments, which is particularly problematic in the case of pipelines transporting hydrocarbons to industrial end users. MIC is notoriously difficult to detect and monitor and, as a consequence, is a particularly difficult corrosion mechanism to manage. Despite the advent of molecular tools and improved microbial monitoring strategies for oil and gas operations, specific underlying MIC mechanisms in pipelines remain largely enigmatic. Emerging mechanistic understanding of methanogenic MIC derived from pure culture work allowed us to develop a qPCR assay that distinguishes technically problematic from benign methanogens in a West African oil field. Detection of the same gene in geographically diverse samples from North America hints at the widespread applicability of this assay. The research presented here offers a step toward a mechanistic understanding of biocorrosion in oil fields and introduces a binary marker for (methanogenic) MIC that can find application in corrosion management programs in industrial settings.
| S-EPMC7848899 | biostudies-literature
Project description:The enzyme [FeFe]-hydrogenase (HydA1) contains a unique 6-iron cofactor, the H-cluster, that has unusual ligands to an Fe-Fe binuclear subcluster: CN-, CO, and an azadithiolate (adt) ligand that provides 2 S bridges between the 2 Fe atoms. In cells, the H-cluster is assembled by a collection of 3 maturases: HydE and HydF, whose roles aren't fully understood, and HydG, which has been shown to construct a [Fe(Cys)(CO)2(CN)] organometallic precursor to the binuclear cluster. Here, we report the in vitro assembly of the H-cluster in the absence of HydG, which is functionally replaced by adding a synthetic [Fe(Cys)(CO)2(CN)] carrier in the maturation reaction. The synthetic carrier and the HydG-generated analog exhibit similar infrared spectra. The carrier allows HydG-free maturation to HydA1, whose activity matches that of the native enzyme. Maturation with 13CN-containing carrier affords 13CN-labeled enzyme as verified by electron paramagnetic resonance (EPR)/electron nuclear double-resonance spectra. This synthetic surrogate approach complements existing biochemical strategies and greatly facilitates the understanding of pathways involved in the assembly of the H-cluster. As an immediate demonstration, we clarify that Cys is not the source of the carbon and nitrogen atoms in the adt ligand using pulse EPR to target the magnetic couplings introduced via a 13C3,15N-Cys-labeled synthetic carrier. Parallel mass-spectrometry experiments show that the Cys backbone is converted to pyruvate, consistent with a cysteine role in donating S in forming the adt bridge. This mechanistic scenario is confirmed via maturation with a seleno-Cys carrier to form HydA1-Se, where the incorporation of Se was characterized by extended X-ray absorption fine structure spectroscopy.
| S-EPMC6800375 | biostudies-literature
Project description:The complex cation in the title compound, (carbonyl-1?C)(1?5-penta-methyl-cyclo-penta-dien-yl)(?-2,3,9,10-tetra-methyl-1,4,8,11-tetra-thia-undeca-2,9-diene-1,11-diido-1?2S,S''':2?4S,S',S'',S''')ironnickel(Fe-Ni) hexa-fluoro-phosphate, [FeNi(C10H15)(C11H18S4)(CO)]PF6 or [Ni(L')FeCp*(CO)]PF6, is composed of the nickel complex fragment [Ni(L')] coordinated as a metalloligand (using S1 and S4) to the [FeCp*(CO)]+ fragment, where (L')2- is [S-C(Me)=C(Me)-S-(CH2)3-S-C(Me)=C(Me)-S]2- and where Cp*- is cyclo-C5(Me)5- (penta-methyl-cyclo-penta-dien-yl). The ratio of hexa-fluoro-phosphate anion per complex cation is 1:1. The structure at 150?K has ortho-rhom-bic (Pbcn) symmetry. The atoms of the complex cation are located on general positions (multiplicity = 8), whereas there are two independent hexa-fluoro-phosphate anions, each located on a twofold axis (Wyckoff position 4c; multiplicity = 4). The structure of the new dimetallic cation [Ni(L')FeCp*(CO)]+ can be described as containing a three-legged piano-stool environment for iron [Cp*Fe(CO)'S2'] and an approximately square-planar 'S4' environment for Ni. The NiS2Fe diamond-shaped substructure is notably folded at the S-S hinge: the angle between the NiS2 plane and the FeS2 plane normals is 64.85?(6)°. Largely because of this fold, the nickel-iron distance is relatively short, at 2.9195?(8)?Å. The structural data for the complex cation, which contains a new unsaturated 'S4' ligand (two C=C double bonds), provide an inter-esting comparison with the known NiFe hydrogenase models containing a saturated 'S4'-ligand analogue having the same number of carbon atoms in the ligand backbone, namely with the structures of [Ni(L)FeCp(CO)]+ (as the PF6- salt, CH2Cl2 solvate) and [Ni(L)FeCp*(CO)]+ (as the PF6- salt), where (L)2- is [S-CH2-CH2-S-(CH2)3-S-CH2-CH2-S]2- and Cp- is cyclo-penta-dienyl. The saturated analogues [Ni(L)FeCp(CO)]+ and [Ni(L)FeCp*(CO)]+ have similar Ni-Fe distances: 3.1727?(6), 3.1529?(7)?Å (two independent mol-ecules in the unit cell) and 3.111?(5)?Å, respectively, for the two complexes, whereas [Ni(L')FeCp*(CO)]+ described here stands out with a much shorter Ni-Fe distance [2.9196?(8)?Å]. Also, [Ni(L)FeCp(CO)]+ and [Ni(L)FeCp*(CO)]+ show inter-planar fold angles that are similar between the two: 39.56?(5), 41.99?(5) (independent mol-ecules in the unit cell) and 47.22?(9) °, respectively, whereas [Ni(L')FeCp*(CO)]+ possesses a much more pronounced fold [64.85?(6)°]. Given that larger fold angles and shorter Ni-Fe distances are considered to be structurally closer to the enzyme, unsaturation in an 'S4'-ligand of the type (S-C2-S-C3-S-C2-S)2- seems to increase structural resemblance to the enzyme for structural models of the type [Ni('S4')FeCp R (CO)]+ (Cp R = Cp or Cp*).
| S-EPMC6127701 | biostudies-literature
Project description:A non-bifurcating NADH-dependent, dimeric [FeFe]-hydrogenase (HydAB) from Syntrophus aciditrophicus was heterologously produced in Escherichia coli, purified and characterized. Purified recombinant HydAB catalyzed NAD+ reduction coupled to hydrogen oxidation and produced hydrogen from NADH without the involvement of ferredoxin. Hydrogen partial pressures (2.2-40.2 Pa) produced by the purified recombinant HydAB at NADH to NAD+ ratios of 1-5 were similar to the hydrogen partial pressures generated by pure and cocultures of S. aciditrophicus (5.9-36.6 Pa). Thus, the hydrogen partial pressures observed in metabolizing cultures and cocultures of S. aciditrophicus can be generated by HydAB if S. aciditrophicus maintains NADH to NAD+ ratios greater than one. The flavin-containing beta subunits from S. aciditrophicus HydAB and the non-bifurcating NADH-dependent S. wolfei Hyd1ABC share a number of conserved residues with the flavin-containing beta subunits from non-bifurcating NADH-dependent enzymes such as NADH:quinone oxidoreductases and formate dehydrogenases. A number of differences were observed between sequences of these non-bifurcating NADH-dependent enzymes and [FeFe]-hydrogenases and formate dehydrogenases known to catalyze electron bifurcation including differences in the number of [Fe-S] centers and in conserved residues near predicted cofactor binding sites. These differences can be used to distinguish members of these two groups of enzymes and may be relevant to the differences in ferredoxin-dependence and ability to mediate electron-bifurcation. These results show that two phylogenetically distinct syntrophic fatty acid-oxidizing bacteria, Syntrophomonas wolfei a member of the phylum Firmicutes, and S. aciditrophicus, a member of the class Deltaproteobacteria, possess functionally similar [FeFe]-hydrogenases that produce hydrogen from NADH during syntrophic fatty acid oxidation without the involvement of reduced ferredoxin. The reliance on a non-bifurcating NADH-dependent [FeFe]-hydrogenases may explain the obligate requirement that many syntrophic metabolizers have for a hydrogen-using partner microorganism when grown on fatty, aromatic and alicyclic acids.
| S-EPMC7311640 | biostudies-literature
Project description:Structural genes coding for two membrane-associated NiFe hydrogenases in the phototrophic purple sulfur bacterium Thiocapsa roseopersicina (hupSL and hynSL) have recently been isolated and characterized. Deletion of both hydrogenase structural genes did not eliminate hydrogenase activity in the cells, and considerable hydrogenase activity was detected in the soluble fraction. The enzyme responsible for this activity was partially purified, and the gene cluster coding for a cytoplasmic, NAD+-reducing NiFe hydrogenase was identified and sequenced. The deduced gene products exhibited the highest similarity to the corresponding subunits of the cyanobacterial bidirectional soluble hydrogenases (HoxEFUYH). The five genes were localized on a single transcript according to reverse transcription-PCR experiments. A sigma54-type promoter preceded the gene cluster, suggesting that there was inducible expression of the operon. The Hox hydrogenase was proven to function as a truly bidirectional hydrogenase; it produced H2 under nitrogenase-repressed conditions, and it recycled the hydrogen produced by the nitrogenase in cells fixing N2. In-frame deletion of the hoxE gene eliminated hydrogen evolution derived from the Hox enzyme in vivo, although it had no effect on the hydrogenase activity in vitro. This suggests that HoxE has a hydrogenase-related role; it likely participates in the electron transfer processes. This is the first example of the presence of a cyanobacterial-type, NAD+-reducing hydrogenase in a phototrophic bacterium that is not a cyanobacterium. The potential physiological implications are discussed.
| S-EPMC348915 | biostudies-literature
Project description:The [4Fe-4S] cluster containing scaffold complex HypCD is the central construction site for the assembly of the [Fe](CN)2CO cofactor precursor of [NiFe]-hydrogenase. While the importance of the HypCD complex is well established, not much is known about the mechanism by which the CN- and CO ligands are transferred and attached to the iron ion. We report an efficient expression and purification system producing the HypCD complex from E. coli with complete metal content. This enabled in-depth spectroscopic characterizations. The results obtained by EPR and Mössbauer spectroscopy demonstrate that the [Fe](CN)2CO cofactor and the [4Fe-4S] cluster of the HypCD complex are redox active. The data indicate a potential-dependent interconversion of the [Fe]2+/3+ and [4Fe-4S]2+/+ couple, respectively. Moreover, ATR FTIR spectroscopy reveals potential-dependent disulfide formation, which hints at an electron confurcation step between the metal centers. MicroScale thermophoresis indicates preferable binding between the HypCD complex and its in vivo interaction partner HypE under reducing conditions. Together, these results provide comprehensive evidence for an electron inventory fit to drive multi-electron redox reactions required for the assembly of the CN- and CO ligands on the scaffold complex HypCD.
| S-EPMC8454700 | biostudies-literature
Project description:Hydrogenases are the most active molecular catalysts for hydrogen production and uptake, and could therefore facilitate the development of new types of fuel cell. In [FeFe]-hydrogenases, catalysis takes place at a unique di-iron centre (the [2Fe] subsite), which contains a bridging dithiolate ligand, three CO ligands and two CN(-) ligands. Through a complex multienzymatic biosynthetic process, this [2Fe] subsite is first assembled on a maturation enzyme, HydF, and then delivered to the apo-hydrogenase for activation. Synthetic chemistry has been used to prepare remarkably similar mimics of that subsite, but it has failed to reproduce the natural enzymatic activities thus far. Here we show that three synthetic mimics (containing different bridging dithiolate ligands) can be loaded onto bacterial Thermotoga maritima HydF and then transferred to apo-HydA1, one of the hydrogenases of Chlamydomonas reinhardtii algae. Full activation of HydA1 was achieved only when using the HydF hybrid protein containing the mimic with an azadithiolate bridge, confirming the presence of this ligand in the active site of native [FeFe]-hydrogenases. This is an example of controlled metalloenzyme activation using the combination of a specific protein scaffold and active-site synthetic analogues. This simple methodology provides both new mechanistic and structural insight into hydrogenase maturation and a unique tool for producing recombinant wild-type and variant [FeFe]-hydrogenases, with no requirement for the complete maturation machinery.
| S-EPMC3793303 | biostudies-literature