Types Of Hydrogenases Research Articles

Homogeneous HER electrocatalysis using monothiolate ligand-based {FeS} complexes: A review

Renewable energy sources are considered as efficient, low cost and sustainable energy systems with the capability of achieving a decarbonized world. Of particular interest has been the use of hydrogen as an affordable and clean energy for achieving a sustainable (renewable) energy economy. The hydrogenases discovered almost 90 years ago and found in green algae and anaerobic bacteria, are known to be highly efficient biological catalysts for hydrogen evolution in nature. Out of the three types of hydrogenases ([FeFe], [NiFe] and [Fe] only) the [FeFe] hydrogenases have drawn particular attention due to their higher activity/efficiency and their ability to reversibly reduce protons to dihydrogen. Several models of the [FeFe] hydrogenase enzymes have been reported over the last three decades. This review article mainly describes in details the characteristics of mono- and di-nuclear {FeS} complexes with monothiolates (-SR) as the bridging ligands that have been reported as electrocatalysts for the hydrogen evolution reaction (HER).

Groundwater cable bacteria conserve energy by sulfur disproportionation

Cable bacteria of the family Desulfobulbaceae couple spatially separated sulfur oxidation and oxygen or nitrate reduction by long-distance electron transfer, which can constitute the dominant sulfur oxidation process in shallow sediments. However, it remains unknown how cells in the anoxic part of the centimeter-long filaments conserve energy. We found 16S rRNA gene sequences similar to groundwater cable bacteria in a 1-methylnaphthalene-degrading culture (1MN). Cultivation with elemental sulfur and thiosulfate with ferrihydrite or nitrate as electron acceptors resulted in a first cable bacteria enrichment culture dominated >90% by 16S rRNA sequences belonging to the Desulfobulbaceae. Desulfobulbaceae-specific fluorescence in situ hybridization (FISH) unveiled single cells and filaments of up to several hundred micrometers length to belong to the same species. The Desulfobulbaceae filaments also showed the distinctive cable bacteria morphology with their continuous ridge pattern as revealed by atomic force microscopy. The cable bacteria grew with nitrate as electron acceptor and elemental sulfur and thiosulfate as electron donor, but also by sulfur disproportionation when Fe(Cl)2 or Fe(OH)3 were present as sulfide scavengers. Metabolic reconstruction based on the first nearly complete genome of groundwater cable bacteria revealed the potential for sulfur disproportionation and a chemo-litho-autotrophic metabolism. The presence of different types of hydrogenases in the genome suggests that they can utilize hydrogen as alternative electron donor. Our results imply that cable bacteria not only use sulfide oxidation coupled to oxygen or nitrate reduction by LDET for energy conservation, but sulfur disproportionation might constitute the energy metabolism for cells in large parts of the cable bacterial filaments.

Understanding the Special Properties of [NiFeSe] Hydrogenases through the Use of Computational Methodologies

Hydrogenases are metalloenzymes that catalyze the reversible reaction H2 ⇄ 2H+ +2e- . In order to use H2 as fuel in a sustainable way, we should learn how to use hydrogenases' unique ability to oxidize and produce H2 without the need for high temperatures, high over potentials and noble metals.Two main families of hydrogenases can be distinguished: the [FeFe] and the [NiFe] hydrogenases. Among the last ones, there is a subgroup with outstanding properties - the [NiFeSe] hydrogenases. They have higher activities and are less inhibited by product during H2 production, and they are more tolerant to the inhibition by O2 than the standard [NiFe] hydrogenases. However, the structural determinants responsible for these special properties remain unknown. The replacement of the one of the active site cysteines by a selenocysteine, apparently, is not enough to explain the differences between the standard [NiFe] and the [NiFeSe] hydrogenases. In addition, it is also not understood, why some [NiFeSe] hydrogenases can exist in a membrane form and in a soluble form, and why is the membrane form more active when the only difference between them is a lipidic tail for membrane anchoring.Our aim is to the answer the open questions regarding the special features of [NiFeSe] hydrogenases using computational methodologies such as molecular dynamics and continuum electrostatics. Our first results indicate that the [NiFeSe] hydrogenases have an alternative channel for H2 diffusion between the protein exterior and the deeply buried active site non-existing in standard [NiFe] hydrogenases. We have also been able to identify differences in the proton transfer pathways between the two types of hydrogenases.

The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics

Dehalobacter restrictus strain PER-K23 is an obligate organohalide respiring bacterium, which displays extremely narrow metabolic capabilities. It grows only via coupling energy conservation to anaerobic respiration of tetra- and trichloroethene with hydrogen as sole electron donor. Dehalobacter restrictus represents the paradigmatic member of the genus Dehalobacter, which in recent years has turned out to be a major player in the bioremediation of an increasing number of organohalides, both in situ and in laboratory studies. The recent elucidation of the D. restrictus genome revealed a rather elaborate genome with predicted pathways that were not suspected from its restricted metabolism, such as a complete corrinoid biosynthetic pathway, the Wood-Ljungdahl (WL) pathway for CO2 fixation, abundant transcriptional regulators and several types of hydrogenases. However, one important feature of the genome is the presence of 25 reductive dehalogenase genes, from which so far only one, pceA, has been characterized on genetic and biochemical levels. This study describes a multi-level functional genomics approach on D. restrictus across three different growth phases. A global proteomic analysis allowed consideration of general metabolic pathways relevant to organohalide respiration, whereas the dedicated genomic and transcriptomic analysis focused on the diversity, composition and expression of genes associated with reductive dehalogenases.

Electronic Elements Governing the Binding of Small Molecules to a [Fe]‐Hydrogenase Mimic

Abstract[Fe]‐hydrogenase, one of three types of hydrogenases, activates molecular hydrogen. Here, using DFT computations, we examine the electronic elements governing the binding of small ligands to a recently synthesized [Fe]‐hydrogenase biomimic. Computed reaction free energies indicate that anionic species, such as CN– and H–, and π acceptors, such as CO, bind favourably with the Fe centre. Ligands such as H2O, CH3CN, and H2, however, do not bind iron. Protonation of an adjacent thiolate ligand on the mimic significantly increases the energies of ligand binding. Additional computational analysis reveals that the degree of electron donation from the ligand to the mimic correlates strongly with overall binding ability. The results give insights into the electronic elements of iron–small‐molecule interaction in these model complexes.

Extended X-ray absorption fine structure of the [Fe]-hydrogenase Hmd active site

Hydrogenases are enzymes that catalyze the reversible oxidation of molecular hydrogen. Although their structure and catalytic mechanism are of considerable applied interest as models for the development of efficient catalysts for hydrogen fueled processes, the understanding of how hydrogenases react with H2 is only in its infancy. Two of the three known types of hydrogenases are iron-sulfur proteins that contain a dinuclear metal center, either [NiFe] or [FeFe]. In contrast, [Fe]-hydrogenase is the only mononuclear hydrogenase and thus a perfect system for studying the structural and electronic determinants of these enzymes. Here we summarize recent improvements in modeling based on the EXAFS signal and the geometric structure of this metalloenzyme in its as isolated or reconstituted form. The individual contributions to the EXAFS resulting in two different structural models are presented and discussed. Inspired by the new crystal structure, we show an advanced EXAFS model for the enzyme from Methanothermobacter marburgensis.

The Iron-Sulfur Cluster-free Hydrogenase (Hmd) Is a Metalloenzyme with a Novel Iron Binding Motif

The iron-sulfur cluster-free hydrogenase (Hmd) from methanogenic archaea harbors an iron-containing cofactor of yet unknown structure. X-ray absorption spectroscopy of the active, as isolated enzyme from Methanothermobacter marburgensis (mHmd) and of the active, reconstituted enzyme from Methanocaldococcus jannaschii (jHmd) revealed the presence of mononuclear iron with two CO, one sulfur and one or two N/O in coordination distance. In jHmd, the single sulfur ligand is most probably provided by Cys176, as deduced from a comparison of the activity and of the x-ray absorption and Mössbauer spectra of the enzyme mutated in any of the three conserved cysteines. In the isolated Hmd cofactor, two CO, one sulfur, and two nitrogen/oxygen atoms coordinate the iron, the sulfur ligand being most probably provided by mercaptoethanol, which is absolutely required for the extraction of the iron-containing cofactor from the holoenzyme and for the stabilization of the extracted cofactor. In active mHmd holoenzyme, the number of iron ligands increased by one when one of the Hmd inhibitors (CO or KCN) were present, indicating that in active Hmd, the iron contains an open coordination site, which is proposed to be the site of H2 interaction.

Biodiversity of Hydrogenases in Frankia

Eighteen Frankia strains originally isolated from nine different host plants were used to study the biodiversity of hydrogenase in Frankia. In the physiological analysis, the activities of uptake hydrogenase and bidirectional hydrogenase were performed by monitoring the oxidation of hydrogen after supplying the cells with 1% hydrogen and the evolution of hydrogen using methyl viologen as an electron donor, respectively. These analyses were supported with a study of the immunological relationship between Frankia hydrogenase and other different known hydrogenases from other microorganisms. Uptake hydrogenase activity was recorded from all the Frankia strains investigated. A methyl-viologen-mediated hydrogen evolution was recorded from only four Frankia strains irrespective of the source of Frankia. From the immunological and physiological studies, we here report that there are at least three types of hydrogenases in Frankia: Ni-Fe uptake hydrogenase, hydrogen-evolving hydrogenase, and [Fe]-hydrogenase. An immunogold localization study, by cryosection technique, of the effect of nickel on the intercellular distribution of hydrogenase proteins in Frankia indicated that nickel affects the transfer of hydrogenase proteins into the membrane.

Localization and specificity of cytochromes and other electron transfer proteins from sulfate-reducing bacteria

Recently data have accumulated concerning the electron transfer chains of sulfate-reducing bacteria in general and of the genus Desulfovibrio in particular. Because of the ever growing number of newly discovered individual redox proteins, it has of these proteins within the bacterial cell and the specificity of electron transfer between the three types of hydrogenases which become essential to try to assign them to physiologically relevant chains. This work presents some new data concerning the localization have been found so far in Desulfovibrio, namely the iron-only, the iron-nickel and the iron-nickel-selenium enzymes. The iron-only hydrogenase reduces cytochromes which have bis-histidinyl heme ligation or histidinyl-methionyl heme ligation. In contrast, the iron-nickel and iron-nickel-selenium hydrogenases cannot reduce cytochromes having a His-Met heme ligation, but are very active toward the cytochromes having a bis-histidinyl ligand. This observation has been used to demonstrate that the tetraheme cytochrome c 3 can exchange electrons with the monoheme cytochrome c 553. No clear specificity has been established for the reaction of hydrogenases toward the hexadecaheme cytochromes from either D vulgaris of D gigas.

Structure-function relationships among the nickel-containing hydrogenases.

The enzymology of the heterodimeric (NiFe) and (NiFeSe) hydrogenases, the monomeric nickel-containing hydrogenases plus the multimeric F420-(NiFe) and NAD(+)-(NiFe) hydrogenases are summarized and discussed in terms of subunit localization of the redox-active nickel and non-heme iron clusters. It is proposed that nickel is ligated solely by amino acid residues of the large subunit and that the non-heme iron clusters are ligated by other cysteine-rich polypeptides encoded in the hydrogenase operons which are not necessarily homologous in either structure or function. Comparison of the hydrogenase operons or putative operons and their hydrogenase genes indicate that the arrangement, number and types of genes in these operons are not conserved among the various types of hydrogenases except for the gene encoding the large subunit. Thus, the presence of the gene for the large subunit is the sole feature common to all known nickel-containing hydrogenases and unites these hydrogenases into a large but diverse gene family. Although the different genes for the large subunits may possess only nominal general derived amino acid homology, all large subunit genes sequenced to date have the sequence R-X-C-X-X-C fully conserved in the amino terminal region of the polypeptide chain and the sequence of D-P-C-X-X-C fully conserved in the carboxyl terminal region. It is proposed that these conserved motifs of amino acids provide the ligands required for the binding of the redox-active nickel. The existing EXAFS (Extended X-ray Absorption Fine Structure) information is summarized and discussed in terms of the numbers and types of ligands to the nickel and the various redox species of nickel defined by EPR spectroscopy. New information concerning the ligands to nickel is presented based on site-directed mutagenesis of the gene encoding the large subunit of the (NiFe) hydrogenase-1 of Escherichia coli. Based on considerations of the biochemical, molecular and biophysical information, ligand environments of the nickel in different redox states of the (NiFe) hydrogenase are proposed.

Structure-function relationships among the nickel-containing hydrogenases

The enzymology of the heterodimeric (NiFe) and (NiFeSe) hydrogeneses, the monomeric nickel-containing hydrogenases plus the multimeric F 420-(NiFe) and NAD +-(NiFe) hydrogenases are summarized and discussed in terms of subunit localization of the redox-active nickel and non-heme iron clusters. It is proposed that nickel is ligated solely by amino acid residues of the large subunit and that the non-heme iron clusters are ligated by other cysteine-rich polypeptides encoded in the hydrogenase operons which are not necessarily homologous in either structure or function. Comparison of the hydrogenase operons or putative operons and their hydrogenase genes indicate that the arrangement, number and types of genes in these operons are not conserved among the various types of hydrogenases except for the gene encoding the large subunit. Thus, the presence of the gene for the large subunit is the sole feature common to all known nickel-containing hydrogenases and unites these hydrogenases into a large but diverse gene family. Although the different genes for the large subunits may possess only nominal general derived amino acid homology, all large subunit genes sequenced to date have the sequence R-X-C-X-X-C fully conserved in the amino terminal region of the polypeptide chain and the sequence D-P-C-X-X-C fully conserved in the carboxyl terminal region. It is proposed that these conserved motifs of amino acids provide the ligands required for the binding of the redox-active nickel. The existing EXAFS (Extended X-ray Absorption Fine Structure) information is summarized and discussed in terms of the numbers and types of ligands to the nickel and the various redox species of nickel defined by EPR spectroscopy. New information concerning the ligands to nickel is presented based on site-directed mutagenesis of the gene encoding the large subunit of the (NiFe) hydrogenase-1 of Escherichia coli. Based on considerations of the biochemical, molecular and biophysical information, ligand environments of the nickel in different redox states of the (NiFe) hydrogenase are proposed.

Utilization of cathodically-produced hydrogen from mild steel byDesulfovibrio species with different types of hydrogenases

Desulfovibrio (D.) vulgaris Hildenborough with a highly active Fe-containing periplasmic hydrogenase,D. salexigens British Guiana with a Fe−Ni−Se periplasmic hydrogenase, andD. multispirans with a Fe−Ni cytoplasmic hydrogenase utilized cathodically-produced hydrogen from mild steel as the only energy source for activity and growth. Changes on the mild steel surface occurred during growth of these bacteria. The concentration of iron sulfide, a corrosion product of mild steel, increased over time, andDesulfovibrio species had an active hydrogenase when they were grown in lactate/sulfate media. This hydrogenase may be any of the three types found in the genus,Desulfovibrio. The concentration of iron in the media affected the production and activity of the Fe-hydrogenase fromD. vulgaris Hildenborough. With an iron-limited medium, the specific activity and the total amount of the periplasmic hydrogenase was less than found with a non-iron limited media.

The three classes of hydrogenases from sulfate-reducing bacteria of the genus Desulfovibrio.

Three types of hydrogenases have been isolated from the sulfate-reducing bacteria of the genus Desulfovibrio. They differ in their subunit and metal compositions, physico-chemical characteristics, amino acid sequences, immunological reactivities, gene structures and their catalytic properties. Broadly, the hydrogenases can be considered as 'iron only' hydrogenases and nickel-containing hydrogenases. The iron-sulfur-containing hydrogenase ([Fe] hydrogenase) contains two ferredoxin-type (4Fe-4S) clusters and an atypical iron-sulfur center believed to be involved in the activation of H2. The [Fe] hydrogenase has the highest specific activity in the evolution and consumption of hydrogen and in the proton-deuterium exchange reaction and this enzyme is the most sensitive to CO and NO2-. It is not present in all species of Desulfovibrio. The nickel-(iron-sulfur)-containing hydrogenases [( NiFe] hydrogenases) possess two (4Fe-4S) centers and one (3Fe-xS) cluster in addition to nickel and have been found in all species of Desulfovibrio so far investigated. The redox active nickel is ligated by at least two cysteinyl thiolate residues and the [NiFe] hydrogenases are particularly resistant to inhibitors such as CO and NO2-. The genes encoding the large and small subunits of a periplasmic and a membrane-bound species of the [NiFe] hydrogenase have been cloned in Escherichia (E.) coli and sequenced. Their derived amino acid sequences exhibit a high degree of homology (70%); however, they show no obvious metal-binding sites or homology with the derived amino acid sequence of the [Fe] hydrogenase. The third class is represented by the nickel-(iron-sulfur)-selenium-containing hydrogenases [( NiFe-Se] hydrogenases) which contain nickel and selenium in equimolecular amounts plus (4Fe-4S) centers and are only found in some species of Desulfovibrio. The genes encoding the large and small subunits of the periplasmic hydrogenase from Desulfovibrio (D.) baculatus (DSM 1743) have been cloned in E. coli and sequenced. The derived amino acid sequence exhibits homology (40%) with the sequence of the [NiFe] hydrogenase and the carboxy-terminus of the gene for the large subunit contains a codon (TGA) for selenocysteine in a position homologous to a codon (TGC) for cysteine in the large subunit of the [NiFe] hydrogenase. EXAFS and EPR studies with the 77Se-enriched D. baculatus hydrogenase indicate that selenium is a ligand to nickel and suggest that the redox active nickel is ligated by at least two cysteinyl thiolate and one selenocysteine selenolate residues.(ABSTRACT TRUNCATED AT 400 WORDS)

The three classes of hydrogenases from sulfate-reducing bacteria of the genus Desulfovibrio

Three types of hydrogenases have been isolated from the sulfate-reducing bacteria of the genus Desulfobibrio. They differ in their subunit and metal compositions, physico-chemical characteristics, amino acid sequences, immunological ractivities, gene structures and their catalytic properties. Broadly, the hydrogenases can be considered as ‘iron only’ hydrogenases and nickel-containing hydrogenases. The iron-sulfur-containg hydrogenase ([Fe] hydrogenase) contains two ferredoxin-type (4Fe-4S) clusters and an atypical iron-sulfur center belived to be involved in the activation of H 2. The [Fe] hydrogenase has the highest specific activity in the evolution and consumption of hydrogen and in the proton-deuterium exchange reaction and this enzyme is the most sensitive to CO and NO 2 −. It is not present in all species of Desulfovibrio The nickel-(iron-sulfur)-containing hydrogenases ([NiFe] hydrogenase) posses two (4Fe-4S) centers and one (3Fe- xS) cluster in addition to nickel and have been found in all species of Desulfovibrio so far investigated. The redox active nickel is ligated by at least two cysteinyl thiolate residues and the [NiFe] hydrogenases are particularly resistant to inhibitors such as CO and NO 2 −. The genes encoding the large and small subunits of a periplasmic and a membrane-bound species of the [NiFe] hydrogenase have been cloned in Eschierichia (E.) coli and sequenced. Their derived amino acid sequences exhibit a high degree of homology (70%); however, they show no obvious metal-binding sites or homology with the derived amino acid sequence of the [Fe] hydrogenase. The third class is represented by the nickel-iron-sulfur)-selenium-containing hydrogenases ([NiFe-Se] hydrohenases) which contain nickel and selenium in equimoleular amounts plus (4Fe-4S) centers and are only found in some species of Desulfovibrio. The genes encoding the large and small subunits of the periplasmic hydrogenase from Desulfrovibio (D) baculatus (DSM 1743) (for abbrviations see appendix) have been cloned

Characterization and partial purification of the reversible hydrogenase of Anabaena cylindrica

Three types of hydrogenases are recognized in the literature; a reversible hydrogenase which has been highly purified and characterized from saccharolytic bacteria [ 11, an uptake hydrogenase which is seemingly incapable of evolving hydrogen and differs from the reversible hydrogenase in being saturated at low pH2 [2], and the ATP-driven hydrogen evolution catalyzed by nitrogenase in the absence of other reducible substrates [3]. Species of cyanobacteria such as Anabaena cylindrica contain all three types of hydrogenase under some conditions [4]. Hydrogen evolution by nitrogenase in this organism has been studied in some detail [5-71. The presence of an uptake hydrogenase, similar to the Azofobacter hydrogenase, has been demonstrated [&lo]. The presence of reversible hydrogenase activity can be directly shown with cultures of A. cylindrica that lack nitrogenase activity either through growth in the presence of tungsten instead of molybdenum, or through ammonium repression [ 11 ,12 1. Hydrogen is produced by isolated heterocysts or vegetative cell fragments supplied with artificial electron donors [ 131. In [ 14,151 crude extracts with hydrogenase activity were prepared from nitrate-grown cultures of A. cylindrica incubated anaerobically in the dark under an atmosphere of hydrogen. It was found that phenazine methosulphate, methylene blue, dichlorophenol-indophenol and toluidine blue were effective as electron acceptors, but the results suggested that redox coupling between the hydrogenase and ferredoxin had a very low efficiency. When crude extracts