Hydrogen isotope effects in the reactions catalyzed by H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase from methanogenic Archaea

[Fe]-Hydrogenase, Cofactor Biosynthesis and Engineering

[Fe]-hydrogenase catalyzes the heterolytic cleavage of H2 and reversible hydride transfer to methenyl-tetrahydromethanopterin. The iron-guanylylpyridinol (FeGP) cofactor is the prosthetic group of this enzyme, in which mononuclear Fe(II) is ligated with a pyridinol and two CO ligands. The pyridinol ligand fixes the iron by an acyl carbon and a pyridinol nitrogen. Biosynthetic proteins for this cofactor are encoded in the hmd co-occurring (hcg) genes. The function of HcgB, HcgC, HcgD, HcgE, and HcgF was studied by using structure-to-function analysis, which is based on the crystal structure of the proteins and subsequent enzyme assays. Recently, we reported the catalytic properties of HcgA and HcgG, novel radical S-adenosyl methionine enzymes, by using an in vitro biosynthesis assay. Here, we review the properties of [Fe]-hydrogenase and the FeGP cofactor, and the biosynthesis of the FeGP cofactor. Finally, we discuss the expected engineering of [Fe]-hydrogenase and the FeGP cofactor.

Scaffold-Based Functional Models of [Fe]-Hydrogenase (Hmd): Building the Bridge between Biological Structure and Molecular Function

The well-known dinuclear [FeFe] and [NiFe] hydrogenase enzymes are redox-based proton reduction and H₂ oxidation catalysts. In comparison, the structural and functional aspects of the mononuclear nonredox hydrogenase, known as [Fe]-hydrogenase or Hmd, have been less explored because of the relatively recent crystallographic elucidation of the enzyme active site. Additionally, the synthetic challenges posed by the highly substituted and asymmetric coordination environment of the iron guanylylpyridinol (FeGP) cofactor have hampered functional biomimetic modeling studies to a large extent. The active site contains an octahedral low-spin Fe(II) center with the following coordination motifs: a bidentate acyl-pyridone moiety (C,N) and cysteinyl-S in a facial arrangement; two cis carbonyl ligands; and a H₂O/H₂ binding site. In [Fe]-hydrogenase, heterolytic H₂ activation putatively by the pendant pyridone/pyridonate-O base serving as a proton acceptor. Following H₂ cleavage, an intermediate Fe-H species is thought to stereoselectively transfer a hydride to the substrate methenyl-H₄MPT⁺, thus forming methylene-H₄MPT. In the past decade, chemists, inspired by the elegant organometallic chemistry inherent to the FeGP cofactor, have synthesized a number of faithful structural models. However, functional systems are still relatively limited and often rely on abiological ligands or metal centers that obfuscate a direct correlation to nature's design.Our group has developed a bioinspired suite of synthetic analogues of Hmd to better understand the effects of structure on the stability and functionality of the Hmd active site, with a special emphasis on using a scaffold-based ligand design. This systematic approach has contributed to a deeper understanding of the unique ligand array of [Fe]-hydrogenase in nature and has ultimately resulted in the first functional synthetic models without the aid of abiological ligands. This Account reviews the reactivity of the functional anthracene-scaffolded synthetic models developed by our group in the context of current mechanistic understanding drawn from both protein crystallography and computational studies. Furthermore, we introduce a novel thermodynamic framework to place the reactivity of our model systems in context and provide an outlook on the future study of [Fe]-hydrogenase synthetic models through both a structural and functional lens.

Isotopic fractionation associated with [NiFe]- and [FeFe]-hydrogenases

RATIONALE

Hydrogenases catalyze the reversible formation of H2 from electrons and protons with high efficiency. Understanding the relationships between H2 production, H2 uptake, and H2-H2O exchange can provide insight into the metabolism of microbial communities in which H2 is an essential component in energy cycling.

METHODS

We used stable H isotopes (1H and 2H) to probe the isotope effects associated with three [FeFe]-hydrogenases and three [NiFe]-hydrogenases.

RESULTS

All six hydrogenases displayed fractionation factors for H2 formation that were significantly less than 1, producing H2 that was severely depleted in 2H relative to the substrate, water. Consistent with differences in their active site structure, the fractionation factors for each class appear to cluster, with the three [NiFe]-hydrogenases (α = 0.27–0.40) generally having smaller values than the three [FeFe]-hydrogenases (α = 0.41–0.55). We also obtained isotopic fractionation factors associated with H2 uptake and H2-H2O exchange under conditions similar to those utilized for H2 production, providing a more complete picture of the reactions catalyzed by hydrogenases.

CONCLUSIONS

The fractionation factors determined in our studies can be used as signatures for different hydrogenases to probe their activity under different growth conditions and to ascertain which hydrogenases are most responsible for H2 production and/or uptake in complex microbial communities.

Hydrogen-activation mechanism of [Fe] hydrogenase revealed by multi-scale modeling

A complete atomistic model of [Fe] hydrogenase reveals important details of its mechanism.

Kinetic modeling of hydrogen conversion at [Fe] hydrogenase active-site models

By means of density functional theory, we investigate the catalytic cycle of active-site model complexes of [Fe] hydrogenase and study how ligand substitutions in the first coordination sphere of the reactive Fe center affect the free-energy surface of the whole reaction pathway. Interestingly, dispersion interactions between the active site and the hydride acceptor MPT render the hydride transfer step less endergonic and lower its barrier. Substitution of CO by CN(-), which resembles [FeFe] hydrogenase-like coordination, inverts the elementary steps H(-) transfer and H2 cleavage. A simplified kinetic model reveals the specifics of the interplay between active-site composition and catalysis. Apparently, the catalytic efficiency of [Fe] hydrogenase can be attributed to a flat energy profile throughout the catalytic cycle. Intermediates that are too stable, as they occur, e.g., when one CO ligand is substituted by CN(-), significantly slow down the turnover rate of the enzyme. The catalytic activity of the wild-type form of the active-site model could, however, be enhanced by a PH3 ligand substitution of the CO ligand.

Evolution in the understanding of [Fe]-hydrogenase

Hydrogenases catalyse redox reactions with molecular hydrogen, either as substrate or product. The enzymes harness hydrogen as a reductant using metals that are abundant and economical, namely, nickel and iron, and should provide new pointers for the economic use of hydrogen in manmade devices. The most recently discovered and perhaps the most enigmatic of the hydrogenases is the [Fe]-hydrogenase, used by certain microorganisms in the pathway that reduces carbon dioxide to methane. Since its discovery some twenty years ago, [Fe]-hydrogenase has consistently provided structural and mechanistic surprises, often requiring complete re-evaluation of its mechanism of action. This tutorial review combines recent advances in X-ray crystallography and other analytical techniques, as well as in computational studies and in chemical synthesis to provide a platform for understanding this remarkable enzyme type.

Amidine dications: isolation and [Fe]-hydrogenase-related hydrogenation

This commmunication demonstrates the preparation, isolation, and full characterization of superelectrophilic salts based on amidine dications in organic solvent, as their triflate salts. These dications are highly activated toward regiospecific reaction with hydrogen gas under mild conditions in the presence of a metal catalyst (Pd/C), mimicking the behavior of the natural substrate, N⁵,N¹⁰-methenyltetrahydromethanopterin, in the iron−sulfur cluster-free [Fe]-hydrogenase.

Carbon Monoxide as Intrinsic Ligand to Iron in the Active Site of [Fe]-Hydrogenase

Structural and spectroscopic studies on [Fe]-hydrogenase revealed an active site mononuclear low spin iron coordinated by the Cys176 sulfur, two CO, and the sp2 hybridized nitrogen of a 2-pyridinol compound with back bonding properties similar to those of cyanide. Thus, [Fe]-hydrogenases are endowed with an iron-ligation pattern related to that found in the active site of [NiFe]- and [FeFe]-hydrogenases although the three hydrogenases and the enzymes involved in their posttranslational maturation have evolved independently and although CO and cyanide ligands are not found in any other metallo-enzymes. Obviously, low-spin iron complexed with thiolate(s), CO, and cyanide or a cyanide functional analogue plays an essential role in H2 activation.

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

[Fe] hydrogenase (iron-sulfur-cluster-free hydrogenase) catalyzes the reversible reduction of methenyltetrahydromethanopterin (methenyl-H4MPT+) with H2 to methylene-H4MPT, a reaction involved in methanogenesis from H2 and CO2 in many methanogenic archaea. The enzyme harbors an iron-containing cofactor, in which a low-spin iron is complexed by a pyridone, two CO and a cysteine sulfur. [Fe] hydrogenase is thus similar to [NiFe] and [FeFe] hydrogenases, in which a low-spin iron carbonyl complex, albeit in a dinuclear metal center, is also involved in H2 activation. Like the [NiFe] and [FeFe] hydrogenases, [Fe] hydrogenase catalyzes an active exchange of H2 with protons of water; however, this activity is dependent on the presence of the hydride-accepting methenyl-H4MPT+. In its absence the exchange activity is only 0.01% of that in its presence. The residual activity has been attributed to the presence of traces of methenyl-H4MPT+ in the enzyme preparations, but it could also reflect a weak binding of H2 to the iron in the absence of methenyl-H4MPT+. To test this we reinvestigated the exchange activity with [Fe] hydrogenase reconstituted from apoprotein heterologously produced in Escherichia coli and highly purified iron-containing cofactor and found that in the absence of added methenyl-H4MPT+ the exchange activity was below the detection limit of the tritium method employed (0.1 nmol min(-1) mg(-1)). The finding reiterates that for H2 activation by [Fe] hydrogenase the presence of the hydride-accepting methenyl-H4MPT+ is essentially required. This differentiates [Fe] hydrogenase from [FeFe] and [NiFe] hydrogenases, which actively catalyze H2/H2O exchange in the absence of exogenous electron acceptors.

Carbon Monoxide as an Intrinsic Ligand to Iron in the Active Site of the Iron−Sulfur-Cluster-Free Hydrogenase H2-Forming Methylenetetrahydromethanopterin Dehydrogenase As Revealed by Infrared Spectroscopy

The iron-sulfur-cluster-free hydrogenase Hmd (H(2)-forming methylenetetrahydromethanopterin dehydrogenase) from methanogenic archaea has recently been found to contain one iron associated tightly with an extractable cofactor of yet unknown structure. We report here that Hmd contains intrinsic CO bound to the Fe. Chemical analysis of Hmd revealed the presence of 2.4 +/- 0.2 mol of CO/mol of iron. Fourier transform infrared spectra of the native enzyme showed two bands of almost equal intensity at 2011 and 1944 cm(-)(1), interpreted as the stretching frequencies of two CO molecules bound to the same iron in an angle of 90 degrees . We also report on the effect of extrinsic (12)CO, (13)CO, (12)CN(-), and (13)CN(-) on the IR spectrum of Hmd.

UV-A/blue-light inactivation of the 'metal-free' hydrogenase (Hmd) from methanogenic archaea

H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) is an unusual hydrogenase present in many methanogenic archaea. The homodimeric enzyme dubbed 'metal-free' hydrogenase does not contain iron-sulfur clusters or nickel and thus differs from [Ni-Fe] and [Fe-Fe] hydrogenases, which are all iron-sulfur proteins. Hmd preparations were found to contain up to 1 mol iron per 40 kDa subunit, but the iron was considered to be a contaminant as none of the catalytic and spectroscopic properties of the enzyme indicated that it was an essential component. Hmd does, however, harbour a low molecular mass cofactor of yet unknown structure. We report here that the iron found in Hmd is most probably functional after all. Further investigation was initiated by the discovery that Hmd is inactivated upon exposure to UV-A (320-400 nm) or blue-light (400-500 nm). Enzyme purified in the dark exhibited an absorption spectrum with a maximum at approximately 360 nm and which mirrored its sensitivity towards light. In UV-A/blue-light the enzyme was bleached. The cofactor extracted from active Hmd was also light sensitive. It showed an UV/visible spectrum similar to that of the active enzyme and was bleached upon exposure to light. Photobleached cofactor no longer had the ability to reconstitute active Hmd from the apoenzyme. When purified in the dark, Hmd consistently contained per monomer about one Fe, which was tightly bound to the cofactor. The iron was released from the enzyme and from the cofactor upon light inactivation. Hmd activity was inhibited by high concentrations of CO and CO protected the enzyme from light inactivation indicating that the iron in Hmd is of functional importance. Therefore, reference to Hmd as 'metal-free' hydrogenase is no longer appropriate.

Activation of dihydrogen without transition metals

The metal-free hydrogenase from methanogenic archaea (Hmd) is a unique enzyme: it catalyzes the reaction of its substrate, methenyl-tetrahydromethanopterin, with molecular hydrogen without the aid of a transition metal. In other words, Hmd is currently the only example of a purely organic hydrogenation catalyst. Recent results from various fields have shed new light on this enzyme. In biochemistry, there is experimental proof that a tightly bound (and metal-free) cofactor exists. Ab initio calculations have revealed that the concerted action of the Lewis-acidic substrate and a Brønsted-base appears to induce facile heterolysis of the hydrogen molecule. In chemical model studies, a transition-metal-free hydrogenation of ketones was achieved in the presence of catalytic base. Taken together, the experimental results available to date point to an enzymatic mechanism in which the hydrogen molecule is heterolyzed by the joint action of the Lewis-acidic substrate methenyl-tetrahydromethanopterin and a Brønsted-base in the active site (i.e. by bifunctional catalysis).

Enzymology of one-carbon metabolism in methanogenic pathways

Methanoarchaea, the largest and most phylogenetically diverse group in the Archaea domain, have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. All of the pathways have in common the two-electron reduction of methyl-coenzyme M to methane catalyzed by methyl-coenzyme M reductase but deviate in the source of the methyl group transferred to coenzyme M. Most of the methane produced in nature derives from acetate in a pathway where the activated substrate is cleaved by CO dehydrogenase/acetyl-CoA synthase and the methyl group is transferred to coenzyme M via methyltetrahydromethanopterin or methyltetrahydrosarcinapterin. Electrons for reductive demethylation of the methyl-coenzyme M originate from oxidation of the carbonyl group of acetate to carbon dioxide by the synthase. In the other major pathway, formate or H2 is oxidized to provide electrons for reduction of carbon dioxide to the methyl level and reduction of methyl-coenzyme to methane. Methane is also produced from the methyl groups of methanol and methylamines. In these pathways specialized methyltransferases transfer the methyl groups to coenzyme M. Electrons for reduction of the methyl-coenzyme M are supplied by oxidation of the methyl groups to carbon dioxide by a reversal of the carbon dioxide reduction pathway. Recent progress on the enzymology of one-carbon reactions in these pathways has raised the level of understanding with regard to the physiology and molecular biology of methanogenesis. These advances have also provided a foundation for future studies on the structure/function of these novel enzymes and exploitation of the recently completed sequences for the genomes from the methanoarchaea Methanobacterium thermoautotrophicum and Methanococcus jannaschii.

Unleashing hydrogenase activity in carbon monoxide dehydrogenase/acetyl-CoA synthase and pyruvate:ferredoxin oxidoreductase

These results demonstrate that two well-studied metalloenzymes, carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) and pyruvate:ferredoxin oxidoreductase (PFOR), can reduce protons to H2 and, at much lower rates, oxidize H2 to protons and electrons. To our knowledge, this if the first time that PFOR has been shown to have hydrogenase activity. CODH/ACS and PFOR evolved H2 at maximum rates when CO and pyruvate were the electron donors, respectively, and when electron acceptors are absent; dithionite was a very poor substitute. PFOR, when purified to greater than 99% homogeneity, exhibited a specific activity for pyruvate-dependent H2 production of 135 nmol min-1 mg-1. The H2 evolution activity divided by the H2 uptake activity was 282:1; the highest ratio previously reported (22:1) was with the membrane-bound hydrogenase from Rhodospirillum rubrum [Fox, J.D., Kerby, R. L., Roberts, G. P., & Ludden, P. W. (1996) J. Bacteriol. 178, 1515-1524]. Highly purified samples of CODH/ACS (> 99% homogeneity) exhibited a specific activity of CO-dependent H2 evolution in the absence of electron carrier of 590 nmol min-1 mg-1. Equivalent rates of CO oxidation and H2 production were observed when determined in the absence of electron acceptor. This level of activity can account for the rate of H2 production that has been observed by growing cultures of Clostridium thermoaceticum and could solve the paradox that the highly CO-sensitive hydrogenases from acetogenic bacteria evolve H2 when grown on CO. The ratio of the rates of (H2 evolution):(H2 uptake) for purified CODH/ACS is between 20:1 and 30:1. H2 evolution and uptake by CODH/ACS were strongly inhibited by cyanide (ki = 1 microM), indicating that these reactions are catalyzed by cluster C, the site of CO oxidation. Our results extend earlier findings that the CODHs from Methanosarcina barkeri [Bhatnagar, L., Krzycki, J. A., & Zeikus, J. G. (1987) FEMS Microbiol. Lett. 41, 337-343] and Oligotropha carboxydovorans [Santiago, B., & Meyer, O. (1996) FEMS Microbiol. Lett. 136, 157-162] exhibit hydrogenase activity. Mechanistic implications of hydrogenase activity are discussed. Several physiological roles for proton reduction by CODH/ACS and PFOR are discussed, including the prevention of radical formation from reduced metal clusters when electron carriers (ferredoxin, flavodoxin, etc.) are limiting.

Purification, properties and primary structure of H2-forming N5 ,N10 -methylenetetrahydromethanopterin dehydrogenase from Methanococcus thermolithotrophicus

H2-Forming N5,N10 -methylenetetrahydromethanopterin dehydrogenase (Hmd) is a novel type of hydrogenase found in methanogenic Achaea that contains neither nickel nor iron-sulfur clusters. The enzyme has previously been characterized from Methanobacterium thermoautotrophicum and from Methanopyrus kandleri. We report here on the purification and properties of the enzyme from Methanococcus thermolithotrophicus. The hmd gene was cloned and sequenced. The results indicate that the enzyme from Mc. thermolithotrophicus is functionally and structurally closely related to the H2-forming methylene tetrahydromethanopterin dehydrogenase from Mb. thermoautotrophicum and Mp. kandleri. From amino acid sequence comparisons of the three enzymes, a phylogenetic tree was deduced that shows branching orders similar to those derived from sequence comparisons of the 16S rRNA of the orders Methanococcales, Methanobacteriales, and Methanopyrales.