Organometallic Fe2(μ-SH)2(CO)4(CN)2 Cluster Allows the Biosynthesis of the [FeFe]-Hydrogenase with Only the HydF Maturase

Pnictogen-functionalised isocyanide ligands

The reactions of a range of cyanometallate salts with ClAtBu2 (A = P, As, Sb, A ≠ Bi) afford the new phosphino, arsino and stibino-isonitrile complexes [M(CNAtBu2)(CO)5] (M = W, A = P, As, Sb) and [MLn(CNPtBu2)] [MLn = Cr(CO)5, Mo(CO)5, Mn(CO)2(η5-C5H5), Re(CO)2(η5-C5H5), Fe(CO)4, Fe(CO)3(PPh3)] allowing crystallographic spectroscopic and computational interrogation of isonitrile compexes functionalised by the heavier pnictogens.

HydE Catalytic Mechanism Is Powered by a Radical Relay with Redox-Active Fe(I)-Containing Intermediates

[FeFe]-hydrogenases are enzymes that catalyze the redox interconversion of H+ and H2 using a six-iron active site, known as the H-cluster, which consists of a structurally unique [2Fe]H subcluster linked to a [4Fe-4S]H subcluster. A set of enzymes, HydG, HydE, and HydF, are responsible for the biosynthesis of the [2Fe]H subcluster. Among them, it is well established that HydG cleaves tyrosine into CO and CN- and forms a mononuclear [Fe(II)(Cys)(CO)2(CN)] complex. Recent work using EPR spectroscopy and X-ray crystallography show that HydE uses this organometallic Fe complex as its native substrate. The low spin Fe(II) center is reduced into an adenosylated Fe(I) species, which is proposed to form an Fe(I)Fe(I) dimer within HydE. The highly unusual transformation catalyzed by HydE draws interest in both biochemistry and organometallic chemistry. Due to the instability of the substrate, the intermediates, and the proposed product, experimental characterization of the detailed HydE mechanism and its final product is challenging. Herein, the catalytic mechanism of HydE is studied using hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. A radical relay mechanism was found for the cleavage of the cysteine S-Cβ bond that is energetically favored with respect to a closed-shell mechanism involving unconventional proton transfer. In addition, we propose a pathway for the dimerization of two Fe(I) complexes within the HydE hydrophobic cavity, which is consistent with the recent experimental result that HydF can perform [FeFe]-hydrogenase maturation with a synthetic dimer complex as the substrate. These simulation results take us further down the path to a more complete understanding of these enzymes that synthesize one of Nature's most efficient energy conversion catalysts.

From [2Mn2S] Diamond Cores to Butterfly Rhombs: Transformations That Highlight Alternating Peptide Binding Sites

Thiocarboxamide chelates are known to assemble [2Mn2S] diamond core complexes via μ-S bridges that connect two MnI(CO)3 fragments. These can exist as syn- and anti-isomers and interconvert via 16-electron, monomeric intermediates. Herein, we demonstrate that reduction of such Mn2 derivatives leads to a loss of one thiocarboxamide ligand and a switch of ligand binding mode from an O- to N-donor of the amide group, yielding a dianionic butterfly rhomb with a short Mn0-Mn0 distance, 2.52 Å. Structural and chemical analyses suggest that reduction of the Mn(I) centers is dependent on the protonation state of the amide-H, as total deprotonation followed by reduction does not result in the reduction of the Mn2 core. Partial deprotonation followed by reduction suggests a pathway that involves monomeric Mn(CO)3(S-O) and Mn(CO)3(S-N) intermediates. Ligand modifications to tertiary amides that remove the possibility of amide-H reduction led to complexes that preserve the [2Mn2S] diamond core during chemical reduction. Further comparison with the tethered system, linking the Mn(CO)3(S-O) sites together, suggests that dimer dissociation is necessary for the overall reductive transformation. These results highlight organomanganese carbonyl chemistry to establish illustrations of peptide fragment binding modes in the uptake of low-valent metal carbonyls related to binuclear active sites of biocatalysts.

Role of ammonia-lyases in the synthesis of the dithiomethylamine ligand during [FeFe]-hydrogenase maturation

The generation of an active [FeFe]-hydrogenase requires the synthesis of a complex metal center, the H-cluster, by three dedicated maturases: the radical S-adenosyl-l-methionine (SAM) enzymes HydE and HydG, and the GTPase HydF. A key step of [FeFe]-hydrogenase maturation is the synthesis of the dithiomethylamine (DTMA) bridging ligand, a process recently shown to involve the aminomethyl-lipoyl-H-protein from the glycine cleavage system, whose methylamine group originates from serine and ammonium. Here we use functional assays together with electron paramagnetic resonance and electron-nuclear double resonance spectroscopies to show that serine or aspartate together with their respective ammonia-lyase enzymes can provide the nitrogen for DTMA biosynthesis during in vitro [FeFe]-hydrogenase maturation. We also report bioinformatic analysis of the hyd operon, revealing a strong association with genes encoding ammonia-lyases, suggesting important biochemical and metabolic connections. Together, our results provide evidence that ammonia-lyases play an important role in [FeFe]-hydrogenase maturation by delivering the ammonium required for dithiomethylamine ligand synthesis.

The H-cluster of [FeFe] Hydrogenases: Its Enzymatic Synthesis and Parallel Inorganic Semisynthesis

Nature's prototypical hydrogen-forming catalysts─hydrogenases─have attracted much attention because they catalyze hydrogen evolution at near zero overpotential and ambient conditions. Beyond any possible applications in the energy sphere, the hydrogenases feature complicated active sites, which implies novel biosynthetic pathways. In terms of the variety of cofactors, the [FeFe]-hydrogenase is among the most complex. For more than a decade, we have worked on the biosynthesis of the active site of [FeFe] hydrogenases. This site, the H-cluster, is a six-iron ensemble consisting of a [4Fe-4S]H cluster linked to a [2Fe]H cluster that is coordinated to CO, cyanide, and a unique organic azadithiolate ligand. Many years ago, three enzymes, namely, HydG, HydE, and HydF, were shown to be required for the biosynthesis and the in vitro maturation of [FeFe] hydrogenases. The structures of the maturases were determined crystallographically, but still little progress was made on the biosynthetic pathway. As described in this Account, the elucidation of the biosynthetic pathway began in earnest with the identification of a molecular iron-cysteinate complex produced within HydG.In this Account, we present our most recent progress toward the molecular mechanism of [2Fe]H biosynthesis using a collaborative approach involving cell-free biosynthesis, isotope and element-sensitive spectroscopies, as well as inorganic synthesis of purported biosynthetic intermediates. Our study starts from the radical SAM enzyme HydG that lyses tyrosine into CO and cyanide and forms an Fe(CO)2(CN)-containing species. Crystallographic identification of a unique auxiliary 5Fe-4S cluster in HydG leads to a proposed catalytic cycle in which a free cysteine-chelated "dangler" Fe serves as the platform for the stepwise formation of a [4Fe-4S][Fe(CO)(CN)(cysteinate)] intermediate, which releases the [Fe(CO)2(CN)(cysteinate)] product, Complex B. Since Complex B is unstable, we applied synthetic organometallic chemistry to make an analogue, syn-B, and showed that it fully replaces HydG in the in vitro maturation of the H-cluster. Syn-B serves as the substrate for the next radical SAM enzyme HydE, where the low-spin Fe(II) center is activated by 5'-dAdo• to form an adenosylated Fe(I) intermediate. We propose that this Fe(I) species strips the carbon backbone and dimerizes in HydE to form a [Fe2(SH)2(CO)4(CN)2]2- product. This mechanistic scenario is supported by the use of a synthetic version of this dimer complex, syn-dimer, which allows for the formation of active hydrogenase with only the HydF maturase. Further application of this semisynthesis strategy shows that an [Fe2(SCH2NH2)2(CO)4(CN)2]2- complex can activate the apo hydrogenase, marking it as the last biosynthetic intermediate en route to the H-cluster. This combined enzymatic and semisynthetic approach greatly accelerates our understanding of H-cluster biosynthesis. We anticipate additional mechanistic details regarding H-cluster biosynthesis to be gleaned, and this methodology may be further applied in the study of other complex metallocofactors.

A Conserved Binding Pocket in HydF is Essential for Biological Assembly and Coordination of the Diiron Site of [FeFe]-Hydrogenases

The active site cofactor of [FeFe]-hydrogenases consists of a cubane [4Fe-4S]-cluster and a unique [2Fe-2S]-cluster, harboring unusual CO- and CN--ligands. The biosynthesis of the [2Fe-2S]-cluster requires three dedicated maturation enzymes called HydG, HydE and HydF. HydG and HydE are both involved in synthesizing a [2Fe-2S]-precursor, still lacking parts of the azadithiolate (adt) moiety that bridge the two iron atoms. This [2Fe-2S]-precursor is then finalized within the scaffold protein HydF, which binds and transfers the [2Fe-2S]-precursor to the hydrogenase. However, its exact binding mode within HydF is still elusive. Herein, we identified the binding location of the [2Fe-2S]-precursor by altering size and charge of a highly conserved protein pocket via site directed mutagenesis (SDM). Moreover, we identified two serine residues that are essential for binding and assembling the [2Fe-2S]-precursor. By combining SDM and molecular docking simulations, we provide a new model on how the [2Fe-2S]-cluster is bound to HydF and demonstrate the important role of one highly conserved aspartate residue, presumably during the bioassembly of the adt moiety.

Final Stages in the Biosynthesis of the [FeFe]-Hydrogenase Active Site

The paper aims to elucidate the final stages in the biosynthesis of the [2Fe]H active site of the [FeFe]-hydrogenases. The recently hypothesized intermediate [Fe2(SCH2NH2)2(CN)2(CO)4]2- ([1]2-) was prepared by a multistep route from [Fe2(S2)(CN)(CO)5]-. The following synthetic intermediates were characterized in order: [Fe2(SCH2NHFmoc)2(CNBEt3)(CO)5]-, [Fe2(SCH2NHFmoc)2(CN)-(CO)5]-, and [Fe2(SCH2NHFmoc)2(CN)2(CO)4]2-, where Fmoc is fluorenylmethoxycarbonyl). Derivatives of these anions include [K(18-crown-6)]+, PPh4 + and PPN+ salts as well as the 13CD2-isotopologues. These Fe2 species exist as a mixture of two isomers attributed to diequatorial (ee) and axial-equatorial (ae) stereochemistry at sulfur. In vitro experiments demonstrate that [1]2- maturates HydA1 in the presence of HydF and a cocktail of reagents. HydA1 can also be maturated using a highly simplified cocktail, omitting HydF and other proteins. This result is consistent with HydA1 participating in the maturation process and refines the roles of HydF.

Maturation of the [FeFe]-Hydrogenase: Direct Transfer of the (κ3 -cysteinate)FeII (CN)(CO)2 Complex B from HydG to HydE

[FeFe]-hydrogenases efficiently catalyze the reversible oxidation of molecular hydrogen. Their prowess stems from the intricate H-cluster, combining a [Fe4 S4 ] center with a binuclear iron center ([2Fe]H ). In the latter, each iron atom is coordinated by a CO and CN ligand, connected by a CO and an azadithiolate ligand. The synthesis of this active site involves a unique multiprotein assembly, featuring radical SAM proteins HydG and HydE. HydG initiates the transformation of L-tyrosine into cyanide and carbon monoxide to generate complex B, which is subsequently transferred to HydE to continue the biosynthesis of the [2Fe]H -subcluster. Due to its instability, complex B isolation for structural or spectroscopic characterization has been elusive thus far. Nevertheless, the use of a biomimetic analogue of complex B allowed circumvention of the need for the HydG protein during in vitro functional investigations, implying a similar structure for complex B. Herein, we used the HydE protein as a nanocage to encapsulate and stabilize the complex B product generated by HydG. Using X-ray crystallography, we successfully determined its structure at 1.3 Å resolution. Furthermore, we demonstrated that complex B is directly transferred from HydG to HydE, thus not being released into the solution post-synthesis, highlighting a transient interaction between the two proteins.

Fully Refined Semisynthesis of the [FeFe] Hydrogenase H-Cluster

[FeFe] hydrogenases contain a 6-Fe cofactor that serves as the active site for efficient redox interconversion between H2 and protons. The biosynthesis of the so-called H-cluster involves unusual enzymatic reactions that synthesize organometallic Fe complexes containing azadithiolate, CO, and CN- ligands. We have previously demonstrated that specific synthetic [Fe(CO)x(CN)y] complexes can be used to functionally replace proposed Fe intermediates in the maturation reaction. Here, we report the results from performing such cluster semisynthesis in the context of a recent fully defined cluster maturation procedure, which eliminates unknown components previously employed from Escherichia coli cell lysate and demonstrate this provides a concise route to H-cluster synthesis. We show that formaldehyde can be used as a simple reagent as the carbon source of the bridging adt ligand of H-cluster in lieu of serine/serine hydroxymethyltransferase. In addition to the actual H-cluster, we observe the formation of several H-cluster-like species, the identities of which are probed by cryogenic photolysis combined with EPR/ENDOR spectroscopy.

Hybrids of [FeFe]- and [NiFe]-H2ase Active Site Models

Complexes of the type (diphosphine)Ni(μ-SR)2Fe(CO)3 are investigated with azadithiolate (adt, HN(CH2S-)2) as the dithiolate. The resulting complexes are hybrid models for the active sites of the [NiFe]- and [FeFe]-hydrogenases. The key complex (dppv)Ni(μ-adt)Fe(CO)3 (3) was prepared from the complex Ni[(SCH2)2NCbz](dppv), which contains a Cbz-protected adt ligand (Cbz = C(O)OCH2Ph, dppv = cis-1,2-(Ph2P)2C2H2). This complex combines with Fe2(CO)9 to give (dppv)Ni[(μ-SCH2)2NCbz]Fe(CO)3, which is readily deprotected to give 3. Complex 3 undergoes protonation at both Fe and N to give successively [(dppv)Ni(μ-adt)FeH(CO)3]+ ([H3]+) and [(dppv)Ni(μ-adtH)FeH(CO)3]2+ ([H3H]2+). The redox properties and dynamics of these complexes resemble previously reported analogues with propanedithiolate. Solutions of [H3]+ readily degrade to [(dppv)Ni[(μ-SCH2)2NCH2]Fe(CO)3]+ ([4]+), which features a methylene group linking N and Fe. Complex [4]+ can be made in high yield by reaction of [H3]+ with CH2O, and this conversion was also demonstrated with 13CH2O. Complex [4]+ undergoes hydrogenolysis by photochemical reaction with H2 to give [(dppv)Ni[(μ-SCH2)2NMe]FeH(CO)3]+, the N-methylated analogue of [H3]+. Upon treatment ith Me3O+, [4]+ undergoes quaternization, giving [(dppv)Ni[(μ-SCH2)2N(Me)CH2]Fe(CO)3]2+. In contrast with the lability of [H3]+, the phosphine-substituted derivative [(dppv)Ni(μ-adt)FeH(CO)2(PPh3)]+ did not degrade. Most complexes were characterized by X-ray crystallography.

Semisynthetic maturation of [FeFe]-hydrogenase using [Fe2(μ-SH)2(CN)2(CO)4]2-: key roles for HydF and GTP

Here we describe maturation of the [FeFe]-hydrogenase from its [4Fe-4S]-bound precursor state by using the synthetic complex [Fe₂(μ-SH)₂(CN)₂(CO)₄]^2- together with HydF and components of the glycine cleavage system, but in the absence of the maturases HydE and HydG. This semisynthetic and fully-defined maturation provides new insights into the nature of H-cluster biosynthesis.

A personal account on 25 years of scientific literature on [FeFe]-hydrogenase

[FeFe]-hydrogenases are gas-processing metalloenzymes that catalyze H₂ oxidation and proton reduction (H₂ release) in microorganisms. Their high turnover frequencies and lack of electrical overpotential in the hydrogen conversion reaction has inspired generations of biologists, chemists, and physicists to explore the inner workings of [FeFe]-hydrogenase. Here, we revisit 25 years of scientific literature on [FeFe]-hydrogenase and propose a personal account on 'must-read' research papers and review article that will allow interested scientists to follow the recent discussions on catalytic mechanism, O₂ sensitivity, and the in vivo synthesis of the active site cofactor with its biologically uncommon ligands carbon monoxide and cyanide. Focused on-but not restricted to-structural biology and molecular biophysics, we highlight future directions that may inspire young investigators to pursue a career in the exciting and competitive field of [FeFe]-hydrogenase research.

Investigating the role of the strong field ligands in [FeFe] hydrogenase: spectroscopic and functional characterization of a semi-synthetic mono-cyanide active site

Artificial maturation of hydrogenases provides a path towards generating new semi-synthetic enzymes with novel catalytic properties. Here enzymes featuring a synthetic asymmetric mono-cyanide cofactor have been prepared using two different hydrogenase scaffolds. Their structure and reactivity was investigated in order to elucidate the design rationale behind the native di-cyanide cofactor, and by extension the second coordination sphere of the active-site pocket. Surprisingly, the choice of host enzyme was found to have a dramatic impact on reactivity. Moreover, the study shows that synthetic manipulations of the active-site can significantly increase inhibitor tolerance, as compared to native [FeFe] hydrogenase, while retaining the enzyme's native capacity for reversible catalysis.

Artificial Metalloproteins: At the Interface between Biology and Chemistry

Artificial metalloproteins (ArMs) have recently gained significant interest due to their potential to address issues in a broad scope of applications, including biocatalysis, biotechnology, protein assembly, and model chemistry. ArMs are assembled by the incorporation of a non-native metallocofactor into a protein scaffold. This can be achieved by a number of methods that apply tools of chemical biology, computational de novo design, and synthetic chemistry. In this Perspective, we highlight select systems in the hope of demonstrating the breadth of ArM design strategies and applications and emphasize how these systems address problems that are otherwise difficult to do so with strictly biochemical or synthetic approaches.

Synthesis and Dynamics of Ferrous Polychalcogenides [Fe(Ex)(CN)2(CO)2]2- (E = S, Se, or Te)

Elemental chalcogens react with [Fe(CN)2(CO)3]2- to give the following ferrous derivatives: [K(18-crown-6)]2[Fe(S5)(CN)2(CO)2], [K(18-crown-6)]2[Fe(S2)(CN)2(CO)2], [K(18-crown-6)]2[Fe(Se4)(CN)2(CO)2], [K(18-crown-6)]2[Fe(Te2)(CN)2(CO)2], and (NEt4)2[Fe(Te2)(CN)2(CO)2]. While these complex anions crystallized in a single stereochemistry (i.e., trans dicyanides or cis dicyanides), they isomerize in solution upon irradiation. The results are benchmarked by the corresponding studies on benzyl thiolate [K(18-crown-6)]2[Fe(SBn)2(CN)2(CO)2].