Histidine-Gated Proton-Coupled Electron Transfer to the CuA Site of Nitrous Oxide Reductase

Revisiting the metal sites of nitrous oxide reductase in a low-dose structure from Marinobacter nauticus

Copper-containing nitrous oxide reductase catalyzes a 2-electron reduction of the green-house gas N2O to yield N2. It contains two metal centers, the binuclear electron transfer site CuA, and the unique, tetranuclear CuZ center that is the site of substrate binding. Different forms of the enzyme were described previously, representing variations in oxidation state and composition of the metal sites. Hypothesizing that many reported discrepancies in the structural data may be due to radiation damage during data collection, we determined the structure of anoxically isolated Marinobacter nauticus N2OR from diffraction data obtained with low-intensity X-rays from an in-house rotating anode generator and an image plate detector. The data set was of exceptional quality and yielded a structure at 1.5 Å resolution in a new crystal form. The CuA site of the enzyme shows two distinct conformations with potential relevance for intramolecular electron transfer, and the CuZ cluster is present in a [4Cu:2S] configuration. In addition, the structure contains three additional types of ions, and an analysis of anomalous scattering contributions confirms them to be Ca2+, K+, and Cl-. The uniformity of the present structure supports the hypothesis that many earlier analyses showed inhomogeneities due to radiation effects. Adding to the earlier description of the same enzyme with a [4Cu:S] CuZ site, a mechanistic model is presented, with a structurally flexible CuZ center that does not require the complete dissociation of a sulfide prior to N2O binding.

Conformational coupling of redox-driven Na+-translocation in Vibrio cholerae NADH:quinone oxidoreductase

In the respiratory chain, NADH oxidation is coupled to ion translocation across the membrane to build up an electrochemical gradient. In the human pathogen Vibrio cholerae, the sodium-pumping NADH:quinone oxidoreductase (Na+-NQR) generates a sodium gradient by a so far unknown mechanism. Here we show that ion pumping in Na+-NQR is driven by large conformational changes coupling electron transfer to ion translocation. We have determined a series of cryo-EM and X-ray structures of the Na+-NQR that represent snapshots of the catalytic cycle. The six subunits NqrA, B, C, D, E, and F of Na+-NQR harbor a unique set of cofactors that shuttle the electrons from NADH twice across the membrane to quinone. The redox state of a unique intramembranous [2Fe-2S] cluster orchestrates the movements of subunit NqrC, which acts as an electron transfer switch. We propose that this switching movement controls the release of Na+ from a binding site localized in subunit NqrB.

Control of charge transport in electronically active systems towards integrated biomolecular circuits (IbC)

The miniaturization of traditional silicon-based electronics will soon reach its limitation as quantum tunneling and heat become serious problems at the several-nanometer scale. Crafting integrated circuits via self-assembly of electronically active molecules using a "bottom-up" paradigm provides a potential solution to these technological challenges. In particular, integrated biomolecular circuits (IbC) offer promising advantages to achieve this goal, as nature offers countless examples of functionalities entailed by self-assembly and examples of controlling charge transport at the molecular level within the self-assembled structures. To this end, the review summarizes the progress in understanding how charge transport is regulated in biosystems and the key redox-active amino acids that enable the charge transport. In addition, charge transport mechanisms at different length scales are also reviewed, offering key insights for controlling charge transport in IbC in the future.

Cu4S Cluster in "0-Hole" and "1-Hole" States: Geometric and Electronic Structure Variations for the Active CuZ* Site of N2O Reductase

The active site of nitrous oxide reductase (N2OR), a key enzyme in denitrification, features a unique μ4-sulfido-bridged tetranuclear Cu cluster (the so-called CuZ or CuZ* site). Details of the catalytic mechanism have remained under debate and, to date, synthetic model complexes of the CuZ*/CuZ sites are extremely rare due to the difficulty in building the unique {Cu4(μ4-S)} core structure. Herein, we report the synthesis and characterization of [Cu4(μ4-S)]n+ (n = 2, 2; n = 3, 3) clusters, supported by a macrocyclic {py2NHC4} ligand (py = pyridine, NHC = N-heterocyclic carbene), in both their 0-hole (2) and 1-hole (3) states, thus mimicking the two active states of the CuZ* site during enzymatic N2O reduction. Structural and electronic properties of these {Cu4(μ4-S)} clusters are elucidated by employing multiple methods, including X-ray diffraction (XRD), nuclear magnetic resonance (NMR), UV/vis, electron paramagnetic resonance (EPR), Cu/S K-edge X-ray emission spectroscopy (XES), and Cu K-edge X-ray absorption spectroscopy (XAS) in combination with time-dependent density functional theory (TD-DFT) calculations. A significant geometry change of the {Cu4(μ4-S)} core occurs upon oxidation from 2 (τ4(S) = 0.46, seesaw) to 3 (τ4(S) = 0.03, square planar), which has not been observed so far for the biological CuZ(*) site and is unprecedented for known model complexes. The single electron of the 1-hole species 3 is predominantly delocalized over two opposite Cu ions via the central S atom, mediated by a π/π superexchange pathway. Cu K-edge XAS and Cu/S K-edge XES corroborate a mixed Cu/S-based oxidation event in which the lowest unoccupied molecular orbital (LUMO) has a significant S-character. Furthermore, preliminary reactivity studies evidence a nucleophilic character of the central μ4-S in the fully reduced 0-hole state.

Structural biology of proteins involved in nitrogen cycling

Microbial metabolic processes drive the global nitrogen cycle through sophisticated and often unique metalloenzymes that facilitate difficult redox reactions at ambient temperature and pressure. Understanding the intricacies of these biological nitrogen transformations requires a detailed knowledge that arises from the combination of a multitude of powerful analytical techniques and functional assays. Recent developments in spectroscopy and structural biology have provided new, powerful tools for addressing existing and emerging questions, which have gained urgency due to the global environmental implications of these fundamental reactions. The present review focuses on the recent contributions of the wider area of structural biology to understanding nitrogen metabolism, opening new avenues for biotechnological applications to better manage and balance the challenges of the global nitrogen cycle.

Understanding the anomaly of cis-trans isomerism in Pro-His sequence

The anomalous absence of cisPro stabilizing C^αH^α_Xaa···π_Aro interactions at Xaa-Pro-Aro exclusively when Aro is His, is understood by NMR structural analyses of model peptides, as due to i → i backbone-side chain C₆ H-bond that forms uniquely when Aro is His, which significantly decreases its χ₁-g^- population essential for C^αH^α_Xaa···π_Aro formation.

Orchestrating copper binding: structure and variations on the cupredoxin fold

A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.

Dynamic Pt-OH-·H2O-Ag species mediate coupled electron and proton transfer for catalytic hydride reduction of 4-nitrophenol at the confined nanoscale interface

Generally, the catalytic transformation of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) at heterogeneous metal surfaces follows a Langmuir-Hinshelwood (L-H) mechanism when sodium borohydride (NaBH₄) is used as the sacrificial reductant. Herein, with Pt-Ag bimetallic nanoparticles confined in dendritic mesoporous silica nanospheres (DMSNs) as a model catalyst, we demonstrated that the conversion of 4-NP did not pass through the direct hydrogen transfer route with the hydride equivalents being supplied by borohydride via the bimolecular L-H mechanism, since Fourier transform infrared (FTIR) spectroscopy with the use of isotopically labeled reactants (NaBD₄ and D₂O) showed that the final product of 4-AP was composed of protons (or deuterons) that originated from the solvent water (or heavy water). Combined characterization by X-ray photoelectron spectroscopy (XPS), ¹H nuclear magnetic resonance (NMR) and the optical excitation and photoluminescence spectrum evidenced that the surface hydrous hydroxide complex bound to the metal surface (also called structural water molecules, SWs), due to the space overlap of p orbitals of two O atoms in SWs, could form an ensemble of dynamic interface transient states, which provided the alternative electron and proton transfer channels for selective transformation of 4-NP. The cationic Pt species in the Ag-Pt bimetallic catalyst mainly acts as a dynamic adsorption center to temporally anchor SWs and related reactants, and not as the active site for hydrogen activation.

NosZ gene cloning, reduction performance and structure of Pseudomonas citronellolis WXP-4 nitrous oxide reductase

Nitrous oxide reductase (N₂OR) is the only known enzyme that can reduce the powerful greenhouse gas nitrous oxide (N₂O) to harmless nitrogen at the final step of bacterial denitrification. To alleviate the N₂O emission, emerging approaches aim at microbiome biotechnology. In this study, the genome sequence of facultative anaerobic bacteria Pseudomonas citronellolis WXP-4, which efficiently degrades N₂O, was obtained by de novo sequencing for the first time, and then, four key reductase structure coding genes related to complete denitrification were identified. The single structural encoding gene nosZ with a length of 1914 bp from strain WXP-4 was cloned in Escherichia coli BL21(DE3), and the N₂OR protein (76 kDa) was relatively highly efficiently expressed under the optimal inducing conditions of 1.0 mM IPTG, 5 h, and 30 °C. Denitrification experiment results confirmed that recombinant E. coli had strong denitrification ability and reduced 10 mg L⁻¹ of N₂O to N₂ within 15 h under the optimal conditions of pH 7.0 and 40 °C, its corresponding N₂O reduction rate was almost 2.3 times that of Alcaligenes denitrificans strain TB, but only 80% of that of wild strain WXP-4, meaning that nos gene cluster auxiliary gene deletion decreased the activity of N₂OR. The 3D structure of N₂OR predicted on the basis of sequence homology found that electron transfer center CuA had only five amino acid ligands, and the S2 of the catalytically active center CuZ only bound one Cu_I atom. The unique 3D structure was different from previous reports and may be closely related to the strong N₂O reduction ability of strain WXP-4 and recombinant E. coli. The findings show a potential application of recombinant E. coli in alleviating the greenhouse effect and provide a new perspective for researching the relationship between structure and function of N₂OR.

Nitrous oxide reductase (N₂OR) is the only known enzyme that can reduce the powerful greenhouse gas nitrous oxide (N₂O) to harmless nitrogen at the final step of bacterial denitrification. The recombinant E. coli and wild strain WXP-4 demonstrate strong N₂O reduction ability.

Dimeric Copper and Lithium Thiolates: Comparison of Copper Thiolates with Their Lithium Congeners

The direct reactions of the large terphenyl thiols HSAr^iPr4 (Ar^iPr4= -C₆H₃-2,6-(C₆H₃-2,6-iPr₂)₂) and HSAr^iPr6 (Ar^iPr6= -C₆H₃-2,6-(C₆H₂-2,4,6-iPr₃)₂) with stoichiometric amounts of mesitylcopper(I) in THF at ca. 80 °C afforded the first well-characterized dimeric copper thiolato species {CuSAr^iPr4}₂ (1) and {CuSAr^iPr6}₂ (2) with elimination of mesitylene. The complexes 1 and 2 were characterized by NMR and electronic spectroscopy as well as by X-ray crystallography. They have dimeric Cu₂S₂ core structures in which the two copper atoms are bridged by the sulfurs from the thiolato ligands and feature short Cu--Cu distances near 2.4 Å as well as a weak copper-flanking aryl ring interaction from a terphenyl substituent. The structures of the planar Cu₂S₂ cores bear a resemblance to the Cu_A site in nitrous oxide reductase in which two cysteines also bridge two copper atoms. The related dimeric Li₂S₂ structural motif was also observed in the lithium congeners {LiSAr^iPr4}₂ (3) and {LiSAr^iPr6}₂ (4) which were synthesized directly from the thiols and n-BuLi in hexanes. However, despite the very similar effective ionic radii of the Li⁺ (0.59 Å) and Cu⁺ (0.60 Å) ions, the Li--Li structures display very much longer (by more than ca. 0.5 Å) separations than the corresponding Cu--Cu distances in 1 and 2, which may be due to weaker dispersion interactions.

Surface electronic states mediate concerted electron and proton transfer at metal nanoscale interfaces for catalytic hydride reduction of -NO2 to -NH2

Concerted electron and proton transfer is a key step for the reversible conversion of molecular hydrogen in both heterogeneous nanocatalysis and metalloenzyme catalysis. However, its activation mechanism involving electron and proton transfer kinetics remains elusive. With the most widely used catalytic hydride reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) as a model reaction, we evaluate the catalytic activity of noble metal nanoparticles (NPs) trapped in porous silica in aqueous NaBH4 solution. By virtue of a novel combination of catalyst design, reaction kinetics, isotope labeling, and multiple spectroscopic techniques, the real catalytic site for the conversion of -NO2 to -NH2 is identified to be the water-hydroxyl transition metal complex, which could further react with NaBH4 to form a new triangular configuration metal complex of H3B-water-hydroxyl with dynamic features. It yields an ensemble of surface electronic states (SESs) though space overlapping of p orbitals of one B and several O atoms (including the O atoms of 4-NP), which could act as an alternative channel for concerted electron and proton transfer. This work highlights the critical role of the conceptual SESs model in heterogeneous catalysis to tune the chemical reactivity and also sheds light on the intricate working of the [FeFe]-hydrogenases.

Radical transfer but not heme distal residues is essential for pH dependence of dye-decolorizing activity of peroxidase from Vibrio cholerae

Dye-decolorizing peroxidase (DyP) is a heme-containing enzyme that catalyzes the degradation of anthraquinone dyes. A main feature of DyP is the acidic optimal pH for dye-decolorizing activity. In this study, we constructed several mutant DyP enzymes from Vibrio cholerae (VcDyP), with a view to identifying the decisive factor of the low pH preference of DyP. Initially, distal Asp144, a conserved residue, was replaced with His, which led to significant loss of dye-decolorizing activity. Introduction of His into a position slightly distant from heme resulted in restoration of activity but no shift in optimal pH, indicating that distal residues do not contribute to the pH dependence of catalytic activity. His178, an essential residue for dye decolorization, is located near heme and forms hydrogen bonds with Asp138 and Thr278. While Trp and Tyr mutants of His178 were inactive, the Phe mutant displayed ~35% activity of wild-type VcDyP, indicating that this position is a potential radical transfer route from heme to the active site on the protein surface. The Thr278Val mutant displayed similar enzymatic properties as WT VcDyP, whereas the Asp138Val mutant displayed significantly increased activity at pH 6.5. On the basis of these findings, we propose that neither distal amino acid residues, including Asp144, nor hydrogen bonds between His178 and Thr278 are responsible while the hydrogen bond between His178 and Asp138 plays a key role in the pH dependence of activity.