Role of Calcium in Secondary Structure Stabilization during Maturation 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.

Photocatalytic Removal of the Greenhouse Gas Nitrous Oxide by Liposomal Microreactors

Nitrous oxide (N₂ O) is a potent greenhouse and ozone-reactive gas for which emissions are growing rapidly due to increasingly intensive agriculture. Synthetic catalysts for N₂ O decomposition typically contain precious metals and/or operate at elevated temperatures driving a desire for more sustainable alternatives. Here we demonstrate self-assembly of liposomal microreactors enabling catalytic reduction of N₂ O to the climate neutral product N₂ . Photoexcitation of graphitic N-doped carbon dots delivers electrons to encapsulated N₂ O Reductase enzymes via a lipid-soluble biomolecular wire provided by the MtrCAB protein complex. Within the microreactor, electron transfer from MtrCAB to N₂ O Reductase is facilitated by the general redox mediator methyl viologen. The liposomal microreactors use only earth-abundant elements to catalyze N₂ O removal in ambient, aqueous conditions.

Photocatalytic Removal of the Greenhouse Gas Nitrous Oxide by Liposomal Microreactors

Nitrous oxide (N2O) is a potent greenhouse and ozone-reactive gas for which emissions are growing rapidly due to increasingly intensive agriculture. Synthetic catalysts for N2O decomposition typically contain precious metals and/or operate at elevated temperatures driving a desire for more sustainable alternatives. Here we demonstrate self-assembly of liposomal microreactors enabling catalytic reduction of N2O to the climate neutral product N2. Photoexcitation of graphitic N-doped carbon dots delivers electrons to encapsulated N2O Reductase enzymes via a lipid-soluble biomolecular wire provided by the MtrCAB protein complex. Within the microreactor, electron transfer from MtrCAB to N2O Reductase is facilitated by the general redox mediator methyl viologen. The liposomal microreactors use only earth-abundant elements to catalyze N2O removal in ambient, aqueous conditions.

Molecular interplay of an assembly machinery for nitrous oxide reductase

Emissions of the critical ozone-depleting and greenhouse gas nitrous oxide (N₂O) from soils and industrial processes have increased considerably over the last decades^1-3. As the final step of bacterial denitrification, N₂O is reduced to chemically inert N₂ (refs. ^1,4) in a reaction that is catalysed by the copper-dependent nitrous oxide reductase (N₂OR) (ref. ⁵). The assembly of its unique [4Cu:2S] active site cluster Cu_Z requires both the ATP-binding-cassette (ABC) complex NosDFY and the membrane-anchored copper chaperone NosL (refs. ^4,6). Here we report cryo-electron microscopy structures of Pseudomonas stutzeri NosDFY and its complexes with NosL and N₂OR, respectively. We find that the periplasmic NosD protein contains a binding site for a Cu⁺ ion and interacts specifically with NosL in its nucleotide-free state, whereas its binding to N₂OR requires a conformational change that is triggered by ATP binding. Mutually exclusive structures of NosDFY in complex with NosL and with N₂OR reveal a sequential metal-trafficking and assembly pathway for a highly complex copper site. Within this pathway, NosDFY acts as a mechanical energy transducer rather than as a transporter. It links ATP hydrolysis in the cytoplasm to a conformational transition of the NosD subunit in the periplasm, which is required for NosDFY to switch its interaction partner so that copper ions are handed over from the chaperone NosL to the enzyme N₂OR.

Coordination chemistry of the CuZ site in nitrous oxide reductase and its synthetic mimics

Atmospheric nitrous oxide (N2O) has garnered significant attention recently due to its dual roles as an ozone depletion agent and a potent greenhouse gas. Anthropogenic N2O emissions occur primarily through agricultural disruption of nitrogen homeostasis causing N2O to build up in the atmosphere. The enzyme responsible for N2O fixation within the geochemical nitrogen cycle is nitrous oxide reductase (N2OR), which catalyzes 2H+/2e- reduction of N2O to N2 and H2O at a tetranuclear active site, CuZ. In this review, the coordination chemistry of CuZ is reviewed. Recent advances in the understanding of biological CuZ coordination chemistry is discussed, as are significant breakthroughs in synthetic modeling of CuZ that have emerged in recent years. The latter topic includes both structurally faithful, synthetic [Cu4(µ4-S)] clusters that are able to reduce N2O, as well as dicopper motifs that shed light on reaction pathways available to the critical CuI-CuIV cluster edge of CuZ. Collectively, these advances in metalloenzyme studies and synthetic model systems provide meaningful knowledge about the physiologically relevant coordination chemistry of CuZ but also open new questions that will pose challenges in the near future.

A [3Cu:2S] cluster provides insight into the assembly and function of the CuZ site of nitrous oxide reductase

Nitrous oxide reductase (N₂OR) is the only known enzyme reducing environmentally critical nitrous oxide (N₂O) to dinitrogen (N₂) as the final step of bacterial denitrification. The assembly process of its unique catalytic [4Cu:2S] cluster Cu_Z remains scarcely understood. Here we report on a mutagenesis study of all seven histidine ligands coordinating this copper center, followed by spectroscopic and structural characterization and based on an established, functional expression system for Pseudomonas stutzeri N₂OR in Escherichia coli. While no copper ion was found in the Cu_Z binding site of variants H129A, H130A, H178A, H326A, H433A and H494A, the H382A variant carried a catalytically inactive [3Cu:2S] center, in which one sulfur ligand, S_Z2, had relocated to form a weak hydrogen bond to the sidechain of the nearby lysine residue K454. This link provides sufficient stability to avoid the loss of the sulfide anion. The UV-vis spectra of this cluster are strikingly similar to those of the active enzyme, implying that the flexibility of S_Z2 may have been observed before, but not recognized. The sulfide shift changes the metal coordination in Cu_Z and is thus of high mechanistic interest.

Variants of all seven histidine ligands of the [4Cu:2S] active site of nitrous oxide reductase mostly result in loss of the metal site. However, a H382A variant retains a [3Cu:2S] cluster that hints towards a structural flexibility also present in the intact site.

Identification and Physicochemical Characterization of a New Allergen from Ascaris lumbricoides

To analyze the impact of Ascaris lumbricoides infection on the pathogenesis and diagnosis of allergic diseases, new allergens should be identified. We report the identification of a new Ascaris lumbricoides allergen, Asc l 5. The aim of this study was to evaluate the physicochemical and immunological features of the Asc l 5 allergen. We constructed an A. lumbricoides cDNA library and Asc l 5 was identified by immunoscreening. After purification, rAsc l 5 was physicochemically characterized. Evaluation of its allergenic activity included determination of Immunoglobulin E (IgE) binding frequency (in two populations: 254 children and 298 all-age subjects), CD203c based-basophil activation tests (BAT) and a passive cutaneous anaphylaxis (PCA) mouse model. We found by amino acid sequence analysis that Asc l 5 belongs to the SXP/RAL-2 protein family of nematodes. rAsc l 5 is a monomeric protein with an alpha-helical folding. IgE sensitization to rAsc l 5 was around 52% in general population; positive BAT rate was 60%. rAsc l 5 induced specific IgE production in mice and a positive PCA reaction. These results show that Asc l 5 has structural and immunological characteristics to be considered as a new allergen from A. lumbricoides.

Biological and Bioinspired Inorganic N-N Bond-Forming Reactions

The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.

Functional assembly of nitrous oxide reductase provides insights into copper site maturation

The multicopper enzyme nitrous oxide reductase reduces the greenhouse gas N₂O to uncritical N₂ as the final step of bacterial denitrification. Its two metal centers require an elaborate assembly machinery that so far has precluded heterologous production as a prerequisite for bioremediatory applications in agriculture and wastewater treatment. Here, we report on the production of active holoenzyme in Escherichia coli using a two-plasmid system to produce the entire biosynthetic machinery as well as the structural gene for the enzyme. Using this recombinant system to probe the role of individual maturation factors, we find that the ABC transporter NosFY and the accessory NosD protein are essential for the formation of the [4Cu:2S] site Cu_Z, but not the electron transfer site Cu_A Depending on source organism, the heterologous host E. coli can, in some cases, compensate for the lack of the Cu chaperone NosL, while in others this protein is strictly required, underlining the case for designing a recombinant system to be entirely self-contained.

NosL is a dedicated copper chaperone for assembly of the CuZ center of nitrous oxide reductase

Nitrous oxide reductase (N₂OR) is the terminal enzyme of the denitrification pathway of soil bacteria that reduces the greenhouse gas nitrous oxide (N₂O) to dinitrogen. In addition to a binuclear Cu_A site that functions in electron transfer, the active site of N₂OR features a unique tetranuclear copper cluster bridged by inorganic sulfide, termed Cu_Z. In copper-limited environments, N₂OR fails to function, resulting in truncation of denitrification and rising levels of N₂O released by cells to the atmosphere, presenting a major environmental challenge. Here we report studies of nosL from Paracoccus denitrificans, which is part of the nos gene cluster, and encodes a putative copper binding protein. A Paracoccus denitrificans ΔnosL mutant strain had no denitrification phenotype under copper-sufficient conditions but failed to reduce N₂O under copper-limited conditions. N₂OR isolated from ΔnosL cells was found to be deficient in copper and to exhibit attenuated activity. UV-visible absorbance spectroscopy revealed that bands due to the Cu_A center were unaffected, while those corresponding to the Cu_Z center were significantly reduced in intensity. In vitro studies of a soluble form of NosL without its predicted membrane anchor showed that it binds one Cu(i) ion per protein with attomolar affinity, but does not bind Cu(ii). Together, the data demonstrate that NosL is a copper-binding protein specifically required for assembly of the Cu_Z center of N₂OR, and thus represents the first characterised assembly factor for the Cu_Z active site of this key environmental enzyme, which is globally responsible for the destruction of a potent greenhouse gas.

Gene cloning, expression, and reducing property enhancement of nitrous oxide reductase from Alcaligenes denitrificans strain TB

Nitrous oxide (N₂O) is a potent greenhouse gas and tends to accumulate as an intermediate in the process of bacteria denitrification. To achieve complete reduction of nitrogen oxide (NO_x) in bacteria denitrification, the structural gene nosZ encoding nitrous oxide reductase (N₂OR) was cloned from Alcaligenes denitrificans strain TB (GenBank JQ044686). The recombinant plasmid containing the nosZ gene was built, and the expression of nosZ gene in Escherichia coli was determined. Results show that the nosZ gene consisting of 1917 nucleotides achieves heterologous expression successfully by codon optimization strategy under optimal conditions (pre-induction inoculum OD₆₀₀ of 0.67, final IPTG concentration of 0.5 mM, inducing time of 6 h, and inducing temperature of 28 °C). Determination result of gas chromatography confirms that N₂O degradation efficiency of recombinant E. coli is strengthened by at least 1.92 times compared with that of original strain TB when treated with N₂O as substrate. Moreover, N₂OR activity in recombinant strain is 2.09 times higher than that in wild strain TB, which validates the aforementioned result and implies that the recombinant E. coli BL21 (DE3)-pET28b-nosZ is a potential candidate to control N₂O accumulation and alleviate greenhouse effect. In addition, the N₂OR structure and the possible N₂O binding site in Alcaligenes sp. TB are predicted, which open an avenue for further research on the relationship between N₂OR activity and its structure.

The catalytic cycle of nitrous oxide reductase - The enzyme that catalyzes the last step of denitrification

The reduction of the potent greenhouse gas nitrous oxide requires a catalyst to overcome the large activation energy barrier of this reaction. Its biological decomposition to the inert dinitrogen can be accomplished by denitrifiers through nitrous oxide reductase, the enzyme that catalyzes the last step of the denitrification, a pathway of the biogeochemical nitrogen cycle. Nitrous oxide reductase is a multicopper enzyme containing a mixed valence CuA center that can accept electrons from small electron shuttle proteins, triggering electron flow to the catalytic sulfide-bridged tetranuclear copper "CuZ center". This enzyme has been isolated with its catalytic center in two forms, CuZ*(4Cu1S) and CuZ(4Cu2S), proven to be spectroscopic and structurally different. In the last decades, it has been a challenge to characterize the properties of this complex enzyme, due to the different oxidation states observed for each of its centers and the heterogeneity of its preparations. The substrate binding site in those two "CuZ center" forms and which is the active form of the enzyme is still a matter of debate. However, in the last years the application of different spectroscopies, together with theoretical calculations have been useful in answering these questions and in identifying intermediate species of the catalytic cycle. An overview of the spectroscopic, kinetics and structural properties of the two forms of the catalytic "CuZ center" is given here, together with the current knowledge on nitrous oxide reduction mechanism by nitrous oxide reductase and its intermediate species.

CheckMyMetal: a macromolecular metal-binding validation tool

Metals are essential in many biological processes, and metal ions are modeled in roughly 40% of the macromolecular structures in the Protein Data Bank (PDB). However, a significant fraction of these structures contain poorly modeled metal-binding sites. CheckMyMetal (CMM) is an easy-to-use metal-binding site validation server for macromolecules that is freely available at http://csgid.org/csgid/metal_sites. The CMM server can detect incorrect metal assignments as well as geometrical and other irregularities in the metal-binding sites. Guidelines for metal-site modeling and validation in macromolecules are illustrated by several practical examples grouped by the type of metal. These examples show CMM users (and crystallographers in general) problems they may encounter during the modeling of a specific metal ion.

The flavinyl transferase ApbE of Pseudomonas stutzeri matures the NosR protein required for nitrous oxide reduction

The copper-containing enzyme nitrous oxide reductase (N₂OR) catalyzes the transformation of nitrous oxide (N₂O) to dinitrogen (N₂) in microbial denitrification. Several accessory factors are essential for assembling the two copper sites Cu_A and Cu_Z, and for maintaining the activity. In particular, the deletion of either the transmembrane iron-sulfur flavoprotein NosR or the periplasmic protein NosX, a member of the ApbE family, abolishes N₂O respiration. Here we demonstrate through biochemical and structural studies that the ApbE protein from Pseudomonas stutzeri, where the nosX gene is absent, is a monomeric FAD-binding protein that can serve as the flavin donor for NosR maturation via covalent flavinylation of a threonine residue. The flavin transfer reaction proceeds both in vivo and in vitro to generate post-translationally modified NosR with covalently bound FMN. Only FAD can act as substrate and the reaction requires a divalent cation, preferably Mg²⁺ that was also present in the crystal structure. In addition, the reaction is species-specific to a certain extent.