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The Copper Chaperone NosL Forms a Heterometal Site for Cu Delivery to Nitrous Oxide Reductase.

ABSTRACT: The final step of denitrification is the reduction of nitrous oxide (N₂ O) to N₂ , mediated by Cu-dependent nitrous oxide reductase (N₂ OR). Its metal centers, Cu_A and Cu_Z , are assembled through sequential provision of twelve Cu^I ions by a metallochaperone that forms part of a nos gene cluster encoding the enzyme and its accessory factors. The chaperone is the nosL gene product, an 18 kDa lipoprotein predicted to reside in the outer membrane of Gram-negative bacteria. In order to better understand the assembly of N₂ OR, we have produced NosL from Shewanella denitrificans and determined the structure of the metal-loaded chaperone by X-ray crystallography. The protein assembled a heterodinuclear metal site consisting of Zn^II and Cu^I , as evidenced by anomalous X-ray scattering. While only Cu^I is delivered to the enzyme, the stabilizing presence of Zn^II is essential for the functionality and structural integrity of the chaperone.

SUBMITTER: Prasser B

PROVIDER: S-EPMC8457098 | biostudies-literature |

REPOSITORIES: biostudies-literature

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

Project description: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 CuA site that functions in electron transfer, the active site of N2OR features a unique tetranuclear copper cluster bridged by inorganic sulfide, termed CuZ. 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 CuA center were unaffected, while those corresponding to the CuZ 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 CuZ center of N2OR, and thus represents the first characterised assembly factor for the CuZ active site of this key environmental enzyme, which is globally responsible for the destruction of a potent greenhouse gas.

| S-EPMC6530538 | biostudies-literature

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

Project description: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 CuZ, but not the electron transfer site CuA 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.

| S-EPMC6601269 | biostudies-literature

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

Project description: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 CuZ 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 CuZ 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, SZ2, 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 SZ2 may have been observed before, but not recognized. The sulfide shift changes the metal coordination in CuZ and is thus of high mechanistic interest.

| S-EPMC8179356 | biostudies-literature

Protonation state of the Cu4S2 CuZ site in nitrous oxide reductase: redox dependence and insight into reactivity.

Project description:Spectroscopic and computational methods have been used to determine the protonation state of the edge sulfur ligand in the Cu4S2 CuZ form of the active site of nitrous oxide reductase (N2OR) in its 3CuICuII (1-hole) and 2CuI2CuII (2-hole) redox states. The EPR, absorption, and MCD spectra of 1-hole CuZ indicate that the unpaired spin in this site is evenly delocalized over CuI, CuII, and CuIV. 1-hole CuZ is shown to have a μ2-thiolate edge ligand from the observation of S-H bending modes in the resonance Raman spectrum at 450 and 492 cm-1 that have significant deuterium isotope shifts (-137 cm-1) and are not perturbed up to pH 10. 2-hole CuZ is characterized with absorption and resonance Raman spectroscopies as having two Cu-S stretching vibrations that profile differently. DFT models of the 1-hole and 2-hole CuZ sites are correlated to these spectroscopic features to determine that 2-hole CuZ has a μ2-sulfide edge ligand at neutral pH. The slow two electron (+1 proton) reduction of N2O by 1-hole CuZ is discussed and the possibility of a reaction between 2-hole CuZ and O2 is considered.

| S-EPMC4583207 | biostudies-literature

Determination of the active form of the tetranuclear copper sulfur cluster in nitrous oxide reductase.

Project description:N2OR has been found to have two structural forms of its tetranuclear copper active site, the 4CuS Cu(Z)* form and the 4Cu2S Cu(Z) form. EPR, resonance Raman, and MCD spectroscopies have been used to determine the redox states of these sites under different reductant conditions, showing that the Cu(Z)* site accesses the 1-hole and fully reduced redox states, while the Cu(Z) site accesses the 2-hole and 1-hole redox states. Single-turnover reactions of N2OR for Cu(Z) and Cu(Z)* poised in these redox states and steady-state turnover assays with different proportions of Cu(Z) and Cu(Z)* show that only fully reduced Cu(Z)* is catalytically competent in rapid turnover with N2O.

| S-EPMC3927536 | biostudies-literature

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

Project description: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.

| S-EPMC7939133 | biostudies-literature

Experimental evidence for a link among cupredoxins: red, blue, and purple copper transformations in nitrous oxide reductase.

Project description:The cupredoxin fold is an important motif in numerous proteins that are central to several critical cellular processes ranging from aerobic and anaerobic respiration to catalysis and iron homeostasis. Three types of copper sites have been found to date within cupredoxin folds: blue type 1 (T1) copper, red type 2 (T2) copper, and purple Cu(A). Although as much as 90% sequence difference has been observed among some members of this superfamily of proteins that span several kingdoms, sequence alignment and phylogenic trees strongly suggest an evolutionary link and common ancestry. However, experimental evidence for such a link has been lacking. We report herein the observation of pH-dependent transformation between blue T1 copper, red T2 copper, and the native purple Cu(A) centers of nitrous oxide reductase (N2OR) from Paracoccus denitrificans. The blue and red copper centers form initially before they are transformed into purple Cu(A) center. This transformation process is pH-dependent, with lower pH resulting in fewer trapped T1 and T2 coppers and faster transition to purple Cu(A). These observations suggest that the purple Cu(A) site contains the essential elements of T1 and T2 copper centers and that the Cu(A) center is preferentially formed at low pH. Therefore, this work provides an underlying link between the various cupredoxin copper sites and possible experimental evidence in vitro for the evolutionary relationship between the cupredoxin proteins. The findings also lend physiological relevance to cupredoxin site biosynthesis.

| S-EPMC2430339 | biostudies-literature

Crystallization of purple nitrous oxide reductase from Pseudomonas stutzeri.

Project description:Nitrous oxide reductase (N(2)OR) from Pseudomonas stutzeri catalyzes the final step in denitrification: the two-electron reduction of nitrous oxide to molecular dinitrogen. Crystals of the enzyme were grown under strict exclusion of dioxygen by sitting-drop vapour diffusion using 2R,3R-butanediol as a cryoprotectant. N(2)OR crystallized in either space group P1 or P6(5). Interestingly, the key determinant for the resulting space group was the crystallization temperature. Crystals belonging to space group P1 contained four 130 kDa dimers in the asymmetric unit, while crystals belonging to space group P6(5) contained a single dimer in the asymmetric unit. Diffraction data were collected to resolutions better than 2 Å.

| S-EPMC3001670 | biostudies-literature

Requirements for Cu(A) and Cu-S center assembly of nitrous oxide reductase deduced from complete periplasmic enzyme maturation in the nondenitrifier Pseudomonas putida.

Project description:Bacterial nitrous oxide (N(2)O) reductase is the terminal oxidoreductase of a respiratory process that generates dinitrogen from N(2)O. To attain its functional state, the enzyme is subjected to a maturation process which involves the protein-driven synthesis of a unique copper-sulfur cluster and metallation of the binuclear Cu(A) site in the periplasm. There are seven putative maturation factors, encoded by nosA, nosD, nosF, nosY, nosL, nosX, and sco. We wanted to determine the indispensable proteins by expressing nos genes from Pseudomonas stutzeri in the nondenitrifying organism Pseudomonas putida. An in silico study of denitrifying bacteria revealed that nosL, nosX (or a homologous gene, apbE), and sco, but not nosA, coexist consistently with the N(2)O reductase structural gene and other maturation genes. Nevertheless, we found that expression of only three maturation factors (periplasmic protein NosD, cytoplasmic NosF ATPase, and the six-helix integral membrane protein NosY) together with nosRZ in trans was sufficient to produce catalytically active holo-N(2)O reductase in the nondenitrifying background. We suggest that these obligatory factors are required for Cu-S center assembly. Using a mutational approach with P. stutzeri, we also studied NosA, the Cu-containing outer membrane protein previously thought to have Cu insertase function, and ScoP, a putative membrane-anchored chaperone for Cu(A) metallation. Both of these were found to be dispensable elements for N(2)O reductase biosynthesis. Our experimental and in silico data were integrated in a model of N(2)O reductase maturation.

| S-EPMC142834 | biostudies-literature

Multiple forms of the catalytic centre, CuZ, in the enzyme nitrous oxide reductase from Paracoccus pantotrophus.

Project description:Nitrous oxide reductase catalyses the reduction of nitrous oxide to dinitrogen at a unique tetranuclear copper site, called Cu(Z), which has a central inorganic sulphide ligand. Limited incubation with oxygen during the preparation of nitrous oxide reductase from Paracoccus pantotrophus results in changed redox properties of the catalytic centre by comparison with anaerobic preparations. While the anaerobically purified enzyme has a catalytic centre which performs a single electron step at a midpoint potential of E(m)=+60 mV versus the standard hydrogen electrode (n=1), the altered centre shows no redox change under similar experimental conditions. Spectroscopic properties of this 'redox fixed' centre are similar to spectra of the reduced 'redox active' form of CuZ, although the positions and intensities of a number of transitions are changed in the optical spectrum. These observations are interpreted in terms of two forms of the catalytic centre, called CuZ and CuZ*. The structural relationship between these forms is unclear. EPR and magnetic circular dichroism spectra suggest that the basic Cu4S structure is common to both. Curiously, steady-state activity of the aerobic enzyme preparation is slightly increased despite the fact the catalytic centre does not undergo detectable redox changes.

| S-EPMC1222630 | biostudies-other

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