Pseudoazurin dramatically enhances the reaction profile of nitrite reduction by Paracoccus pantotrophus cytochrome cd1 and facilitates release of product nitric oxide

Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis

Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.

A 60-heme reductase complex from an anammox bacterium shows an extended electron transfer pathway

The hydroxylamine oxidoreductase/hydrazine dehydrogenase (HAO/HDH) protein family constitutes an important group of octaheme cytochromes c (OCCs). The majority of these proteins form homotrimers, with their subunits being covalently attached to each other via a rare cross-link between the catalytic heme moiety and a conserved tyrosine residue in an adjacent subunit. This covalent cross-link has been proposed to modulate the active-site heme towards oxidative catalysis by distorting the heme plane. In this study, the crystal structure of a stable complex of an HAO homologue (KsHAOr) with its diheme cytochrome c redox partner (KsDH) from the anammox bacterium Kuenenia stuttgartiensis was determined. KsHAOr lacks the tyrosine cross-link and is therefore tuned to reductive catalysis. The molecular model of the KsHAOr–KsDH complex at 2.6 Å resolution shows a heterododecameric (α6β6) assembly, which was also shown to be the oligomeric state in solution by analytical ultracentrifugation and multi-angle static light scattering. The 60-heme-containing protein complex reveals a unique extended electron transfer pathway and provides deeper insights into catalysis and electron transfer in reductive OCCs.

Periplasmic Nicotine Dehydrogenase NdhAB Utilizes Pseudoazurin as Its Physiological Electron Acceptor in Agrobacterium tumefaciens S33

Agrobacterium tumefaciens S33 can grow with nicotine as the sole source of carbon, nitrogen, and energy via a novel hybrid of the pyridine pathway and the pyrrolidine pathway. Characterization of the enzymes involved in the hybrid pathway is important for understanding its biochemical mechanism. Here, we report that the molybdenum-containing nicotine dehydrogenase (NdhAB), which catalyzes the initial step of nicotine degradation, is located in the periplasm of strain S33, while the 6-hydroxynicotine oxidase and 6-hydroxypseudooxynicoine oxidase are in the cytoplasm. This is consistent with the fact that NdhA has a Tat signal peptide. Interestingly, an open reading frame (ORF) adjacent to the ndhAB gene was verified to encode a copper-containing electron carrier, pseudoazurin (Paz), which has a signal peptide typical of bacterial Paz proteins. Both were transported into the periplasm after being produced in the cytoplasm. We purified NdhAB from the periplasmic fraction of strain S33 and found that with Paz as the physiological electron acceptor, NdhAB catalyzed the hydroxylation of nicotine at a specific rate of 110.52 ± 8.09 μmol · min^-1 · mg of protein^-1, where the oxygen atom in the hydroxyl group of the product 6-hydroxynicotine was derived from H₂O. The apparent K_m values for nicotine and Paz were 1.64 ± 0.07 μM and 3.61 ± 0.23 μM, respectively. NAD(P)⁺, O₂, and ferredoxin could not serve as electron acceptors. Disruption of the paz gene disabled the strain for nicotine degradation, indicating that Paz is required for nicotine catabolism in the strain. These findings help our understanding of electron transfer during nicotine degradation in bacteria.IMPORTANCE Nicotine is a toxic and addictive N-heterocyclic aromatic alkaloid produced in tobacco. Its catabolism in organisms and degradation in tobacco wastes have become major concerns for human health and the environment. Bacteria usually decompose nicotine using the classical strategy of hydroxylating the pyridine ring with the help of activated oxygen by nicotine dehydrogenase, which binds one molybdopterin, two [2Fe2S] clusters, and usually one flavin adenine dinucleotide (FAD) as well. However, the physiological electron acceptor for the reaction is still unknown. In this study, we found that the two-component nicotine dehydrogenase from Agrobacterium tumefaciens S33, naturally lacking an FAD-binding domain, is located in the periplasmic space and uses a copper-containing electron carrier, pseudoazurin, as its physiological electron acceptor. We report here the role of pseudoazurin in a reaction catalyzed by a molybdopterin-containing hydroxylase occurring in the periplasmic space. These results provide new biochemical knowledge on microbial degradation of N-heterocyclic aromatic compounds.

The functional role of the structure of the dioxo-isobacteriochlorin in the catalytic site of cytochrome cd1 for the reduction of nitrite

Cytochrome cd1 is a key enzyme in bacterial denitrification and catalyzes one-electron reduction of nitrite (NO2-) to nitric oxide (NO) at the heme d1 center under anaerobic conditions. The heme d1 has a unique dioxo-isobacteriochlorin structure and is present only in cytochrome cd1. To reveal the functional role of the unique heme d1 in the catalytic nitrite reduction, we studied effect of the porphyrin macrocycle on each reaction step of the catalytic cycle of cytochrome cd1 using synthetic model complexes. The complexes investigated are iron complexes of dioxo-octaethylisobacteriochlorin (1), mono-oxo-octaethylchlorin (2) and octaethylporphyrin (3). We show here that the reduction potential for the transition from the ferric state to the ferrous state and the binding constant for binding of NO2- to the ferrous complex increases with a trend of 3 < 2 < 1. However, the reactivity of the ferrous nitrite complex with protons increases in the reversed order, 1 < 2 < 3. We also show that the iron bound NO of the ferric NO complex is readily replaced by addition of 1 equiv. of p-nitrophenolate. These results indicate that the dioxo-isobacteriochlorin structure is superior to porphyrin and mono-oxo-chlorin structures in the first iron reduction step, the second nitrite binding step, and the NO dissociation step, but inferior in the third nitrite reduction step. These results suggest that the heme d1 has evolved as the catalytic site of cytochrome cd1 to catalyze the nitrite reduction at the highest possible redox potential while maintaining its catalytic activity.

Observation of fast release of NO from ferrous d₁ haem allows formulation of a unified reaction mechanism for cytochrome cd₁ nitrite reductases

Cytochrome cd1 nitrite reductase is a haem-containing enzyme responsible for the reduction of nitrite into NO, a key step in the anaerobic respiratory process of denitrification. The active site of cytochrome cd1 contains the unique d1 haem cofactor, from which NO must be released. In general, reduced haems bind NO tightly relative to oxidized haems. In the present paper, we present experimental evidence that the reduced d1 haem of cytochrome cd1 from Paracoccus pantotrophus releases NO rapidly (k=65-200 s(-1)); this result suggests that NO release is the rate-limiting step of the catalytic cycle (turnover number=72 s(-1)). We also demonstrate, using a complex of the d1 haem and apomyoglobin, that the rapid dissociation of NO is largely controlled by the d1 haem cofactor itself. We present a reaction mechanism proposed to be applicable to all cytochromes cd1 and conclude that the d1 haem has evolved to have low affinity for NO, as compared with other ferrous haems.

The catalytic mechanism of Pseudomonas aeruginosa cd1 nitrite reductase

The cd1 NiRs (nitrite reductases) are enzymes catalysing the reduction of nitrite to NO (nitric oxide) in the bacterial energy conversion denitrification process. These enzymes contain two distinct redox centres: one covalently bound c-haem, which is reduced by external electron donors, and another peculiar porphyrin, the d1-haem (3,8-dioxo-17-acrylate-porphyrindione), where nitrite is reduced to NO. In the present paper, we summarize the most recent results on the mechanism of nitrite reduction by the cd1 NiR from Pseudomonas aeruginosa. We discuss the essential catalytic features of this enzyme, with special attention to the allosteric regulation of the enzyme's activity and to the mechanism employed to avoid product inhibition, i.e. trapping of the active-site reduced haem by the product NO. These results shed light on the reactivity of cd1 NiRs and assign a central role to the unique d1-haem, present only in this class of enzymes.

The 1.4 A resolution structure of Paracoccus pantotrophus pseudoazurin

Pseudoazurins are small type 1 copper proteins that are involved in the flow of electrons between various electron donors and acceptors in the bacterial periplasm, mostly under denitrifying conditions. The previously determined structure of Paracoccus pantotrophus pseudoazurin in the oxidized form was improved to a nominal resolution of 1.4 A, with R and R(free) values of 0.188 and 0.206, respectively. This high-resolution structure makes it possible to analyze the interactions between the monomers and the solvent structure in detail. Analysis of the high-resolution structure revealed the structural regions that are responsible for monomer-monomer recognition during dimer formation and for protein-protein interaction and that are important for partner recognition. The pseudoazurin structure was compared with other structures of various type 1 copper proteins and these were grouped into families according to similarities in their secondary structure; this may be useful in the annotation of copper proteins in newly sequenced genomes and in the identification of novel copper proteins.

d(1) haem biogenesis - assessing the roles of three nir gene products

The synthesis of the modified tetrapyrrole known as d(1) haem requires several dedicated proteins which are coded for by a set of genes that are often found adjacent to the structural gene, nirS, for cytochrome cd(1) nitrite reductase. NirE, the product of the first gene in the nir biogenesis operon, was anticipated to catalyse the conversion of uroporphyrinogen III into precorrin-2; this was confirmed, but it was shown that this enzyme is less sensitive to product inhibition than similar enzymes that function in other biosynthetic pathways. Sequence analysis suggesting that one of these proteins, NirN, is a c-type cytochrome, and has similarity to the part of cytochrome cd(1) that binds d(1), was validated by recombinant production and characterization of NirN. A NirN-d(1) haem complex was demonstrated to release the cofactor to a semi-apo form of cytochrome cd(1) from which d(1) was extracted, suggesting a role for NirN in the assembly of cytochrome cd(1) (NirS). However, inactivation of nirN surprisingly led to only a marginal attenuation of growth of Paracoccus pantotrophus under anaerobic denitrifying conditions. As predicted, NirC is a c-type cytochrome; it was shown in vitro to be an electron donor to the NirN-d(1) complex.

Fast ferrous heme-NO oxidation in nitric oxide synthases

During catalysis, the heme in nitric oxide synthase (NOS) binds NO before releasing it to the environment. Oxidation of the NOS ferrous heme-NO complex by O2 is key for catalytic cycling, but the mechanism is unclear. We utilized stopped-flow methods to study the reaction of O2 with ferrous heme-NO complexes of inducible and neuronal NOS enzymes. We found that the reaction does not involve heme-NO dissociation, but instead proceeds by a rapid direct reaction of O2 with the ferrous heme-NO complex. This behavior is novel and may distinguish heme-thiolate enzymes, such as NOS, from related heme proteins.

Intramolecular electron transfer in Pseudomonas aeruginosa cd(1) nitrite reductase: thermodynamics and kinetics

The cd(1) nitrite reductases, which catalyze the reduction of nitrite to nitric oxide, are homodimers of 60 kDa subunits, each containing one heme-c and one heme-d(1). Heme-c is the electron entry site, whereas heme-d(1) constitutes the catalytic center. The 3D structure of Pseudomonas aeruginosa nitrite reductase has been determined in both fully oxidized and reduced states. Intramolecular electron transfer (ET), between c and d(1) hemes is an essential step in the catalytic cycle. In earlier studies of the Pseudomonas stutzeri enzyme, we observed that a marked negative cooperativity is controlling this internal ET step. In this study we have investigated the internal ET in the wild-type and His369Ala mutant of P. aeruginosa nitrite reductases and have observed similar cooperativity to that of the Pseudomonas stutzeri enzyme. Heme-c was initially reduced, in an essentially diffusion-controlled bimolecular process, followed by unimolecular electron equilibration between the c and d(1) hemes (k(ET) = 4.3 s(-1) and K = 1.4 at 298 K, pH 7.0). In the case of the mutant, the latter ET rate was faster by almost one order of magnitude. Moreover, the internal ET rate dropped (by approximately 30-fold) as the level of reduction increased in both the WT and the His mutant. Equilibrium standard enthalpy and entropy changes and activation parameters of this ET process were determined. We concluded that negative cooperativity is a common feature among the cd(1) nitrite reductases, and we discuss this control based on the available 3D structure of the wild-type and the H369A mutant, in the reduced and oxidized states.

Neutralizing a surface charge on the FMN subdomain increases the activity of neuronal nitric-oxide synthase by enhancing the oxygen reactivity of the enzyme heme-nitric oxide complex

Nitric-oxide synthases (NOSs) are calmodulin-dependent flavoheme enzymes that oxidize l-Arg to nitric oxide (NO) and l-citrulline. Their catalytic behaviors are complex and are determined by their rates of heme reduction (k(r)), ferric heme-NO dissociation (k(d)), and ferrous heme-NO oxidation (k(ox)). We found that point mutation (E762N) of a conserved residue on the enzyme's FMN subdomain caused the NO synthesis activity to double compared with wild type nNOS. However, in the absence of l-Arg, NADPH oxidation rates suggested that electron flux through the heme was slower in E762N nNOS, and this correlated with the mutant having a 60% slower k(r). During NO synthesis, little heme-NO complex accumulated in the mutant, compared with approximately 50-70% of the wild-type nNOS accumulating as this complex. This suggested that the E762N nNOS is hyperactive because it minimizes buildup of an inactive ferrous heme-NO complex during NO synthesis. Indeed, we found that k(ox) was 2 times faster in the E762N mutant than in wild-type nNOS. The mutational effect on k(ox) was independent of calmodulin. Computer simulation and experimental measures both indicated that the slower k(r) and faster k(ox) of E762N nNOS combine to lower its apparent K(m,O(2)) for NO synthesis by at least 5-fold, which in turn increases its V/K(m) value and enables it to be hyperactive in steady-state NO synthesis. Our work underscores how sensitive nNOS activity is to changes in the k(ox) and reveals a novel means for the FMN module or protein-protein interactions to alter nNOS activity.

New insights into the activity of Pseudomonas aeruginosa cd1 nitrite reductase

The cytochrome cd(1) nitrite reductases are enzymes that catalyse the reduction of nitrite to nitric oxide (NO) in the bacterial energy conversion denitrification process. These enzymes contain two different redox centres: one covalently bound c-haem, which is reduced by external donors, and one peculiar d(1)-haem, where catalysis occurs. In the present paper, we summarize the current understanding of the reaction of nitrite reduction in the light of the most recent results on the enzyme from Pseudomonas aeruginosa and discuss the differences between enzymes from different organisms. We have evidence that release of NO from the ferrous d(1)-haem occurs rapidly enough to be fully compatible with the turnover, in contrast with previous hypotheses, and that the substrate nitrite is able to displace NO from the d(1)-haem iron. These results shed light on the mechanistic details of the activity of cd(1) nitrite reductases and on the biological role of the d(1)-haem, whose presence in this class of enzymes has to date been unexplained.