Correlation of optical and EPR signals with the P460 heme of hydroxylamine oxidoreductase from Nitrosomonas europaea

Influences of the heme-lysine crosslink in cytochrome P460 over redox catalysis and nitric oxide sensitivity

Ammonia (NH₃)-oxidizing bacteria (AOB) derive total energy for life from the multi-electron oxidation of NH₃ to nitrite (NO₂^-). One obligate intermediate of this metabolism is hydroxylamine (NH₂OH), which can be oxidized to the potent greenhouse agent nitrous oxide (N₂O) by the AOB enzyme cytochrome (cyt) P460. We have now spectroscopically characterized a 6-coordinate (6c) {FeNO}⁷ intermediate on the NH₂OH oxidation pathway of cyt P460. This species has two fates: it can either be oxidized to the {FeNO}⁶ that then undergoes attack by NH₂OH to ultimately generate N₂O, or it can lose its axial His ligand, thus generating a stable, off-pathway 5-coordinate (5c) {FeNO}⁷ species. We show that the wild type (WT) cyt P460 exhibits a slow nitric oxide (NO)-independent conversion (k_His-off = 2.90 × 10^-3 s^-1), whereas a cross-link-deficient Lys70Tyr cyt P460 mutant protein underwent His dissociation via both a NO-independent (k_His-off = 3.8 × 10^-4 s^-1) and a NO-dependent pathway [k_His-off(NO) = 790 M^-1 s^-1]. Eyring analyses of the NO-independent pathways for these two proteins revealed a significantly larger (ca. 27 cal mol^-1 K^-1) activation entropy (ΔS^‡) in the cross-link-deficient mutant. Our results suggest that the Lys-heme cross-link confers rigidity to the positioning of the heme P460 cofactor to avoid the fast NO-dependent His dissociation pathway and subsequent formation of the off-pathway 5c {FeNO}⁷ species. The relevance of these findings to NO signaling proteins such as heme-nitric oxide/oxygen binding (H-NOX) is also discussed.

Characterization of Anammox Hydrazine Dehydrogenase, a Key N2-producing Enzyme in the Global Nitrogen Cycle

Anaerobic ammonium-oxidizing (anammox) bacteria derive their energy for growth from the oxidation of ammonium with nitrite as the electron acceptor. N2, the end product of this metabolism, is produced from the oxidation of the intermediate, hydrazine (N2H4). Previously, we identified N2-producing hydrazine dehydrogenase (KsHDH) from the anammox organism Kuenenia stuttgartiensis as the gene product of kustc0694 and determined some of its catalytic properties. In the genome of K. stuttgartiensis, kustc0694 is one of 10 paralogs related to octaheme hydroxylamine (NH2OH) oxidoreductase (HAO). Here, we characterized KsHDH as a covalently cross-linked homotrimeric octaheme protein as found for HAO and HAO-related hydroxylamine-oxidizing enzyme kustc1061 from K. stuttgartiensis Interestingly, the HDH trimers formed octamers in solution, each octamer harboring an amazing 192 c-type heme moieties. Whereas HAO and kustc1061 are capable of hydrazine oxidation as well, KsHDH was highly specific for this activity. To understand this specificity, we performed detailed amino acid sequence analyses and investigated the catalytic and spectroscopic (electronic absorbance, EPR) properties of KsHDH in comparison with the well defined HAO and kustc1061. We conclude that HDH specificity is most likely derived from structural changes around the catalytic heme 4 (P460) and of the electron-wiring circuit comprising seven His/His-ligated c-type hemes in each subunit. These nuances make HDH a globally prominent N2-producing enzyme, next to nitrous oxide (N2O) reductase from denitrifying microorganisms.

Theoretical insight into the hydroxylamine oxidoreductase mechanism

The multiheme enzyme hydroxylamine oxidoreductase from the autotrophic bacteria Nitrosomonas europaea catalyzes the conversion of hydroxylamine to nitrite, with a complicate arrangement of heme groups in three subunits. As a distinctive feature, the protein has a covalent linkage between a tyrosyl residue of one subunit and a meso carbon atom of the heme active site of another. We studied the influence of this bond in the catalysis from a theoretical perspective through electronic structure calculations at the density functional theory level, starting from the crystal structure of the protein. Geometry optimizations of proposed reaction intermediates were used to calculate the dissociation energy of different nitrogen containing ligands, considering the presence and absence of the meso tyrosyl residue. The results indicate that the tyrosine residue enhances the binding of hydroxylamine, and increases the stability of a Fe(III)NO intermediate, while behaving indifferently in the Fe(II)NO form. The calculations performed on model systems including neighboring aminoacids revealed the probable formation of a bidentate hydrogen bond between the Fe(III)H(2)O complex and Asp 257, in a high-spin aquo complex as the resting state. Characterization of non-planar heme distortions showed that the meso-substituent induces significant ruffling in the evaluated intermediates.

NO reductase activity of the tetraheme cytochrome C554 of Nitrosomonas europaea

The tetraheme cytochrome c(554) (cyt c(554)) from Nitrosomonas europaea is believed to function as an electron-transfer protein from hydroxylamine oxidoreductase (HAO). We show here that cyt c(554) also has significant NO reductase activity. The protein contains one high-spin and three low-spin c-type hemes. HAO catalyzed reduction of the cyt c(554), ligand binding, intermolecular electron transfer, and kinetics of NO reduction by cyt c(554) have been investigated. We detect the formation of a NO-bound ferrous heme species in cyt c(554) by EPR and Mössbauer spectroscopies during the HAO catalyzed oxidation of hydroxylamine, indicating that N-oxide intermediates produced from HAO readily bind to cyt c(554). In the half-reduced state of cyt c(554), we detect a spin interaction between the [FeNO](7) state of heme 2 and the low-spin ferric state of heme 4. We find that ferrous cyt c(554) will reduce NO at a rate greater than 16 s(-1), which is comparable to rates of other known NO reductases. Carbon monoxide or nitrite are shown not to bind to the reduced protein, and previous results indicate the reactions with O(2) are slow and that a variety of ligands will not bind in the oxidized state. Thus, the enzymatic site is highly selective for NO. The NO reductase activity of cyt c(554) may be important during ammonia oxidation in N. europaea at low oxygen concentrations to detoxify NO produced by reduction of nitrite or incomplete oxidation of hydroxylamine.

Selective one-electron reduction of Nitrosomonas europaea hydroxylamine oxidoreductase with nitric oxide

Hydroxylamine oxidoreductase (HAO) from the autotrophic bacterium Nitrosomonas europaea catalyzes the 4-e- oxidation of NH2-OH to NO2-. The e- are transferred from NH2OH to an unusual 5-coordinate heme known as P460, which is the active site of HAO, and from there to an array of seven c-type hemes. NO., generated by laser flash photolysis of N,N'-bis(carboxymethyl)-N,N'-dinitroso-1,4-phenylenediamine, is found to act as a 1-e- donor to HAO. Most likely NO. binds P460 to yield a [Fe(NO)]6 moiety, which then hydrolyzes to give the reduced enzyme and NO2-. The [Fe(NO)]6 moiety is also a plausible final intermediate in the oxidation of NH2OH.

Correlations of structure and electronic properties from EPR spectroscopy of hydroxylamine oxidoreductase

Hydroxylamine oxidoreductase (HAO) from the autotrophic nitrifying bacterium Nitrosomonas europaea catalyzes the oxidation of NH(2)OH to HNO(2). The enzyme contains eight hemes per subunit which participate in catalytic function and electron transport. The structure of the enzyme shows a unique spatial arrangement of the eight hemes, subsets of which are now observed in four other proteins. The spatial arrangement displays three types of diheme pairing motifs. At least four of the eight hemes are electronically coupled in two distinguishable pairs and one of these pairs is at the active site of the enzyme. Here, the use of quantitative simulation of the EPR signals allows determination of exchange couplings, and assignments of signals and reduction potentials to hemes of the crystal structure. The absence of any obvious heme-to-heme bonding pathway in the crystal structure suggests that the observed exchange interactions are derived from direct electronic overlap of porphyrin orbitals. This provides evidence for heme pairs which function as biological two-electron redox centers in electron-transfer processes.

Inorganic nitrogen metabolism in bacteria

Enzymatic reactions involving inorganic nitrogen species provide a rich variety of systems with which to study biological chemistry. In many cases, catalysis involves redox chemistry and takes place at metal centres. Recent structures and new spectroscopic data have rapidly advanced our knowledge of nitrogen cycle enzymology, particularly in the areas of nitrogen fixation, hydroxylamine oxidation and nitrite reduction. In the case of the nitrate reductases and nitric oxide reductase, models for structure and catalysis can be designed, based on new structural information that is now available for closely related enzymes. The past two years have also seen significant progress in our understanding of the enzymology of some 'new' reactions of the nitrogen cycle, for example anaerobic ammona oxidation and heterotrophic nitrification.