Purification of cytochrome cd1 nitrite reductase from Pseudomonas stutzeri JM300 and reconstitution with native and synthetic heme d1

Azulichlorins and Benzocarbachlorins Derived Therefrom

Acid-catalyzed condensation of azulidipyrrane aldehydes with a dihydrodipyrrin carbaldehyde afforded the first examples of azulichlorins. These macrocyclic products were isolated in a monoprotonated form, and the free bases proved to be somewhat unstable. The monocations were strongly diatropic, and proton NMR spectroscopy showed the internal C-H at ca. -2 ppm. Addition of TFA gave the related dications, but these exhibited significantly reduced aromatic ring currents. Reaction of an azulichlorin with tert-butyl hydroperoxide and KOH in dichloromethane/methanol gave a benzocarbachlorin and two related aldehydes. The UV-vis spectrum for the benzocarbachlorin showed a split Soret band at 414 and 430 nm, together with a strong chlorin-like absorption at 684 nm. The proton NMR spectrum indicated that the carbachlorin is strongly aromatic and the internal C-H was observed at -4.64 ppm. Addition of TFA afforded a C-protonated dication with a significantly increased diatropic ring current. The proton NMR spectrum, NICS calculations, and AICD plots indicated that the system favors a 22π electron delocalization pathway that runs through the fused benzo unit. Addition of TFA to the benzocarbachlorin aldehydes primarily led to the formation of monocations, and the generation of C-protonated dications was no longer favored due to the presence of electron-withdrawing formyl moieties.

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.

Maturation of the cytochrome cd1 nitrite reductase NirS from Pseudomonas aeruginosa requires transient interactions between the three proteins NirS, NirN and NirF

The periplasmic cytochrome cd₁ nitrite reductase NirS occurring in denitrifying bacteria such as the human pathogen Pseudomonas aeruginosa contains the essential tetrapyrrole cofactors haem c and haem d₁. Whereas the haem c is incorporated into NirS by the cytochrome c maturation system I, nothing is known about the insertion of the haem d₁ into NirS. Here, we show by co-immunoprecipitation that NirS interacts with the potential haem d₁ insertion protein NirN in vivo. This NirS–NirN interaction is dependent on the presence of the putative haem d₁ biosynthesis enzyme NirF. Further, we show by affinity co-purification that NirS also directly interacts with NirF. Additionally, NirF is shown to be a membrane anchored lipoprotein in P. aeruginosa. Finally, the analysis by UV–visible absorption spectroscopy of the periplasmic protein fractions prepared from the P. aeruginosa WT (wild-type) and a P. aeruginosa ΔnirN mutant shows that the cofactor content of NirS is altered in the absence of NirN. Based on our results, we propose a potential model for the maturation of NirS in which the three proteins NirS, NirN and NirF form a transient, membrane-associated complex in order to achieve the last step of haem d₁ biosynthesis and insertion of the cofactor into NirS.

Solvent accessibility in the distal heme pocket of the nitrosyl d(1)-heme complex of Pseudomonas stutzeri cd(1) nitrite reductase

In nitrite reductase (cd(1) NIR), the c-heme mediates electron transfer to the catalytic d(1)-heme where nitrite (NO(2)(-)) is reduced to nitric oxide (NO). An interesting feature of this enzyme is the relative lability of the reaction product NO bound to the d(1)-heme. Marked differences in the c- to d(1)-heme electron-transfer rates were reported for cd(1) NIRs from different sources, such as Pseudomonas stutzeri (P. stutzeri) and Pseudomonas aeruginosa (P. aeruginosa). The three-dimensional structure of the P. aeruginosa enzyme has been determined, but that of the P. stutzeri enzyme is still unknown. The difference in electron transfer rates prompted a comparison of the structural properties of the d(1)-heme pocket of P. stutzeri cd(1) NIR with those of the P. aeruginosa wild type enzyme (WT) and its Y10F using their nitrosyl d(1)-heme complexes. We applied high field pulse electron paramagnetic resonance (EPR) techniques that detect nuclear spins in the close environment of the spin bearing Fe(II)-NO entity. We observed similarities in the rhombic g-tensor and detected a proximal histidine ligand with (14)N hyperfine and quadrupole interactions also similar to those of P. aeruginosa WT and Y10F mutant complexes. In contrast, we also observed significant differences in the H-bond network involving the NO ligand and a larger solvent accessibility for P. stutzeri attributed to the absence of this tyrosine residue. For P. aeruginosa, cd(1) NIR domain swapping allows Tyr(10) to become H-bonded to the bound NO substrate. These findings support a previous suggestion that the large difference in the c- to d(1)-heme electron transfer rates between the two enzymes is related to solvent accessibility of their d(1)-heme pockets.

Determination of the intrinsic kinetic parameters of sulfide-oxidizing autotrophic denitrification in differential reactors containing immobilized biomass

Nitrogen removal coupled with sulfide oxidation has potential for the treatment of effluents from anaerobic reactors because they contain sulfide, which can be used as an endogenous electron donor for denitrification. This work evaluated the intrinsic kinetics of sulfide-oxidizing autotrophic denitrification via nitrate and nitrite in systems containing attached cells. Differential reactors were fed with nitrified synthetic domestic sewage and different sulfide concentrations. The intrinsic kinetic parameters of nitrogen removal were determined when the mass transfer resistance was negligible. This bioprocess could be described by a half-order kinetic model for biofilms. The half-order kinetic coefficients ranged from 0.425 to 0.658 mg N(1/2) L(-1/2) h(-1) for denitrification via nitrite and from 0.190 to 0.609 mg N(1/2) L(-1/2) h(-1) for denitrification via nitrate. In this latter, the lower value was due to the use of electrons donated from intermediary sulfur compounds whose formation and subsequent consumption were detected.

Purification, characterization, and gene cloning of thermophilic cytochrome cd1 nitrite reductase from Hydrogenobacter thermophilus TK-6

A thermophilic, chemolithoautotrophic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6 can grow autotrophically under anaerobic conditions by denitrification. One of the denitrification enzymes, cytochrome cd(1) nitrite reductase, was isolated and its gene was cloned from strain TK-6. The subunit molecular mass of the purified enzyme was 61.5 kDa and the isoelectric point was determined to be 9.3. The optimum temperature and pH for the enzymatic reaction were 70-75 degrees C and 6.5-7.0, respectively. The structural gene for the enzyme, nirS, is probably transcribed as a hexacistronic operon with the following genes encoding a putative diheme cytochrome c and the proteins required for biosynthesis of heme d(1). The NirS sequence was phylogenetically distinct from those of proteobacteria. The consensus -35 and -10 sequences were found in the putative nirS promoter region, but the consensus sequences for the DNR/NnrR-type or the NorR/FhpR-type nitric oxide sensing regulators were not found in this region.

Biology of Pseudomonas stutzeri

Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri.

Cytochrome cd1, reductive activation and kinetic analysis of a multifunctional respiratory enzyme

Paracoccus pantotrophus cytochrome cd(1) is an enzyme of bacterial respiration, capable of using nitrite in vivo and also hydroxylamine and oxygen in vitro as electron acceptors. We present a comprehensive analysis of the steady state kinetic properties of the enzyme with each electron acceptor and three electron donors, pseudoazurin and cytochrome c(550), both physiological, and the non-physiological horse heart cytochrome c. At pH 5.8, optimal for nitrite reduction, the enzyme has a turnover number up to 121 s(-1) per d(1) heme, significantly higher than previously observed for any cytochrome cd(1). Pre-activation of the enzyme via reduction is necessary to establish full catalytic competence with any of the electron donor proteins. There is no significant kinetic distinction between the alternative physiological electron donors in any respect, providing support for the concept of pseudospecificity, in which proteins with substantially different tertiary structures can transfer electrons to the same acceptor. A low level hydroxylamine disproportionase activity that may be an intrinsic property of cytochromes c is also reported. Important implications for the enzymology of P. pantotrophus cytochrome cd(1) are discussed and proposals are made about the mechanism of reduction of nitrite, based on new observations placed in the context of recent rapid reaction studies.

A quantum chemical survey of metalloporphyrin-nitrosyl linkage isomers: insights into the observation of multiple FeNO conformations in a recent crystallographic determination of nitrophorin 4

Using density functional theory-based geometry optimizations, we have searched for eta(1)-NO, eta(1)-ON (isonitrosyl), and eta(2)-NO (side-on bound NO) linkage isomers of a number of metalloporphyrin-NO complexes, M(Por)(NO)(L), where Por = porphinato dianion, M = Mn(II), Fe(II), Fe(III), Ru(II), Ru(III), Co(II), and Rh(II), and L = no ligand, SMe, Ph, and imidazole. The eta(1)-NO isomer had the lowest energy in all cases, and the isonitrosyl isomer was also located as a higher energy potential energy minimum in a number of cases. The eta(2)-NO isomer was only located as a minimum for Mn(II) (L = no ligand), Fe(III) (L = no ligand), and Ru(III) (L = Ph, imidazole, pyrdine), suggesting that an [MNO](6) electron count is important for stabilization of the eta(2) mode of ligation. However, in the presence of axial ligands L, the side-on isomers of [FeNO](6) complexes were not stable and opened up to an unusual geometry where the FeN(O) and NO vectors were tilted in opposite directions relative to the heme normal. Exactly such a geometry, as well as a "normal" upright geometry, has been observed in a recent crystallographic determination of nitrophorin 4 (Nature Struct. Biol. 2000, 7, 551), a salivary protein from the blood-sucking insect Rhodnius prolixus. Together, the calculated and experimental result illustrate the extreme softness of the FeNO potential energy surface toward various forms of tilting and bending deformations.

Time-resolved infrared spectroscopy reveals a stable ferric heme-NO intermediate in the reaction of Paracoccus pantotrophus cytochrome cd1 nitrite reductase with nitrite

Cytochrome cd(1) is a respiratory enzyme that catalyzes the physiological one-electron reduction of nitrite to nitric oxide. The enzyme is a dimer, each monomer containing one c-type cytochrome center and one active site d(1) heme. We present stopped-flow Fourier transform infrared data showing the formation of a stable ferric heme d(1)-NO complex (formally d(1)Fe(II)-NO(+)) as a product of the reaction between fully reduced Paracoccus pantotrophus cytochrome cd(1) and nitrite, in the absence of excess reductant. The Fe-(14)NO nu(NO) stretching mode is observed at 1913 cm(-1) with the corresponding Fe-(15)NO band at 1876 cm(-1). This d(1) heme-NO complex is still readily observed after 15 min. EPR and visible absorption spectroscopic data show that within 4 ms of the initiation of the reaction, nitrite is reduced at the d(1) heme, and a cFe(III) d(1)Fe(II)-NO complex is formed. Over the next 100 ms there is an electron redistribution within the enzyme to give a mixed species, 55% cFe(III) d(1)Fe(II)-NO and 45% cFe(II) d(1)Fe(II)-NO(+). No kinetically competent release of NO could be detected, indicating that at least one additional factor is required for product release by the enzyme. Implications for the mechanism of P. pantotrophus cytochrome cd(1) are discussed.

X-ray crystallographic study of cyanide binding provides insights into the structure-function relationship for cytochrome cd1 nitrite reductase from Paracoccus pantotrophus

We present a 1.59-A resolution crystal structure of reduced Paracoccus pantotrophus cytochrome cd(1) with cyanide bound to the d(1) heme and His/Met coordination of the c heme. Fe-C-N bond angles are 146 degrees for the A subunit and 164 degrees for the B subunit of the dimer. The nitrogen atom of bound cyanide is within hydrogen bonding distance of His(345) and His(388) and either a water molecule in subunit A or Tyr(25) in subunit B. The ferrous heme-cyanide complex is unusually stable (K(d) approximately 10(-6) m); we propose that this reflects both the design of the specialized d(1) heme ring and a general feature of anion reductases with active site heme. Oxidation of crystals of reduced, cyanide-bound, cytochrome cd(1) results in loss of cyanide and return to the native structure with Tyr(25) as a ligand to the d(1) heme iron and switching to His/His coordination at the c-type heme. No reason for unusually weak binding of cyanide to the ferric state can be identified; rather it is argued that the protein is designed such that a chelate-based effect drives displacement by tyrosine of cyanide or a weaker ligand, like reaction product nitric oxide, from the ferric d(1) heme.

Magnetic interactions in the high-spin iron(III) oxooctaethylchlorinato derivative [Fe(oxoOEC)(Cl)] and its pi-cation radical [Fe(oxoOEC.)(Cl)]SbCl6

The preparation and characterization of the beta-oxochlorin derivative [3,3,7,8,12,13,17,18-octaethyl-(3H)-porphin-2-onato(2-)]iron(III) chloride, [Fe(oxoOEC)(Cl)], and its pi-cation radical derivative [Fe(oxoOEC.)(Cl)]SbCl6 is described. Both compounds have been characterized by single-crystal X-ray structure determinations, IR, UV/vis/near-IR, and Mössbauer spectroscopies, and temperature-dependent magnetic susceptibility measurements. The macrocycles of [Fe(oxoOEC)(Cl)] and [Fe(oxoOEC.)(Cl)]SbCl6 are both saddled, and [Fe(oxoOEC.)(Cl)]-SbCl6 is slightly ruffled as well. [Fe(oxoOEC)(Cl)] shows a laterally shifted dimeric unit in the solid state, with a mean plane separation of 3.39 A and a lateral shift of 7.39 A. Crystal data for [Fe(oxoOEC)(Cl)]: triclinic, space group P1, Z = 2, a = 9.174(2) A, b = 13.522(3) A, c = 14.838(3) A, alpha = 95.79(3) degrees, beta = 101.46(2) degrees, gamma = 104.84(3) degrees. Upon oxidation, the inter-ring geometric parameters increase; the mean plane separation and the lateral shift of the dimeric unit of [Fe(oxoOEC.)(Cl)]SbCl6 are 4.82 and 8.79 A, respectively. Crystal data for [Fe(oxoOEC.)(Cl)]SbCl6: monoclinic, space group Cc, Z = 4, a = 19.8419(13) A, b = 10.027(2) A, c = 22.417(4) A, beta = 96.13(2) degrees. A broad near-IR absorption band appears at 1415 nm for the pi-cation radical, [Fe(oxoOEC.)(Cl)]SbCl6. Zero-field Mössbauer measurements at 4.2 K for both [Fe(oxoOEC)(Cl)] and [Fe(oxoOEC.)(Cl)]SbCl6 confirmed that the oxidation state of the iron atom did not change upon chemical oxidation. Solid-state magnetic susceptibility measurements for [Fe(oxoOEC.)(Cl)]SbCl6 resulted in a large temperature dependence of the magnetic moment that can best be fit with a model that includes a zero-field splitting parameter of D = 6 cm-1, antiferromagnetic intermolecular iron-iron coupling (2JFe-Fe = -0.14 cm-1), antiferromagnetic intramolecular iron-radical coupling (2JFe-r = -76 cm-1), and antiferromagnetic radical-radical coupling (2Jr-r = -13 cm-1).

Bacterial nitric oxide synthesis

The structure-function relationships in nitrite reductases, key enzymes in the dissimilatory denitrification pathway which reduce nitrite to nitric oxide (NO), are reviewed in this paper. The mechanisms of NO production are discussed in detail and special attention is paid to new structural information, such as the high resolution structure of the copper- and heme-containing enzymes from different sources. Finally, some implications relevant to regulation of the steady state levels of NO in denitrifiers are presented.

Two enzymes with a common function but different heme ligands in the forms as isolated. Optical and magnetic properties of the heme groups in the oxidized forms of nitrite reductase, cytochrome cd1, from Pseudomonas stutzeri and Thiosphaera pantotropha

It is shown that, in the oxidized state, heme c of Pseudomonas stutzeri (ZoBell strain) cytochrome cd1 has histidine-methionine ligation as observed for cytochrome cd1 from Pseudomonas aeruginosa [Sutherland, J., Greenwood, C., Peterson, J., and Thomson, A. J. (1986) Biochem. J. 233, 893-898]. However, the X-ray structure of Thiosphaera pantotropha cytochrome cd1 reveals bis-histidine ligation for heme c. It is confirmed by EPR and near-infrared (NIR) MCD measurements that the bis-histidine coordination remains unaltered in the solution phase. Hence, the difference between the heme c ligation states defines two distinct classes of oxidized cytochromes cd1 as isolated. A weak feature in the T. pantotropha NIR MCD at 1900 nm suggests that a small population of heme c has histidine-methionine coordination. The ligation state of heme d1 cannot be defined with the same level of confidence, because the porphyrin-to-Fe(III) charge-transfer (CT) bands are less well characterized for this class of partially reduced porphyrin ring. However, variable temperature absorption and MCD spectra show that, in the T. pantotropha enzyme, heme d1 exists in a thermal low-spin/high-spin mixture with the low-spin as the ground state, whereas in P. stutzeri cytochrome cd1, and d1 heme is low-spin at all temperatures. A weak band, assigned as the heme d1 porphyrin-pi(a1u,a2u)-to-ferric(d) charge-transfer transition has been identified for the first time at 2170 nm. Its magnetic properties show the heme d1 to have an unusual (dxz,yz)4(dxy)1 electronic ground state as is found for low-spin Fe(III) chlorins [Cheesman, M. R., and Walker, F. A. (1996) J. Am. Chem. Soc. 118, 7373-7380]. It is proposed that the localization of the Fe(III) unpaired d-electron in an orbital lying in the heme plane may decrease the affinity of the Fe(III) heme for unsaturated ligands such as NO. Although heme d1 in the enzymes from P. stutzeri and T. pantotropha shows different temperature-dependent spin properties, the positions of the low-spin Fe(III) alpha-absorption band, at approximately 640 nm, are very similar to those observed for cytochromes cd1 from eight other sources, suggesting that all have similar strength fields from the axial ligands and, hence, that all have the same coordination, namely histidine-tyrosine or possibly histidine-hydroxide at the heme.

Cell biology and molecular basis of denitrification

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

Cytochrome cd1 structure: unusual haem environments in a nitrite reductase and analysis of factors contributing to beta-propeller folds

The central tunnel of the eight-bladed beta-propeller domain of cytochrome cd1 (nitrite reductase) is seen, from a 1.28 A resolution structure, to contain hydrogen donors and acceptors that are satisfied by interaction either with water or the d1 haem. The d1 haem, although bound by an extensive network of hydrogen bonds, is not distorted in its binding pocket and is confirmed to have exactly the dioxoisobacteriochlorin structure proposed from chemical studies. A biological rationale is advanced for the undistorted structure of the d1 haem and the large number of hydrogen bonds it makes. The beta-propeller domain can be closely superimposed on that of methanol dehydrogenase despite the enzymes sharing no common sequence motifs and using a different set of interactions to "Velcro" close the propeller. The sequence and likely structural relationships between cytochrome cd1 or methanol dehydrogenase and other predicted eight-bladed beta-propeller domains in proteins, such as the pyrolloquinoline quinone-dependent alcohol dehydrogenase, are discussed and compared with other propeller proteins. From sequencing the nirS gene of Thiosphaera pantotropha, it is established that the amino acid sequence deduced previously in part from X-ray diffraction data at lower resolution was largely correct, as was the proposal that eight N-terminal amino acid residues were not seen in the structure. The unusual haem iron environments in both the c-type cytochrome domain, with His/His coordination, and the d1-type cytochrome domain with Tyr/His coordination are related to the functions of the redox centres.

A cytochrome cd1-type nitrite reductase mediates the first step of denitrification in Alcaligenes eutrophus

Respiratory nitrite reductase (NIR) has been purified from the soluble extract of denitrifying cells of Alcaligenes eutrophus strain H16 to apparent electrophoretic homogeneity. The enzyme was induced under anoxic conditions in the presence of nitrite. Purified NIR showed typical features of a cytochrome cd1-type nitrite reductase. It appeared to be a dimer of kDa subunits, its activity was only weakly inhibited by the copper chelator diethyldithiocarbamate, and spectral analysis revealed absorption maxima which were characteristic for the presence of heme c and heme d1. The isoelectric point of 8.6 was considerably higher than the pI determined for cd1 nitrite reductases from pseudomonads. Eighteen amino acids at the N-terminus of the A. eutrophus NIR, obtained by protein sequencing, showed no significant homology to the N-terminal region of nitrite reductases from Pseudomonas stutzeri and Pseudomonas aeruginosa.

Pseudomonas aeruginosa nitrite reductase (or cytochrome oxidase): an overview

The biochemistry and molecular biology of nitrite reductase, a key enzyme in the dissimilatory denitrification pathway of Ps aeruginosa which reduces nitrite to NO, is reviewed in this paper. The enzyme is a non-covalent homodimer, each subunit containing one heme c and one heme d1. The reaction mechanisms of nitrite and oxygen reduction are discussed in detail, as well as the interaction of the enzyme with its macromolecular substrates, azurin and cytochrome c551. Special attention is paid to new structural information, such as the chemistry of the d1 prosthetic group and the primary sequence of the gene and the protein. Finally, results on the expression both in Ps aeruginosa and in heterologous systems are presented.

Characterization of Tn5 mutants deficient in dissimilatory nitrite reduction in Pseudomonas sp. strain G-179, which contains a copper nitrite reductase

Tn5 was used to generate mutants that were deficient in the dissimilatory reduction of nitrite for Pseudomonas sp. strain G-179, which contains a copper nitrite reductase. Three types of mutants were isolated. The first type showed a lack of growth on nitrate, nitrite, and nitrous oxide. The second type grew on nitrate and nitrous oxide but not on nitrite (Nir-). The two mutants of this type accumulated nitrite, showed no nitrite reductase activity, and had no detectable nitrite reductase protein bands in a Western blot (immunoblot). Tn5 insertions in these two mutants were clustered in the same region and were within the structural gene for nitrite reductase. The third type of mutant grew on nitrate but not on nitrite or nitrous oxide (N2O). The mutant of this type accumulated significant amounts of nitrite, NO, and N2O during anaerobic growth on nitrate and showed a slower growth rate than the wild type. Diethyldithiocarbamic acid, which inhibited nitrite reductase activity in the wild type, did not affect NO reductase activity, indicating that nitrite reductase did not participate in NO reduction. NO reductase activity in Nir- mutants was lower than that in the wild type when the strains were grown on nitrate but was the same as that in the wild type when the strains were grown on nitrous oxide. These results suggest that the reduction of NO and N2O was carried out by two distinct processes and that mutations affecting nitrite reduction resulted in reduced NO reductase activity following anaerobic growth with nitrate.

Mutants of Pseudomonas fluorescens deficient in dissimilatory nitrite reduction are also altered in nitric oxide reduction

Five Tn5 mutants of Pseudomonas fluorescens AK-15 deficient in dissimilatory reduction of nitrite were isolated and characterized. Two insertions occurred inside the nitrite reductase structural gene (nirS) and resulted in no detectable nitrite reductase protein on a Western immunoblot. One mutant had Tn5 inserted inside nirC, the third gene in the same operon, and produced a defective nitrite reductase protein. Two other mutants had insertions outside of this nir operon and also produced defective proteins. All of the Nir- mutants characterized showed not only loss of nitrite reductase activity but also a significant decrease in nitric oxide reductase activity. When cells were incubated with 15NO in H2(18)O, about 25% of the oxygen found in nitrous oxide exchanged with H2O. The extent of exchange remained constant throughout the reaction, indicating the incorporation of 18O from H2(18)O reached equilibrium rapidly. In all nitrite reduction-deficient mutants, less than 4% of the 18O exchange was found, suggesting that the hydration and dehydration step was altered. These results indicate that the factors involved in dissimilatory reduction of nitrite influenced the subsequent NO reduction in this organism.

Evidence for a NO-rebound mechanism for production of N2O from nitrite by the copper-containing nitrite reductase from Achromobacter cycloclastes

Reduction of NO2- by the Cu-containing nitrite reductase from Achromobacter cycloclastes produces NO as the primary product initially, but as NO accumulates, NO production levels-off and N2O production becomes significant. Reaction of the enzyme with NO2- in the presence of NO increases the amount of N2O product significantly, while trapping the NO product as nitrosylhemoglobin or rapid removal of NO by sparging results in no detectable N2O production. Reaction of the enzyme with 15NO2- in the presence of 14NO results in rapid formation of the mixed isotope product (14N, 15N)O in ca. 45% yield. In contrast, the presence or absence of NO has no effect on N2O production by a prototypical heme cd1-containing nitrite reductase. These results are consistent with formation of a labile Cu(+)-NO+ species in the copper enzyme, which normally decomposes to NO. Production of N2O requires that the released NO must rebind to the enzyme to combine with a second NO2- or a species derived therefrom.