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PubMed2003

Directing the mode of nitrite binding to a copper-containing nitrite reductase from Alcaligenes faecalis S-6: characterization of an active site isoleucine.

Unlike the heme cd(1)-based nitrite reductase enzymes, the molecular mechanism of copper-containing nitrite reductases remains controversial. A key source of controversy is the productive binding mode of nitrite in the active site. To identify and characterize the molecular determinants associated with nitrite binding, we applied a combinatorial mutagenesis approach to generate a small library of six variants at position 257 in nitrite reductase from Alcaligenes faecalis S-6. The activities of these six variants span nearly two orders of magnitude with one variant, I257V, the only observed natural substitution for Ile257, showing greater activity than the native enzyme. High-resolution (> 1.8 A) nitrite-soaked crystal structures of these variants display different modes of nitrite binding that correlate well with the altered activities. These studies identify for the first time that the highly conserved Ile257 in the native enzyme is a key molecular determinant in directing a catalytically competent mode of nitrite binding in the active site. The O-coordinate bidentate binding mode of nitrite observed in native and mutant forms with high activity supports a catalytic model distinct from the heme cd(1) NiRs. (The atomic coordinates for I257V[NO(2)(-)], I257L[NO(2)(-)], I257A[NO(2)(-)], I257T[NO(2)(-)], I257M[NO(2)(-)] and I257G[NO(2)(-)] AfNiR have been deposited in the Protein Data Bank [PDB identification codes are listed in Table 2].)

Alcaligenes↗
PubMed2000

The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite.

Escherichia coli possesses two distinct nitrite reductase enzymes encoded by the nrfA and nirB operons. The expression of each operon is induced during anaerobic cell growth conditions and is further modulated by the presence of either nitrite or nitrate in the cells' environment. To examine how each operon is expressed at low, intermediate, and high levels of either nitrate or nitrite, anaerobic chemostat culture techniques were employed using nrfA-lacZ and nirB-lacZ reporter fusions. Steady-state gene expression studies revealed a differential pattern of nitrite reductase gene expression where optimal nrfA-lacZ expression occurred only at low to intermediate levels of nitrate and where nirB-lacZ expression was induced only by high nitrate conditions. Under these conditions, the presence of high levels of nitrate suppressed nrfA gene expression. While either NarL or NarP was able to induce nrfA-lacZ expression in response to low levels of nitrate, only NarL could repress at high nitrate levels. The different expression profile for the alternative nitrite reductase operon encoded by nirBDC under high-nitrate conditions was due to transcriptional activation by either NarL or NarP. Neither response regulator could repress nirB expression. Nitrite was also an inducer of nirB and nrfA gene expression, but nitrate was always the more potent inducer by >100-fold. Lastly, since nrfA operon expression is only induced under low-nitrate concentrations, the NrfA enzyme is predicted to have a physiological role only where nitrate (or nitrite) is limiting in the cell environment. In contrast, the nirB nitrite reductase is optimally synthesized only when nitrate or nitrite is in excess of the cell's capacity to consume it. Revised regulatory schemes are presented for NarL and NarP in control of the two operons.

Anaerobiosis↗
PubMed1999

Ion chromatography of nitrite at the ppb level with photometric measurement of iodine formed by post-column reaction of nitrite with iodide.

The difficulty in ion-chromatographic determination of nitrite in aqueous solutions containing a high concentration of chloride arises mainly from incomplete resolution of the peaks for these anions on the separation column whose efficiency is not high. A photometric measurement of iodine formed by a reaction of nitrite with iodide has been found to make it possible to determine, chromatographically, trace amounts of nitrite without any interference from chloride; chloride does not oxidize iodide to produce iodine. The proposed method was based on the separation of nitrite from matrix anions on a silica-based anion-exchange column with a 1.5.10(-3) M phthalate eluent (pH 5.0), followed by photometric measurement of the iodine (as triiodide) formed via a post-column reaction of the separated nitrite with iodide. The optimal conditions for the post-column reaction were established by varying the concentrations of iodide, copper(II) and nitric acid in a post-column-reaction solution and the length of a reaction tube. A calibration graph for nitrite, plotted as peak heights versus concentrations, was linear up to 1.50.10(-5) M (690 ppb). The detection limit, defined at S/N = 3, was 1.00.10(-7) M (4.60 ppb) nitrite. The presence of chloride ions up to 0.01 M did not give any interference to the determination of nitrite. This method was successfully applied to the determination of nitrite in lake water, river water, sewage works water and snow samples without any pretreatment.

Chromatography, Ion Exchange↗
PubMed1993

The purification of a cd1-type nitrite reductase from, and the absence of a copper-type nitrite reductase from, the aerobic denitrifier Thiosphaera pantotropha; the role of pseudoazurin as an electron donor.

Thiosphaera pantotropha has been reported to contain a copper-type nitrite reductase on the basis that the copper chelator diethyldithiocarbamate inhibited the overall process of denitrification. It is now shown that nitrous oxide reduction is 100% inhibited by 10 mM diethyldithiocarbamate or 100 microM azide. We also found that both these inhibitors partially inhibited nitrite reduction in this organism. We purified the nitrite reductase of T. pantotropha and found that it was of the cytochrome cd1 type, contrary to the published report of it being a copper-type nitrite reductase. This is of importance since T. pantotropha is capable of aerobic nitrite reduction. The only detectable nitrite reductase in anaerobically or aerobically grown cells is the cd1 type. We also purified a small copper-containing protein, pseudoazurin. Pseudoazurin was found to be capable of donating electrons to the cd1-type nitrite reductase in vitro, and its copper centre was chelated by diethyldithiocarbamate. Since nitrite reduction is partially inhibited by diethyldithiocarbamate, it is thought that pseudoazurin is an electron donor to nitrite reductase in vivo.

Aerobiosis↗
PubMed2004

Model-based evaluation on the conversion ratio of ammonium to nitrite in a nitritation process for ammonium-rich wastewater treatment.

Modeling for nitritation process was discussed and analyzed quantitatively for the factors that influence nitrite accumulation. The results indicated that pH, inorganic carbon source and Hydraulic Retention Time (HRT) as well as biomass concentration are the main factors that influenced the conversion ratio of ammonium to nitrite. A constant high pH can lead to a high nitritation rate and results in high conversion ratio on condition that free ammonia inhibition do not happen. In a CSTR system, without pH control, this conversion ratio can be monitored by pH variation in the reactor. The pH goes down far from the inlet level means a strongly nitrite accumulation. High concentration of alkalinity can promoted the conversion ratio by means of accelerating the nitritation rate through providing sufficient inorganic carbon source(carbon dioxide). When inorganic carbon source was depleted, the nitritation process stopped. HRT adjustment could be an efficient way to make the nitritation system run more flexible, which to some extent can meet the requirements of the fluctuant of inlet parameters such as ammonium concentration, pH, and temperature and so on. Biomass concentration is the key point, especially for a CSTR system in steady state, which was normally circumscribed by the characteristics of bacteria and may also affected by aeration mode and can be increased by prolonging the HRT on the condition of no nitrate accumulation when no recirculation available. The higher the biomass concentration is, the better the nitrite accumulation can be obtained.

Biomass↗
PubMed1983

15N tracer studies on the reduction of nitrite by the purified dissimilatory nitrite reductase of Pseudomonas aeruginosa. Evidence for direct production of N2O without free NO as an intermediate.

Nitrite reductase (cytochrome c,d1) was purified from Pseudomonas aeruginosa. In the presence of the reducing system, ascorbate-N,N,N',N'-tetramethylphenyl-enediamine, which alone had no ability to reduce nitrite or NO at pH 7.5, the enzyme catalyzed the reduction of nitrite to NO and N2O as major and minor products, respectively, as determined by gas chromatography-mass spectrometry. The rate of reduction of NO to N2O was considerably lower than the rate of reduction of nitrite to N2O and might be zero. The N2O produced in a system containing [15N]nitrite and natural NO was more highly enriched in 15N than was the NO pool and, in this regard, closely resembled the enrichment of the nitrite pool. The amount of 14N in the NO pool changed little, if any, as the result of enzymatic processes. For the enzyme, free NO seems not to be an intermediate between nitrite and N2O, just as was found by this laboratory for certain intact denitrifying bacteria. The results are consistent with reduction of nitrite to enzyme-bound NO, which can partition between release and further reduction.

Kinetics↗
PubMed2002

Acute exposure of Siberian sturgeon (Acipenser baeri, Brandt) yearlings to nitrite: median-lethal concentration (LC(50)) determination, haematological changes and nitrite accumulation in selected tissues.

Exposure of Siberian sturgeon (Acipenser baeri) yearlings (172.0+/-18 g; mean+/-S.D.) to several NO(2)(-)-N concentrations (0, 25, 130, 180 and 275 mg/l) was studied for 72 h in static tests. At 72 h, the median-lethal concentration of NO(2)(-)-N was 130 mg/l in water with high chloride content (130.5 mg/l). Nitrite exposure produced high levels of methaemoglobin (MetHb) but did not seem to cause mortality, as surviving fish showed higher levels (82.7+/-5.6%) than torpid specimens (60.8+/-4.5%). Levels of MetHb were unrelated to environmental and plasmatic nitrite concentrations, as both torpid and surviving fish exposed to the highest nitrite levels (275 mg/l of NO(2)(-)-N) presented similar concentrations of MetHb to those exposed to 25 mg/l of NO(2)(-)-N, thus indicating the ability of Siberian sturgeon yearlings to regulate plasmatic nitrite levels and maintain them lower than the environmental concentration of the toxicant. Nitrite exposure caused changes in the plasmatic electrolyte balance, which is characterised by extracellular hyperkalemia, high plasmatic chloride levels and low plasmatic sodium concentration. Differences between the nitrite concentration in the liver of torpid (46.3+/-9.0 mg/l) and surviving specimens (19.1+/-13.1 mg/l) exposed to several concentrations of NO(2)(-)-N suggest a significant contribution of the liver in nitrite detoxification pathways, and would thus explain a possible nitrite tolerance of Siberian sturgeon yearlings.

Animals↗
PubMed1999

Sources and sinks for ammonia and nitrite on the early Earth and the reaction of nitrite with ammonia.

An analysis of sources and sinks for ammonia and nitrite on the early Earth was conducted. Rates of formation and destruction, and steady state concentrations of both species were determined by steady state kinetics. The importance of the reaction of nitrite with ammonia on the feasibility of ammonia formation from nitrite was evaluated. The analysis considered conditions such as temperature, ferrous iron concentration, and pH. For sinks we considered the reduction of nitrite to ammonia, reaction between nitrite and ammonia, photochemical destruction of both species, and destruction at hydrothermal vents. Under most environmental conditions, the primary sink for nitrite is reduction to ammonia. The reaction between ammonia and nitrite is not an important sink for either nitrite or ammonia. Destruction at hydrothermal vents is important at acidic pH's and at low ferrous iron concentrations. Photochemical destruction, even in a worst case scenario, is unimportant under many conditions except possibly under acidic, low iron concentration, or low temperature conditions. The primary sink for ammonia is photochemical destruction in the atmosphere. Under acidic conditions, more of the ammonia is tied up as ammonium (reducing its vapor pressure and keeping it in solution) and hydrothermal destruction becomes more important.

Ammonia↗
PubMed2003

Nitrite-catalase interaction as an important element of nitrite toxicity.

It was established that nitrite in the presence of chloride, bromide, and thiocyanate decreases the rate of hydrogen peroxide decomposition by catalase. The decrease was recorded by the permanganatometric method and by a method of dynamic calorimetry. Nitrite was not destroyed in the course of the reaction and the total value of heat produced in the process was not changed by its presence. These facts suggest that nitrite induces inhibition of catalase with no change in the essence of the enzymatic process. Even micromolar nitrite concentrations induced a considerable decrease in catalase activity. However, in the absence of chloride, bromide, and thiocyanate inhibition was not observed. In contrast, fluoride protected catalase from nitrite inhibition in the presence of the above-mentioned halides and pseudohalide. As hydrogen peroxide is a necessary factor for triggering a number of important toxic effects of nitrite, the latter increases its toxicity by inhibiting catalase. This was shown by the example of nitrite-induced hemoglobin oxidation. The naturally existing gradient of chloride and other anion concentrations between intra- and extracellular media appears to be the most important mechanism of cell protection from inhibition of intracellular catalase by nitrite. Possible mechanisms of this inhibition are discussed.

Animals↗
PubMed2002

Increased urinary nitrite excretion in primary enuresis: effects of indomethacin treatment on urinary and serum osmolality and electrolytes, urinary volumes and nitrite excretion.

OBJECTIVE: To assess urinary nitrite excretion, a stable end product of nitric oxide (NO), in patients with enuresis and in normal controls, and to evaluate the effects of indomethacin (a potent prostaglandin synthesis inhibitor) on urinary nitrite excretion, other urinary variables and bladder capacity. PATIENTS AND METHODS: The study comprised 10 patients with primary enuresis and 10 normal comparable controls (age range 6-14 years). Nitrite was assayed in 'spot' morning urine samples in both the enuretics and normal controls. Enuretics were then given 50 mg indomethacin suppositories each night; urine volume, urinary osmolality and electrolytes, serum osmolality and electrolytes and urinary nitrite were assayed before indomethacin treatment and after 15 days of treatment. RESULTS: The mean (sd) urinary nitrite excretion was 24.4 (19.6) micromol/L in normal children and 275.9 (111.2) micromol/L in enuretics (P<0.05). With indomethacin, the urinary nitrite concentration was significantly decreased to 141 (45.1) micromol/L (P<0.05) and associated with a significant reduction in bed-wetting episodes and voiding frequency. The functional bladder capacity was <70% of the predicted value for age in six of the patients; they had significant improvements on indomethacin, to values similar to those in patients with a nearly normal functional bladder capacity. Indomethacin decreased the 24-h urinary volume by 41%, the night volume by 40%, clearance of free water by 46% and increased the day : night urinary volume ratio by 55%. The absolute amounts of urinary calcium, magnesium, phosphorus, urea, creatinine, and glucose were lower on indomethacin, although not statistically significantly so. Indomethacin decreased the 24-h urinary and 'spot' morning osmolality and osmotic clearance. There were no significant changes in serum osmolality and electrolyte concentrations. Indomethacin also decreased the absolute amount of urinary sodium, chloride and potassium, fractional sodium and potassium excretion, and filtered sodium. Creatinine clearance was decreased by 20% (P>0.05) and normal 24-h urinary protein was significantly lower, by 47%, after indomethacin treatment (P<0.05). CONCLUSION: Urinary nitrite excretion increased significantly in patients with primary nocturnal enuresis; indomethacin markedly reduced bed-wetting episodes and decreased the frequency of voiding in enuretics with small or normal functional bladder capacity, which was associated with a significant decrease in urinary nitrite excretion. Indomethacin reduced bed-wetting by decreasing the urine volume, clearance of free water and urinary electrolytes, and through possible effects on bladder and urethral contraction, by inhibiting NO and prostaglandin synthesis. NO and prostaglandins might be important in the pathogenesis of primary enuresis.

Adolescent↗
PubMed2002

Protein film voltammetry reveals distinctive fingerprints of nitrite and hydroxylamine reduction by a cytochrome C nitrite reductase.

The cytochrome c nitrite reductases perform a key step in the biological nitrogen cycle by catalyzing the six-electron reduction of nitrite to ammonium. Graphite electrodes painted with Escherichia coli cytochrome c nitrite reductase and placed in solutions containing nitrite (pH 7) exhibit large catalytic reduction currents during cyclic voltammetry at potentials below 0 V. These catalytic currents were not observed in the absence of cytochrome c nitrite reductase and were shown to originate from an enzyme film engaged in direct electron exchange with the electrode. The catalytic current-potential profiles observed on progression from substrate-limited to enzyme-limited nitrite reduction revealed a fingerprint of catalytic behavior distinct from that observed during hydroxylamine reduction, the latter being an alternative substrate for the enzyme that is reduced to ammonium in a two electron process. Cytochrome c nitrite reductase clearly interacts differently with these two substrates. However, similar features underlie the development of the voltammetric response with increasing nitrite or hydroxylamine concentration. These features are consistent with coordinated two-electron reduction of the active site and suggest that the mechanisms for reduction of both substrates are underpinned by common rate-defining processes.

Binding Sites↗
PubMedDate not supplied

[Protonation of nitrite is an obligatory stage in the generation of nitric oxide from nitrite in biological systems].

The yield of nitric oxide from 1 mM sodium nitrite differs 200 times when the process was initiated by 10 mM sodium dithionite in the solution of 5 or 150 mM HEPES-buffer (pH 7.4). Dithionite acted both as a strong reductant and an agent that induced a local acidification of solutions without notable change in pH value. The amount of nitric oxide was estimated by the EPR method by measuring the incorporation of nitric oxide to water-soluble complexes of Fe with N-methyl-D-glucamine dithiocarbamate (MGD), which led to the formation of EPR-detectable mononitrosyl iron complexes with MGD (MNIC-MGD). Ten seconds after dithionite addition, the concentration of MNIC - MGD complexes reached 2 microM in 5 mM HEPES-buffer in contrast to 0.01 microM in 150 mM HEPES-buffer. The difference was suggested to be due to a higher life-time of zones with decreased pH values in a weaker weak buffer solution. The life-time was high enough to ensure the protonation of a part of nitrite. The resulting nitrous acid was decomposed to form nitric oxide. The difference in the formation of nitric oxide from nitrite was also observed in weak and strong buffer solutions in the presence of hemoglobin (0.3 mM) or serum albumin (0.5 mM). However, the ratios of nitric oxide yields in weak and strong buffer did not exceed 3-4 times. The increase in the formation of nitric oxide from nitrite was characteristic for the solutions containing both proteins. Large amounts of nitric oxide formed from nitrite was observed in mouse liver preparation subjected to freezing-thawing procedure followed by incubation in 150 mM HEPES-buffer (pH 7.4) and addition of dithionite. The proposition was made that the presence of zones with low pH value in cells and tissues can ensure the predominant operation of the acid mechanism formation of nitric oxide from nitrite. The contribution of the formation of nitric oxide from nitrite catalyzing with heme-containing proteins nitrite reductases can be minor one under these conditions.

Animals↗
PubMed2006

A random-sequential mechanism for nitrite binding and active site reduction in copper-containing nitrite reductase.

The homotrimeric copper-containing nitrite reductase (NiR) contains one type-1 and one type-2 copper center per monomer. Electrons enter through the type-1 site and are shuttled to the type-2 site where nitrite is reduced to nitric oxide. To investigate the catalytic mechanism of NiR the effects of pH and nitrite on the turnover rate in the presence of three different electron donors at saturating concentrations were measured. The activity of NiR was also measured electrochemically by exploiting direct electron transfer to the enzyme immobilized on a graphite rotating disk electrode. In all cases, the steady-state kinetics fitted excellently to a random-sequential mechanism in which electron transfer from the type-1 to the type-2 site is rate-limiting. At low [NO(-)(2)] reduction of the type-2 site precedes nitrite binding, at high [NO(-)(2)] the reverse occurs. Below pH 6.5, the catalytic activity diminished at higher nitrite concentrations, in agreement with electron transfer being slower to the nitrite-bound type-2 site than to the water-bound type-2 site. Above pH 6.5, substrate activation is observed, in agreement with electron transfer to the nitrite-bound type-2 site being faster than electron transfer to the hydroxyl-bound type-2 site. To study the effect of slower electron transfer between the type-1 and type-2 site, NiR M150T was used. It has a type-1 site with a 125-mV higher midpoint potential and a 0.3-eV higher reorganization energy leading to an approximately 50-fold slower intramolecular electron transfer to the type-2 site. The results confirm that NiR employs a random-sequential mechanism.

Alcaligenes faecalis↗
PubMed2006

pH dependence of copper geometry, reduction potential, and nitrite affinity in nitrite reductase.

Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity.

Binding Sites↗
PubMed1982

Nitrite, nitrite alternatives, and the control of Clostridium botulinum in cured meats.

Historically, nitrite has been a component of meat-curing additives for several centuries. In recent years the safety of nitrite as an additive in cured meats has been questioned mainly because of the possible formation of carcinogenic nitrosamines. Nitrite has many important functions in meat curing including its role in color development, flavor, antioxidant properties, and antimicrobial activity. The inhibition of Clostridium botulinum growth and toxin production is an especially important antimicrobial property of nitrite. This review discusses the effects of processing, curing ingredients (especially nitrite), and storage of cured meats in relation to the control of C. botulinum. If nitrite is eliminated from cured meats or the level of usage decreased, then alternatives for the antibotulinal function of nitrite need to be considered. Several potential alternatives including sorbates, parabens, and biological acidulants are discussed.

Animals↗
PubMed1994

EPR and electron nuclear double resonance (ENDOR) studies show nitrite binding to the type 2 copper centers of the dissimilatory nitrite reductase of Alcaligenes xylosoxidans (NCIMB 11015).

EPR and 1H, 14,15N ENDOR spectra are described for the type 1 and type 2 Cu(II) centers of dissimilatory nitrite reductase (NiR) from Alcaligenes xylosoxidans. The study was carried out on preparations of NiR containing both type 1 and type 2 Cu sites, and also on preparations of lower activity which contained essentially only type 1 Cu centers. This has enabled ENDOR studies of type 1 and type 2 sites to be carried out largely independently of each other, by appropriate choice of the excitation field. Spectra were recorded both in the absence and presence of nitrite, allowing a clear determination of which of the two types of Cu center constitutes the substrate binding site. The EPR results show large changes in the type 2 site gparallel (which decreases by 0.065) and CuAparallel (which increases by 2.0 mT) while the type 1 site EPR is not affected. In addition, both 1H and 14N ENDOR of the type 2 Cu site undergo considerable changes on addition of nitrite whereas the type 1 Cu site ENDOR is unaffected. Our results clearly demonstrate that nitrite binds to the type 2 copper and that this process significantly perturbs the ligation of this copper by the protein histidine residues. No 15N ENDOR resonances were observed from 15N nitrite. The accessibility of the copper sites to solvent has been studied using 2H2O. The results indicate that nitrite binds to the type 2 Cu by displacing a proton, probably on a water molecule bound to the copper atom.

Alcaligenes↗
PubMed1976

Change in the ratio of cytochrome oxidase activity to nitrite reductase activity of Pseudomonas aeruginosa nitrite reductase with the kind of C-type cytochrome used as an electron donor.

The ratio between the nitrite reductase and cytochrome oxidase activities of Pseudomonas aeruginosa nitrite reductase [EC 1.9.3.2.] varies with kind of C-type cytochrome used as the electron donor. Withe cytochrome c-548, 554 (Micrococcus sp.), the nitrite reductase activity is greater than the cytochrome oxidase activity, while the former is smaller than the latter with cytochrome c-554 (Navicula pelliculosa). The aerobic oxidation catalyzed by this enzyme of denitrifying bacterial ferrocytochrome c is greatly accelerated on addition of nitrite, while that of the algal ferrocytochrome c is not affected or is even depressed by the salt. An accelerative effect of nitrite is generally observed with many kinds of C-type cytochromes which react with the enzyme very or fairly rapidly. The difference in the ratio of the two activities of the enzyme seems to arise according to whether or not nitrite affects the interaction of C-type cytochrome with the enzyme.

Cytochrome c Group↗