Nitric-oxide reductase

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nitric oxide reductase
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EC no. 1.7.2.5
CAS no. 37256-43-2
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Nitric oxide reductase, an enzyme, catalyzes the reduction of nitric oxide (NO) to nitrous oxide (N2O). [1] [2] [3] [4] The enzyme participates in nitrogen metabolism and in the microbial defense against nitric oxide toxicity. The catalyzed reaction may be dependent on different participating small molecules: Cytochrome c (EC: 1.7.2.5, Nitric oxide reductase (cytochrome c)), NADPH (EC:1.7.1.14), or Menaquinone (EC:1.7.5.2).

Contents

Nomenclature

Nitric oxide reductase was assigned Enzyme Commission number (EC) 1.7.2.5. Enzyme Commission numbers are the standard naming system used for enzymes. [5] The EC identifies the class, subclass, sub-subclass, and serial number of the enzyme. [5] Nitric oxide reductase is in Class 1, therefore it is an oxidoreductases. [5]

Figure 1. The Nitrogen Cycle. Nitric oxide (NO) and nitrous oxide (N2O) are intermediates in the denitrification of nitrate (NO3 ) to nitrogen gas (N2). Nitric oxide reductase reduces NO to N2O. The nitrogen cycle with the role of DNRA..png
Figure 1. The Nitrogen Cycle. Nitric oxide (NO) and nitrous oxide (N2O) are intermediates in the denitrification of nitrate (NO3 ) to nitrogen gas (N2). Nitric oxide reductase reduces NO to N2O.

Nitric oxide reductase belongs to the family of oxidoreductases, specifically those acting on other nitrogenous compounds as donors with other acceptors. The systematic name of this enzyme class is nitrous-oxide:acceptor oxidoreductase (NO-forming). Other names in common use include nitrogen oxide reductase, and nitrous-oxide:(acceptor) oxidoreductase (NO-forming).

Function

Organisms reduce nitrate (NO3−) to nitrogen gas (N2) through the process of denitrification, see Figure 1. [1] [2] Two important intermediates of the reduction pathway are nitric oxide (NO) and nitrous oxide (N2O). [1] [2] The reducing reaction that transforms NO into N2O is catalyzed by nitric oxide reductase (NOR). [1] [2] [3] [4]

NO is reduced to N2O also to prevent cellular toxicity. [4] [6] N2O, a potent greenhouse gas, is released. [1] [4]

Reaction

In enzymology, a nitric oxide reductase (NOR) catalyzes the chemical reaction:

2 NO + 2 e− + 2 H+ N2O + H2O [4]

The enzyme acts on 2 nitric oxide (substrate). [2] The enzyme converts NO, electrons and protons to products: nitrous oxide, and H2O. [2]

Inputs: 2 molecules of NO, 2 electrons, 2 protons [2]

Outputs: 1 molecule of N2O, 1 molecule of H2O [2]

Mechanism

NOR catalyzes the formation of nitrogen to nitrogen (N--N)  bonding. [1] [3] [6] The conformation changes of the active site and attached ligands (ie. Glu211) allows NO to be positioned in the crowded binuclear center and form N--N bonds. [4]

The precise mechanism of catalysis is still unknown, although hypotheses have been proposed. [3] [4]

Cordas et al. 2013 proposes three options: the trans-mechanism, the cis-FeB and the cis-heme b3 mechanisms. [3]

Based on the structure of the enzyme, Shiro 2012 proposes the following mechanism: (1) NO molecules bind at the binuclear center, (2) electrons are transferred from the ferrous irons to the NO, (3) charged NO molecules have the potential to form N to N bonds, and (4) N to O bonds are potentially broken by water, allowing for the N2O and H2O to be released. [4]

According to Hino et al. 2010, the changing charge of the active site causes NO to bind, form N2O and leave the enzyme. The NOR active site is positioned near two hydrogen bound glutamic acids (Glu). The Glu groups provide an electron-negative charge to the active site. [1] The electro-negative charge reduces the reaction potential for heme b3 and allows NO to bind to the binuclear activation site. [1] Glu residues also provide protons needed for removal of N2O and production of H2O. [1]

Structure

Subunits

NOR is made up of two subunits, NorC (small) and NorB (large), with a binuclear iron centre. [1] [3] [4] The binuclear iron center is the active site. [1] [2] [3] [4] It is composed of two b-type hemes and a non-heme iron (FeB). [1] [2] [3] [4] The ligands are connected through a μ-oxo bridge. [3] Histidine (His) residues are attached to the heme b3 in the small subunit. [1] The hydrophilic region of the larger subunit has His and methionine (Met) ligands. [1] Structure is similar to cytochrome oxidases. [1] [4]

The active site is conserved between cNOR and qNOR, although differences (ie. heme type) occur between cNOR and qNOR. [4]

Folding

Enzymatic folding produced 13 alpha-helices (12 from NorB, 1 from NorC) located within and through the membrane. [1] The folded metalloenzyme [7] transverses the membrane. [2] [3] [4]

Species distribution

Bacteria, archaea and fungi use NOR. [4] [6] qNOR is found in denitrifying bacteria and archaea, as well as pathogenic bacteria not involved in denitrification. [4] Denitrifying fungi reduce NO using P-450nor soluble enzyme. [6]

Types

Three types of NOR were identified from bacteria: cNOR, qNOR, and qCuNOR. [3] cNOR was found in denitrifying bacteria: Paracoccus denitrificans , Halomonas halodenitrificans, Pseudomonas nautica , Pseudomonas stutzeri , and Pseudomonas aeruginosa . [3] cNOR was first isolated from P. aeruginosa. [1] [4] qNOR was isolated from Geobacillus stearothermophilus . [4]

Related Research Articles

<span class="mw-page-title-main">Denitrification</span> Microbially facilitated process

Denitrification is a microbially facilitated process where nitrate (NO3−) is reduced and ultimately produces molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products. Facultative anaerobic bacteria perform denitrification as a type of respiration that reduces oxidized forms of nitrogen in response to the oxidation of an electron donor such as organic matter. The preferred nitrogen electron acceptors in order of most to least thermodynamically favorable include nitrate (NO3−), nitrite (NO2−), nitric oxide (NO), nitrous oxide (N2O) finally resulting in the production of dinitrogen (N2) completing the nitrogen cycle. Denitrifying microbes require a very low oxygen concentration of less than 10%, as well as organic C for energy. Since denitrification can remove NO3−, reducing its leaching to groundwater, it can be strategically used to treat sewage or animal residues of high nitrogen content. Denitrification can leak N2O, which is an ozone-depleting substance and a greenhouse gas that can have a considerable influence on global warming.

<span class="mw-page-title-main">Nitric oxide synthase</span> Enzyme catalysing the formation of the gasotransmitter NO(nitric oxide)

Nitric oxide synthases (NOSs) are a family of enzymes catalyzing the production of nitric oxide (NO) from L-arginine. NO is an important cellular signaling molecule. It helps modulate vascular tone, insulin secretion, airway tone, and peristalsis, and is involved in angiogenesis and neural development. It may function as a retrograde neurotransmitter. Nitric oxide is mediated in mammals by the calcium-calmodulin controlled isoenzymes eNOS and nNOS. The inducible isoform, iNOS, involved in immune response, binds calmodulin at physiologically relevant concentrations, and produces NO as an immune defense mechanism, as NO is a free radical with an unpaired electron. It is the proximate cause of septic shock and may function in autoimmune disease.

<i>Nitrosomonas</i> Genus of bacteria

Nitrosomonas is a genus of Gram-negative bacteria, belonging to the Betaproteobacteria. It is one of the five genera of ammonia-oxidizing bacteria and, as an obligate chemolithoautotroph, uses ammonia as an energy source and carbon dioxide as a carbon source in presence of oxygen. Nitrosomonas are important in the global biogeochemical nitrogen cycle, since they increase the bioavailability of nitrogen to plants and in the denitrification, which is important for the release of nitrous oxide, a powerful greenhouse gas. This microbe is photophobic, and usually generate a biofilm matrix, or form clumps with other microbes, to avoid light. Nitrosomonas can be divided into six lineages: the first one includes the species Nitrosomonas europea, Nitrosomonas eutropha, Nitrosomonas halophila, and Nitrosomonas mobilis. The second lineage presents the species Nitrosomonas communis, N. sp. I and N. sp. II, meanwhile the third lineage includes only Nitrosomonas nitrosa. The fourth lineage includes the species Nitrosomonas ureae and Nitrosomonas oligotropha and the fifth and sixth lineages include the species Nitrosomonas marina, N. sp. III, Nitrosomonas estuarii and Nitrosomonas cryotolerans.

Denitrifying bacteria are a diverse group of bacteria that encompass many different phyla. This group of bacteria, together with denitrifying fungi and archaea, is capable of performing denitrification as part of the nitrogen cycle. Denitrification is performed by a variety of denitrifying bacteria that are widely distributed in soils and sediments and that use oxidized nitrogen compounds in absence of oxygen as a terminal electron acceptor. They metabolise nitrogenous compounds using various enzymes, turning nitrogen oxides back to nitrogen gas or nitrous oxide.

Any enzyme system that includes cytochrome P450 protein or domain can be called a P450-containing system.

Nitrite reductase refers to any of several classes of enzymes that catalyze the reduction of nitrite. There are two classes of NIR's. A multi haem enzyme reduces NO2− to a variety of products. Copper containing enzymes carry out a single electron transfer to produce nitric oxide.

Trimethylamine N-oxide reductase is a microbial enzyme that can reduce trimethylamine N-oxide (TMAO) into trimethylamine (TMA), as part of the electron transport chain. The enzyme has been purified from E. coli and the photosynthetic bacteria Roseobacter denitrificans.

In enzymology, a 4-hydroxybenzoyl-CoA reductase (EC 1.3.7.9) is an enzyme found in some bacteria and archaea that catalyzes the chemical reaction

<span class="mw-page-title-main">Camphor 5-monooxygenase</span>

In enzymology, a camphor 5-monooxygenase (EC 1.14.15.1) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Nitric oxide dioxygenase</span>

Nitric oxide dioxygenase (EC 1.14.12.17) is an enzyme that catalyzes the conversion of nitric oxide (NO) to nitrate (NO−
3) . The net reaction for the reaction catalyzed by nitric oxide dioxygenase is shown below:

In enzymology, a ferredoxin—nitrate reductase (EC 1.7.7.2) is an enzyme that catalyzes the chemical reaction

Hydroxylamine oxidoreductase (HAO) is an enzyme found in the prokaryotic genus Nitrosomonas. It plays a critically important role in the biogeochemical nitrogen cycle as part of the metabolism of ammonia-oxidizing bacteria.

In enzymology, a hydroxylamine reductase (EC 1.7.99.1) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Nitrite reductase (NO-forming)</span> Class of enzymes

In enzymology, a nitrite reductase (NO-forming) (EC 1.7.2.1) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Nitrous-oxide reductase</span> Class of enzymes

In enzymology, a nitrous oxide reductase also known as nitrogen:acceptor oxidoreductase (N2O-forming) is an enzyme that catalyzes the final step in bacterial denitrification, the reduction of nitrous oxide to dinitrogen.

Aerobic denitrification or co-respiration the simultaneous use of both oxygen (O2) and nitrate (NO3−) as oxidizing agents, performed by various genera of microorganisms. This process differs from anaerobic denitrification not only in its insensitivity to the presence of oxygen, but also in that it has a higher potential to create the harmful byproduct nitrous oxide.

Nitric oxide reductase (NAD(P), nitrous oxide-forming) (EC 1.7.1.14, fungal nitric oxide reductase, cytochrome P450nor, NOR (ambiguous)) is an enzyme with systematic name nitrous oxide:NAD(P) oxidoreductase. This enzyme catalyses the following chemical reaction

Nitric oxide reductase (cytochrome c) (EC 1.7.2.5) is an enzyme with systematic name nitrous oxide:ferricytochrome-c oxidoreductase. This enzyme catalyses the following chemical reaction

Nitric oxide reductase (menaquinol) (EC 1.7.5.2) is an enzyme. This enzyme catalyses the following chemical reaction

<span class="mw-page-title-main">Cattle urine patches</span> Grass damage by cattle urine

Urine patches in cattle pastures generate large concentrations of the greenhouse gas nitrous oxide through nitrification and denitrification processes in urine-contaminated soils. Over the past few decades, the cattle population has increased more rapidly than the human population. Between the years 2000 and 2050, the cattle population is expected to increase from 1.5 billion to 2.6 billion. When large populations of cattle are packed into pastures, excessive amounts of urine soak into soils. This increases the rate at which nitrification and denitrification occur and produce nitrous oxide. Currently, nitrous oxide is one of the single most important ozone-depleting emissions and is expected to remain the largest throughout the 21st century.

References

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  2. 1 2 3 4 5 6 7 8 9 10 11 Collman JP, Yang Y, Dey A, Decréau RA, Ghosh S, Ohta T, Solomon EI (October 2008). "A functional nitric oxide reductase model". Proceedings of the National Academy of Sciences of the United States of America. 105 (41): 15660–5. Bibcode:2008PNAS..10515660C. doi: 10.1073/pnas.0808606105 . PMC   2572950 . PMID   18838684.
  3. 1 2 3 4 5 6 7 8 9 10 11 12 Cordas CM, Duarte AG, Moura JJ, Moura I (March 2013). "Electrochemical behaviour of bacterial nitric oxide reductase-evidence of low redox potential non-heme Fe(B) gives new perspectives on the catalytic mechanism". Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1827 (3): 233–8. doi: 10.1016/j.bbabio.2012.10.018 . PMID   23142527.
  4. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 Shiro Y (October 2012). "Structure and function of bacterial nitric oxide reductases: nitric oxide reductase, anaerobic enzymes". Biochimica et Biophysica Acta. 1817 (10): 1907–13. doi: 10.1016/j.bbabio.2012.03.001 . PMID   22425814.
  5. 1 2 3 Moss GP, Webb EC, et al. (International Union of Biochemistry and Molecular Biology. Nomenclature Committee.; IUPAC-IUBMB Joint Commission on Biochemical Nomenclature) (1992). Enzyme nomenclature . Academic Press. ISBN   0122271645. OCLC   715593348.
  6. 1 2 3 4 Hendriks J, Oubrie A, Castresana J, Urbani A, Gemeinhardt S, Saraste M (August 2000). "Nitric oxide reductases in bacteria". Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1459 (2–3): 266–73. doi: 10.1016/S0005-2728(00)00161-4 . PMID   11004439.
  7. ↑ Yeung N, Lin YW, Gao YG, Zhao X, Russell BS, Lei L, et al. (December 2009). "Rational design of a structural and functional nitric oxide reductase". Nature. 462 (7276): 1079–82. Bibcode:2009Natur.462.1079Y. doi:10.1038/nature08620. PMC   4297211 . PMID   19940850.

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