scholarly journals A QM/MM Study of Nitrite Binding Modes in a Three-Domain Heme-Cu Nitrite Reductase

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2997
Author(s):  
Kakali Sen ◽  
Michael Hough ◽  
Richard Strange ◽  
Chin Yong ◽  
Thomas Keal
Keyword(s):  
Nitric Oxide ◽  
Nitrite Reductase ◽  
Binding Mode ◽  
Nitrite Reduction ◽  
Quantum Mechanical ◽  
Binding Modes ◽  
Crystallographic Study ◽  
Nitrite Reductases ◽  
Global Nitrogen Cycle ◽  
Oxygen Mode

Copper-containing nitrite reductases (CuNiRs) play a key role in the global nitrogen cycle by reducing nitrite (NO2−) to nitric oxide, a reaction that involves one electron and two protons. In typical two-domain CuNiRs, the electron is acquired from an external electron-donating partner. The recently characterised Rastonia picketti (RpNiR) system is a three-domain CuNiR, where the cupredoxin domain is tethered to a heme c domain that can function as the electron donor. The nitrite reduction starts with the binding of NO2− to the T2Cu centre, but very little is known about how NO2− binds to native RpNiR. A recent crystallographic study of an RpNiR mutant suggests that NO2− may bind via nitrogen rather than through the bidentate oxygen mode typically observed in two-domain CuNiRs. In this work we have used combined quantum mechanical/molecular mechanical (QM/MM) methods to model the binding mode of NO2− with native RpNiR in order to determine whether the N-bound or O-bound orientation is preferred. Our results indicate that binding via nitrogen or oxygen is possible for the oxidised Cu(II) state of the T2Cu centre, but in the reduced Cu(I) state the N-binding mode is energetically preferred.

New insights into the activity of Pseudomonas aeruginosa cd1 nitrite reductase

2008 ◽  
Vol 36 (6) ◽  
pp. 1155-1159 ◽  
Author(s):  
Serena Rinaldo ◽  
Alessandro Arcovito ◽  
Giorgio Giardina ◽  
Nicoletta Castiglione ◽  
Maurizio Brunori ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Pseudomonas Aeruginosa ◽  
Nitrite Reductase ◽  
Nitrite Reduction ◽  
Nitrite Reductases ◽  
Cytochrome Cd1 ◽  
Haem Iron ◽  
Shed Light ◽  
Denitrification Process

The cytochrome cd1 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 d1-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 d1-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 d1-haem iron. These results shed light on the mechanistic details of the activity of cd1 nitrite reductases and on the biological role of the d1-haem, whose presence in this class of enzymes has to date been unexplained.

scholarly journals Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in Phylum Chloroflexi

2021 ◽  
Author(s):  
Sarah Schwartz ◽  
Lily Momper ◽  
L. Thiberio Rangel ◽  
Cara Magnabosco ◽  
Jan Amend ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Nitrite Reductase ◽  
Phylogenetic Analyses ◽  
Domain Architecture ◽  
Terrestrial Ecosystems ◽  
Genomic Diversity ◽  
Nitric Oxide Reductase ◽  
Fusion Event ◽  
Ecological Carrying Capacity ◽  
Global Nitrogen Cycle

Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from marine and terrestrial ecosystems. The flux of nitrogen species through this pathway has a widespread impact, affecting ecological carrying capacity, agriculture, and climate. Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two central enzymes in this pathway. Here we present a previously unreported Nir domain architecture in members of Phylum Chloroflexi. Phylogenetic analyses of protein domains within Nir indicate that an ancestral horizontal transfer and fusion event produced this chimeric domain architecture. We also identify an expanded genomic diversity of a rarely reported nitric oxide reductase subtype, eNOR. Together, these results suggest a greater diversity of denitrification enzyme arrangements exist than have been previously reported.

scholarly journals Identification, Functional Studies, and Genomic Comparisons of New Members of the NnrR Regulon in Rhodobacter sphaeroides

2009 ◽  
Vol 192 (4) ◽  
pp. 903-911 ◽  
Author(s):  
Angela Hartsock ◽  
James P. Shapleigh
Keyword(s):  
Nitric Oxide ◽  
Rhodobacter Sphaeroides ◽  
Nitrite Reductase ◽  
Reductase Activity ◽  
Nitrite Reduction ◽  
No Production ◽  
Nitric Oxide Reductase ◽  
New Members ◽  
Functional Studies ◽  
The Status

ABSTRACT Analysis of the Rhodobacter sphaeroides 2.4.3 genome revealed four previously unidentified sequences similar to the binding site of the transcriptional regulator NnrR. Expression studies demonstrated that three of these sequences are within the promoters of genes, designated paz, norEF, and cdgA, in the NnrR regulon, while the status of the fourth sequence, within the tat operon promoter, remains uncertain. nnrV, under control of a previously identified NnrR site, was also identified. paz encodes a pseudoazurin that is a donor of electrons to nitrite reductase. paz inactivation did not decrease nitrite reductase activity, but loss of pseudoazurin and cytochrome c2 together reduced nitrite reduction. Inactivation of norEF reduced nitrite and nitric oxide reductase activity and increased the sensitivity to nitrite in a taxis assay. This suggests that loss of norEF increases NO production as a result of decreased nitric oxide reductase activity. 2.4.3 is the only strain of R. sphaeroides with norEF, even though all four of the strains whose genomes have been sequenced have the norCBQD operon and nnrR. norEF was shown to provide resistance to nitrite when it was mobilized into R. sphaeroides strain 2.4.1 containing nirK. Inactivation of the other identified genes did not reveal any detectable denitrification-related phenotype. The distribution of members of the NnrR regulon in R. sphaeroides revealed patterns of coselection of structural genes with the ancillary genes identified here. The strong coselection of these genes indicates their functional importance under real-world conditions, even though inactivation of the majority of them does not impact denitrification under laboratory conditions.

The catalytic mechanism of Pseudomonas aeruginosa cd1 nitrite reductase

2011 ◽  
Vol 39 (1) ◽  
pp. 195-200 ◽  
Author(s):  
Serena Rinaldo ◽  
Giorgio Giardina ◽  
Nicoletta Castiglione ◽  
Valentina Stelitano ◽  
Francesca Cutruzzolà
Keyword(s):  
Nitric Oxide ◽  
Pseudomonas Aeruginosa ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Product Inhibition ◽  
Electron Donors ◽  
Nitrite Reduction ◽  
Nitrite Reductases ◽  
Shed Light ◽  
Denitrification Process

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.

scholarly journals Electron Paramagnetic Resonance Investigation of Nitrite Binding in Myoglobin

2018 ◽  
Author(s):  
Matthew Bawn ◽  
Fraser MacMillan
Keyword(s):  
Electron Paramagnetic Resonance ◽  
High Spin ◽  
Nitrite Reductase ◽  
Binding Mode ◽  
Nitrite Reduction ◽  
Paramagnetic Resonance ◽  
High Ph ◽  
Hypoxic Conditions ◽  
Electron Paramagnetic ◽  
Iron Center

ABSTRACTIt has been proposed that myoglobin (Mb) may act as a nitrite reductase under hypoxic conditions. Any mechanism describing such activity should take into account the binding geometry of the ligand to the heme. Crystal structures of horse-heart Mb and human hemoglobin-nitrite complexes suggest that the anion adopts an uncommon O-nitrito binding mode. Electron Paramagnetic Resonance (EPR) spectroscopy was employed to investigate the nature of nitrite binding to Mb at pH values ranging from 6.5 to 10.8. Results suggest that for ferric Mb at low pH, nitrite binds in the O-bound nitrito mode resulting in a low-spin (LS) iron center. Further a high-spin (HS) iron center is observed at high pH in Mb-Nitrite with spectral values different to that of purely HS-Mb that is proposed to be due to an N-bound nitrite. The yields of these two species were found to be influenced by pH.BackgroundMyoglobin has been theorized to have a role as a nitrite reductase.ResultsO-bound nitrite produces a low-spin ferric heme complex, whilst at high pH a high-spin species is found proposed to be the N-bound form.ConclusionNitrite may bind to heme in myoglobin via N-nitro or O-nitrito mode.SignificanceThe mechanism of any nitrite reduction will depend on its binding to the heme cofactor.

scholarly journals Lewis Acid-Assisted Reduction of Nitrite to Nitric and Nitrous Oxide via the Elusive Nitrite Radical Dianion

2022 ◽  
Author(s):  
Valiallah Hosseininasab ◽  
Ida M. DiMucci ◽  
Pokhraj Ghosh ◽  
Jeffery A. Bertke ◽  
Siddarth Chandrasekharan ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Nitrous Oxide ◽  
Lewis Acid ◽  
Nitrogen Cycle ◽  
Reduction Potential ◽  
Nitrite Reduction ◽  
Redox Active ◽  
Active Transition ◽  
Aqueous Conditions ◽  
Global Nitrogen Cycle

Reduction of nitrite anions [NO2]- takes place in a myriad of environments such as in the soil as part of the biogeochemical nitrogen cycle as well as in acidified nuclear waste. Nitrite reduction typically takes place within the coordination sphere of a redox active transition metal. Lewis acid coordination, however, can dramatically modify the reduction potential of this polyoxoanion to allow for reduction under non-aqueous conditions (-0.74 V vs. NHE). This strategy enables the isolation of a borane-capped nitrite dianion [NO2]2- along with its spectroscopic study consistent with reduction to the N(II) oxidation state. Protonation of the nitrite dianion results in facile loss of nitric oxide (NO) while reaction of the nitrite dianion with nitric oxide results in disproportionation to nitrous oxide (N2O) and nitrite, connecting three redox levels in the global nitrogen cycle.

scholarly journals Purification and characterization of assimilatory nitrite reductase from Candida utilis

1996 ◽  
Vol 317 (1) ◽  
pp. 147-155 ◽  
Author(s):  
Sagar SENGUPTA ◽  
Melkote S. SHAILA ◽  
Gannamani R. RAO
Keyword(s):  
Nitrite Reductase ◽  
Candida Utilis ◽  
Gel Filtration ◽  
Nitrate Assimilation ◽  
Nitrite Reduction ◽  
In Vitro Translation ◽  
Nitrite Reductases ◽  
Stepwise Reduction ◽  
Molecular Masses

Nitrate assimilation in many plants, algae, yeasts and bacteria is mediated by two enzymes, nitrate reductase (EC 1.6.6.2) and nitrite reductase (EC 1.7.7.1). They catalyse the stepwise reduction of nitrate to nitrite and nitrite to ammonia respectively. The nitrite reductase from an industrially important yeast, Candida utilis, has been purified to homogeneity. Purified nitrite reductase is a heterodimer and the molecular masses of the two subunits are 58 and 66 kDa. The native enzyme exhibits a molecular mass of 126 kDa as analysed by gel filtration. The identity of the two subunits of nitrite reductase was confirmed by immunoblotting using antibody for Cucurbita pepo leaf nitrite reductase. The presence of two different sized transcripts coding for the two subunits was confirmed by (a) in vitro translation of mRNA from nitrate-induced C. utilis followed by immunoprecipitation of the in vitro translated products with heterologous nitrite reductase antibody and (b) Northern-blot analysis. The 66 kDa subunit is acidic in nature which is probably due to its phosphorylated status. The enzyme is stable over a range of temperatures. Both subunits can catalyse nitrite reduction, and the reconstituted enzyme, at a higher protein concentration, shows an activity similar to that of the purified enzyme. Each of these subunits has been shown to contain a few unique peptides in addition to a large number of common peptides. Reduced Methyl Viologen has been found to be as effective an electron donor as NADPH in the catalytic process, a phenomenon not commonly seen for nitrite reductases from other systems.

Nitrite reductase activity of heme and copper bound Aβ peptides

2019 ◽  
Vol 48 (21) ◽  
pp. 7451-7461
Author(s):  
Arnab Kumar Nath ◽  
Chandradeep Ghosh ◽  
Madhuparna Roy ◽  
Manas Seal ◽  
Somdatta Ghosh Dey
Keyword(s):  
Nitric Oxide ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Nitrite Reductase ◽  
Reductase Activity ◽  
Aβ Peptides ◽  
Nitrite Reductases ◽  
Nitrite Reductase Activity

The heme(III)-Cu(i)-Aβ complexes relevant to Alzheimer’s disease (AD) can reduce nitrite to nitric oxide (NO) and thus behave as nitrite reductases.

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