Substrate Binding to a Nitrite Reductase Induces a Spin Transition

Martins, G.; Rodrigues, Luisa; Cunha, Filipa; Matos, Daniela; Hildebrandt, Peter; Murgida, Daniel H.; Pereira, Inês A. C.; Todorović, Smilja

doi:10.1021/jp9118502

Cited by 14 publications

(21 citation statements)

References 25 publications

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“…Previous studies showed that the Escherichia coli and Desulfovibrio vulgaris ccNiR ferriheme 1 active sites undergo high-spin to low-spin transitions upon binding nitrite. 43,44 This transition had a minimal effect on the UV/vis spectrum of the wild-type enzyme, but resulted in substantial changes to its EPR spectrum. 43 S. oneidensis ccNiR showed analogous behavior, so nitrite binding to it was monitored by EPR.…”

Section: ■ Resultsmentioning

confidence: 99%

Trapping of a Putative Intermediate in the Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite: Implications for the ccNiR Reaction Mechanism

et al. 2019

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Cytochrome c nitrite reductase (ccNiR) is a periplasmic, decaheme homodimeric enzyme that catalyzes the six-electron reduction of nitrite to ammonia. Under standard assay conditions catalysis proceeds without detected intermediates, and it has been assumed that this is also true in vivo. However, this report demonstrates that it is possible to trap a putative intermediate by controlling the electrochemical potential at which reduction takes place. UV/vis spectropotentiometry showed that nitrite-loaded Shewanella oneidensis ccNiR is reduced in a concerted two-electron step to generate an {FeNO} 7 moiety at the active site, with an associated midpoint potential of +246 mV vs SHE at pH 7. By contrast, cyanide-bound active site reduction is a one-electron process with a midpoint potential of +20 mV, and without a strong-field ligand the active site midpoint potential shifts 70 mV lower still. EPR analysis subsequently revealed that the {FeNO} 7 moiety possesses an unusual spectral signature, different from those normally observed for {FeNO} 7 hemes, that may indicate magnetic interaction of the active site with nearby hemes. Protein film voltammetry experiments previously showed that catalytic nitrite reduction to ammonia by S. oneidensis ccNiR requires an applied potential of at least −120 mV, well below the midpoint potential for {FeNO} 7 formation. Thus, it appears that an {FeNO} 7 active site is a catalytic intermediate in the ccNiR-mediated reduction of nitrite to ammonia, whose degree of accumulation depends exclusively on the applied potential. At low potentials the species is rapidly reduced and does not accumulate, while at higher potentials it is trapped, thus preventing catalytic ammonia formation.

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Section: ■ Resultsmentioning

confidence: 99%

Trapping of a Putative Intermediate in the Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite: Implications for the ccNiR Reaction Mechanism

et al. 2019

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“…vulgaris, [38][39][40][41][42] indicate that it is likely the NrfHA enzyme complex, rather than the sulfite reductase, that allows D. vulgaris to use nitrite as an electron acceptor. While the sulfite reductase can reduce nitrite, its high affinity for nitrite and a low turnover number for nitrite reduction 25 may inhibit its ability to use nitrite efficiently as a terminal electron acceptor.…”

Section: Discussionmentioning

confidence: 99%

Independence of Nitrate and Nitrite Inhibition of Desulfovibrio vulgaris Hildenborough and Use of Nitrite as a Substrate for Growth

Korte

Saini

Trotter

et al. 2015

Environ. Sci. Technol.

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Sulfate-reducing microbes, such as Desulfovibrio vulgaris Hildenborough, cause “souring” of petroleum reservoirs through produced sulfide and precipitate heavy metals, either as sulfides or by alteration of the metal reduction state. Thus, inhibitors of these microbes, including nitrate and nitrite ions, are studied in order to limit their impact. Nitrite is a potent inhibitor of sulfate reducers, and it has been suggested that nitrate does not inhibit these microbes directly but by reduction to nitrite, which serves as the ultimate inhibitor. Here we provide evidence that nitrate inhibition of D. vulgaris can be independent of nitrite production. We also show that D. vulgaris can use nitrite as a nitrogen source or terminal electron acceptor for growth. Moreover, we report that use of nitrite as a terminal electron acceptor requires nitrite reductase (nrfA) as a D. vulgaris nrfA mutant cannot respire nitrite but remains capable of utilizing nitrite as a nitrogen source. These results illuminate previously uncharacterized metabolic abilities of D. vulgaris that may allow niche expansion in low-sulfate environments. Understanding these abilities may lead to better control of sulfate-reducing bacteria in industrial settings and more accurate prediction of their interactions in the environment.

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“…According to the theoretical studies by Bykov and Neese, an intramolecular reaction with Tyr 218 in the final step of the nitrite reduction process led directly to the final product, NH 3 . Dissociation of the final product proceeds concomitantly with a change in heme Fe spin state [ 171 , 197 , 198 ].…”

Section: Reaction Mechanism Of Pentaheme Cytochrome C ...mentioning

confidence: 99%

Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen

Kroneck

2021

J Biol Inorg Chem

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Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2− is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2− to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features. Graphical abstract

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Substrate Binding to a Nitrite Reductase Induces a Spin Transition

Cited by 14 publications

References 25 publications

Trapping of a Putative Intermediate in the Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite: Implications for the ccNiR Reaction Mechanism

Trapping of a Putative Intermediate in the Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite: Implications for the ccNiR Reaction Mechanism

Independence of Nitrate and Nitrite Inhibition of Desulfovibrio vulgaris Hildenborough and Use of Nitrite as a Substrate for Growth

Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen

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