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Bacterial nitric oxide reductase: a mechanism revisited by an ONIOM (DFT:MM) study

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Abstract

Bacterial nitric oxide reductase (cNOR) is an important binuclear iron enzyme responsible for the reduction of nitric oxide to nitrous oxide in the catalytic cycle of bacterial respiration. The reaction mechanism of cNOR as well as the key reactive intermediates of the reaction are still under debate. Here, we report a computational study based on ONIOM (DFT:MM) calculations aimed at investigating the reaction mechanism of cNOR. The results suggest that the reaction proceeds via the mono-nitrosyl mechanism which starts off by the binding of an NO molecule to the heme b3 center, N-N hyponitrite bond formation as a result of the reaction with a second NO molecule was found to proceed with an exothermic energy barrier to yield a hyponitrite adduct forming an open (incomplete) ring conformation with the non-heme FeB center (O-N-N-O-FeB). N-O bond cleavage to yield N2O was shown to be the rate-limiting step with an activation barrier of 22.6 kcal mol-1. The dinitrosyl (trans) mechanism, previously proposed by several studies, was also examined and found unfavorable due to high activation barriers of the resulting intermediates.

Bacterial nitric oxide reductaseᅟ

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Acknowledgments

Funding from the Romanian Ministry of Education and Research (Grant PN-II-ID-PCE-2012-4-0488) is gratefully acknowledged.

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Authors and Affiliations

  1. Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Cluj-Napoca, Romania

    Amr A. A. Attia & Radu Silaghi-Dumitrescu

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  1. Amr A. A. Attia
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  2. Radu Silaghi-Dumitrescu
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Correspondence to Radu Silaghi-Dumitrescu.

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Attia, A.A.A., Silaghi-Dumitrescu, R. Bacterial nitric oxide reductase: a mechanism revisited by an ONIOM (DFT:MM) study. J Mol Model 21, 130 (2015). https://doi.org/10.1007/s00894-015-2679-0

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