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Article

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

1
School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
2
Scientific Computing Department, STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK
*
Author to whom correspondence should be addressed.
Academic Editor: Hai Lin
Molecules 2018, 23(11), 2997; https://doi.org/10.3390/molecules23112997
Received: 29 October 2018 / Revised: 13 November 2018 / Accepted: 14 November 2018 / Published: 16 November 2018
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. View Full-Text
Keywords: nitrite reductases; three-domain CuNiRs; RpNiR; nitrite binding; QM/MM methods nitrite reductases; three-domain CuNiRs; RpNiR; nitrite binding; QM/MM methods
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MDPI and ACS Style

Sen, K.; Hough, M.A.; Strange, R.W.; Yong, C.W.; Keal, T.W. A QM/MM Study of Nitrite Binding Modes in a Three-Domain Heme-Cu Nitrite Reductase. Molecules 2018, 23, 2997. https://doi.org/10.3390/molecules23112997

AMA Style

Sen K, Hough MA, Strange RW, Yong CW, Keal TW. A QM/MM Study of Nitrite Binding Modes in a Three-Domain Heme-Cu Nitrite Reductase. Molecules. 2018; 23(11):2997. https://doi.org/10.3390/molecules23112997

Chicago/Turabian Style

Sen, Kakali, Michael A. Hough, Richard W. Strange, Chin W. Yong, and Thomas W. Keal. 2018. "A QM/MM Study of Nitrite Binding Modes in a Three-Domain Heme-Cu Nitrite Reductase" Molecules 23, no. 11: 2997. https://doi.org/10.3390/molecules23112997

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