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

Sen, Kakali and Hough, Michael and Strange, Richard and Yong, Chin and Keal, Thomas (2018) 'A QM/MM Study of Nitrite Binding Modes in a Three-Domain Heme-Cu Nitrite Reductase.' Molecules, 23 (11). ISSN 1420-3049

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Abstract

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 (RρNiR) 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 RρNiR 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.</jats:p>

Item Type: Article
Uncontrolled Keywords: nitrite reductases; three-domain CuNiRs; RpNiR; nitrite binding; QM/MM methods
Subjects: Q Science > QR Microbiology
Divisions: Faculty of Science and Health > Life Sciences, School of
Depositing User: Elements
Date Deposited: 28 Nov 2018 11:36
Last Modified: 28 Aug 2019 15:15
URI: http://repository.essex.ac.uk/id/eprint/23538

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