A QM/MM Study of Nitrite Binding Modes in a Three-Domain Heme-Cu Nitrite Reductase.
A QM/MM Study of Nitrite Binding Modes in a Three-Domain Heme-Cu Nitrite Reductase.
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DOI：
10.3390/molecules23112997
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发表时间：
2018-11-16
期刊：
影响因子：
--
通讯作者：
Keal TW
中科院分区：
文献类型：
--
作者：
Sen K;Hough MA;Strange RW;Yong CW;Keal TW
含铜亚硝酸盐还原酶（CuNiRs）通过将亚硝酸盐（NO2−）还原为一氧化氮，在全球氮循环中起着关键作用，这一反应涉及一个电子和两个质子。在典型的双域cunir中，电子是从外部给电子的伙伴获得的。最近表征的Rastonia picketti （RpNiR）系统是一个三结构域CuNiR，其中铜氧还蛋白结构域连接到可以作为电子供体的血红素c结构域。亚硝酸盐的还原始于NO2 -与T2Cu中心的结合，但对于NO2 -如何与天然RpNiR结合知之甚少。最近对RpNiR突变体的晶体学研究表明，NO2 -可能通过氮结合，而不是通过双齿氧模式（通常在双畴cunir中观察到）结合。在这项工作中，我们使用联合量子力学/分子力学（QM/MM）方法来模拟NO2−与天然RpNiR的结合模式，以确定n键取向还是o键取向是首选。结果表明，T2Cu中心的氧化态Cu（II）可以通过氮或氧结合，但在还原态Cu(I)中，氮结合模式在能量上是优先的。
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.
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影响因子：
5.6
作者：
Ellis, MJ;Dodd, FE;Hasnain, SS
通讯作者：
Hasnain, SS
影响因子：
3.9
作者：
Dong J;Sasaki D;Eady RR;Antonyuk SV;Hasnain SS
通讯作者：
Hasnain SS
系列晶体学以原子分辨率从一个晶体捕获亚硝酸铜还原酶的酶催化作用。
影响因子：
3.9
作者：
Horrell S;Antonyuk SV;Eady RR;Hasnain SS;Hough MA;Strange RW
通讯作者：
Strange RW
DOI：
10.1073/pnas.0504207102
发表时间：
2005-08-23
影响因子：
11.1
作者：
Antonyuk, SV;Strange, RW;Hasnain, SS
通讯作者：
Hasnain, SS
影响因子：
5.6
作者：
Ellis, MJ;Prudêncio, M;Hasnain, SS
通讯作者：
Hasnain, SS