School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
Scientific Computing Department, STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK.
Molecules. 2018 Nov 16;23(11):2997. doi: 10.3390/molecules23112997.
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 (NiR) system is a three-domain CuNiR, where the cupredoxin domain is tethered to a heme 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 NiR. A recent crystallographic study of an NiR 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 NiR 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.
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（NO）在全球氮循环中起着关键作用，该反应涉及一个电子和两个质子。在典型的双结构域 CuNiRs 中，电子来自外部电子供体伙伴。最近被描述的 （NiR）系统是一个三结构域 CuNiR，其中铜蓝蛋白结构域与可以作为电子供体的血红素结构域连接。亚硝酸盐还原的起始是 NO₂与 T2Cu 中心的结合，但对于 NO₂如何与天然 NiR 结合，我们知之甚少。最近对 NiR 突变体的晶体学研究表明，NO₂可能通过氮而不是通常在双结构域 CuNiRs 中观察到的双齿氧模式结合。在这项工作中，我们使用了组合量子力学/分子力学（QM/MM）方法来模拟 NO₂与天然 NiR 的结合模式，以确定 N 结合或 O 结合的取向是否更优。我们的结果表明，对于 T2Cu 中心的氧化态 Cu(II)，通过氮或氧的结合是可能的，但在还原态 Cu(I)中，N 结合模式在能量上是优先的。
