Qin Xin, Chen Xiaohua
Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, 55 University City South Road, Shapingba District, Chongqing, 401331, P. R. China.
National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, Chongqing University, Chongqing, 401331, P. R. China.
Chembiochem. 2021 Apr 16;22(8):1405-1414. doi: 10.1002/cbic.202000644. Epub 2021 Jan 28.
The copper-containing nitrite reductase (CuNiR) catalyzes the biological conversion of nitrite to nitric oxide; key long-range electron/proton transfers are involved in the catalysis. However, the details of the electron-/proton-transfer mechanism are still unknown. In particular, the driving force of the electron transfer from the type-1 copper (T1Cu) site to the type-2 copper (T2Cu) site is ambiguous. Here, we explored the two possible proton-transfer channels, the high-pH proton channel and the primary proton channel, by using two-layered ONIOM calculations. Our calculation results reveal that the driving force for electron transfer from T1Cu to T2Cu comes from a remote water-mediated triple-proton-coupled electron-transfer mechanism. In the high-pH proton channel, the water-mediated triple-proton transfer occurs from Glu113 to an intermediate water molecule, whereas in the primary channel, the transfer is from Lys128 to His260. Subsequently, the two channels employ another two or three distinct proton-transfer steps to deliver the proton to the nitrite substrate at the T2Cu site. These findings explain the detailed proton-/electron-transfer mechanisms of copper-containing nitrite reductase and could extend our understanding of the diverse proton-coupled electron-transfer mechanisms in complicated proteins.
含铜亚硝酸还原酶（CuNiR）催化亚硝酸盐向一氧化氮的生物转化；关键的远程电子/质子转移参与了该催化过程。然而，电子/质子转移机制的细节仍然未知。特别是，从1型铜（T1Cu）位点到2型铜（T2Cu）位点的电子转移驱动力尚不明确。在此，我们通过使用两层ONIOM计算探索了两种可能的质子转移通道，即高pH质子通道和初级质子通道。我们的计算结果表明，从T1Cu到T2Cu的电子转移驱动力来自远程水介导的三质子耦合电子转移机制。在高pH质子通道中，水介导的三质子转移从Glu113发生到一个中间水分子，而在初级通道中，转移是从Lys128到His260。随后，这两个通道采用另外两个或三个不同的质子转移步骤将质子传递到T2Cu位点的亚硝酸盐底物上。这些发现解释了含铜亚硝酸还原酶详细的质子/电子转移机制，并可能扩展我们对复杂蛋白质中各种质子耦合电子转移机制的理解。
