Lintuluoto Masami, Lintuluoto Juha M
Graduate School of Life and Environmental Sciences, Kyoto Prefectural University , Shimogamohanki-cho, Sakyo, Kyoto 606-8522, Japan.
Graduate School of Engineering, Kyoto University, Katsura Campus , Nishikyo-ku, Kyoto 615-8530, Japan.
Biochemistry. 2016 Jan 12;55(1):210-23. doi: 10.1021/acs.biochem.5b00542. Epub 2015 Dec 29.
Dissimilatory reduction of nitrite by copper-containing nitrite reductase (CuNiR) is an important step in the geobiochemical nitrogen cycle. The proposed mechanisms for the reduction of nitrite by CuNiRs include intramolecular electron and proton transfers, and these two events are understood to couple. Proton-coupled electron transfer is one of the key processes in enzyme reactions. We investigated the geometric structure of bound nitrite and the mechanism of nitrite reduction on CuNiR using density functional theory calculations. Also, the proton transfer pathway, the key residues, and their roles in the reaction mechanism were clarified in this study. In our results, the reduction of T2 Cu site promotes the proton transfer, and the hydrogen bond network around the binding site has an important role not only to stabilize the nitrite binding but also to promote the proton transfer to nitrite.
含铜亚硝酸还原酶（CuNiR）催化的亚硝酸盐异化还原是地球生物化学氮循环中的重要一步。关于CuNiRs催化亚硝酸盐还原的机制，目前提出的包括分子内电子和质子转移，并且这两个过程被认为是相互耦合的。质子耦合电子转移是酶促反应中的关键过程之一。我们使用密度泛函理论计算研究了结合态亚硝酸盐的几何结构以及CuNiR上亚硝酸盐还原的机制。此外，本研究还阐明了质子转移途径、关键残基及其在反应机制中的作用。在我们的结果中，T2铜位点的还原促进了质子转移，结合位点周围的氢键网络不仅对稳定亚硝酸盐结合起着重要作用，而且对促进质子向亚硝酸盐的转移也起着重要作用。
