DFT Study on Nitrite Reduction Mechanism in Copper-Containing Nitrite Reductase

• Published in: Biochemistry (Easton) Vol. 55; no. 1; pp. 210 - 223
• Main Authors: Lintuluoto, Masami, Lintuluoto, Juha M
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 12.01.2016
• Subjects: Copper - metabolism; Crystallography, X-Ray; Electron Transport; Geobacillus - chemistry; Geobacillus - enzymology; Geobacillus - metabolism; Models, Molecular; Nitrite Reductases - chemistry; Nitrite Reductases - metabolism; Nitrites - metabolism; Oxidation-Reduction; Protein Conformation; Protons; Quantum Theory; Thermodynamics
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/acs.biochem.5b00542

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.