Structural, Mechanistic, and Functional Insights into an <i>Arthrobacter nicotinovorans</i> Molybdenum Hydroxylase Involved in Nicotine Degradation

• Main Authors: Lei Wang, Xia Mu, Wenjin Li, Qin Xu, Ping Xu, Liyun Zhang, Yuebin Zhang, Geng Wu
• Format: Article
• Language: English
• Published: MDPI AG 2021-07-01
• Series: Molecules
• Subjects: nicotine degradation; ketone dehydrogenase; Kdh; molybdenum hydroxylase; crystal structure; reaction mechanism
• Online Access: https://www.mdpi.com/1420-3049/26/14/4387

<i>Arthrobacter nicotinovorans</i> decomposes nicotine through the pyridine pathway. 6-hydroxypseudooxynicotine 2-oxidoreductase (also named ketone dehydrogenase, Kdh) is an important enzyme in nicotine degradation pathway of <i>A. nicotinovorans</i>, and is responsible for the second hydroxylation of nicotine. Kdh belongs to the molybdenum hydroxylase family, and catalyzes the oxidation of 6-hydroxy-pseudooxynicotine (6-HPON) to 2,6-dihydroxy-pseudooxynicotine (2,6-DHPON). We determined the crystal structure of the Kdh holoenzyme from <i>A. nicotinovorans</i>, with its three subunits KdhL, KdhM, and KdhS, and their associated cofactors molybdopterin cytosine dinucleotide (MCD), two iron-sulfur clusters (Fe₂S₂), and flavin adenine dinucleotide (FAD), respectively. In addition, we obtained a structural model of the substrate 6-HPON-bound Kdh through molecular docking, and performed molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations to unveil the catalytic mechanism of Kdh. The residues Glu345, Try551, and Glu748 of KdhL were found to participate in substrate binding, and Phe269 and Arg383 of KdhL were found to contribute to stabilize the MCD conformation. Furthermore, site-directed mutagenesis and enzymatic activity assays were performed to support our structural and computational results, which also revealed a trend of increasing catalytic efficiency with the increase in the buffer pH. Lastly, our electrochemical results demonstrated electron transfer among the various cofactors of Kdh. Therefore, our work provides a comprehensive structural, mechanistic, and functional study on the molybdenum hydroxylase Kdh in the nicotine degradation pathway of <i>A. nicotinovorans.</i>