[논문]Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex

Kim, Jun Hoe; Kim, Bong Heon; Brooks, Shelby; Kang, Seung Yeon; Summers, Ryan M.; Song, Hyun Kyu

doi:10.1016/j.jmb.2019.08.004

[해외논문] Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex 원문보기

Journal of molecular biology, v.431 no.19, 2019년, pp.3647 - 3661

Kim, Jun Hoe (Department of Life Sciences, Korea University) , Kim, Bong Heon (Department of Life Sciences, Korea University) , Brooks, Shelby (Department of Chemical and Biological Engineering, The University of Alabama) , Kang, Seung Yeon (Department of Life Sciences, Korea University) , Summers, Ryan M. (Department of Chemical and Biological Engineering, The University of Alabama) , Song, Hyun Kyu (Department of Life Sciences, Korea University)

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Abstract Caffeine, found in many foods, beverages, and pharmaceuticals, is the most used chemical compound for mental alertness. It is originally a natural product of plants and exists widely in environmental soil. Some bacteria, such as Pseudomonas putida CBB5, utilize caffeine as a sole carbon and nitrogen source by degrading it through sequential N-demethylation catalyzed by five enzymes (NdmA, NdmB, NdmC, NdmD, and NdmE). The environmentally friendly enzymatic reaction products, methylxanthines, are high-value biochemicals that are used in the pharmaceutical and cosmetic industries. However, the structures and biochemical properties of bacterial N-demethylases remain largely unknown. Here, we report the structures of NdmA and NdmB, the initial N 1- and N 3-specific demethylases, respectively. Reverse-oriented substrate bindings were observed in the substrate-complexed structures, offering methyl position specificity for proper N-demethylation. For efficient sequential degradation of caffeine, these enzymes form a unique heterocomplex with 3:3 stoichiometry, which was confirmed by enzymatic assays, fluorescent labeling, and small-angle x-ray scattering. The binary structure of NdmA with the ferredoxin domain of NdmD, which is the first structural information for the plant-type ferredoxin domain in a complex state, was also determined to better understand electron transport during N-demethylation. These findings broaden our understanding of the caffeine degradation mechanism by bacterial enzymes and will enable their use for industrial applications. Highlights Crystal structures of bacterial N-demethylase A and B were determined in apo and substrate-bound states. NdmAB forms a unique heterocomplex with 3:3 stoichiometry. Structure of the binary complex between NdmA and a ferredoxin domain of NdmD was determined. The structural and biochemical results provide a framework for engineering of caffeine degradation enzymes and thus increase the reaction products, methylxanthines, which are high-value biochemicals. Graphical abstract [DISPLAY OMISSION]

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[해외논문] Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex 원문보기

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[해외논문] Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex 원문보기

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