6ICM

Pseudomonas putida CBB5 NdmA with ferredoxin domain of NdmD

Summary for 6ICM

• Entry DOI: 10.2210/pdb6icm/pdb
• Descriptor: Methylxanthine N1-demethylase NdmA, Oxidoreductase NdmD, FE2/S2 (INORGANIC) CLUSTER, ... (6 entities in total)
• Functional Keywords: n-demethylase, rieske oxygenase, reductase plant type ferredoxin, metal binding protein-oxidoreductase complex, metal binding protein/oxidoreductase
• Biological source: Pseudomonas putida (Arthrobacter siderocapsulatus); More
• Total number of polymer chains: 4
• Total formula weight: 137862.34

Authors

Kim, J.H.,Kim, B.H.,Kang, S.Y.,Song, H.K. (deposition date: 2018-09-06, release date: 2019-09-04, Last modification date: 2024-03-27)

Primary citation

Kim, J.H.,Kim, B.H.,Brooks, S.,Kang, S.Y.,Summers, R.M.,Song, H.K.
Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.
J.Mol.Biol., 431:3647-3661, 2019

PubMed 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- and N-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.

PubMed: 31412262
DOI: 10.1016/j.jmb.2019.08.004

Experimental method

X-RAY DIFFRACTION (2.961 Å)