EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.
ジャーナル・号・ページ	J Mol Biol, Vol. 431, Issue 19, Page 3647-3661, Year 2019
掲載日	2019年9月6日
著者	Jun Hoe Kim / Bong Heon Kim / Shelby Brooks / Seung Yeon Kang / Ryan M Summers / Hyun Kyu Song /
PubMed 要旨	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 ...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.
リンク	J Mol Biol / PubMed:31412262
手法	SAS (X-ray synchrotron) / X線回折
解像度	1.65 - 2.961 Å
構造データ	SASDFD7: Pseudomonas putida CBB5 NdmAB complex - static (Methylxanthine N1-demethylase NdmA + Methylxanthine N3-demethylase NdmB) 手法: SAXS/SANS SASDFE7: Pseudomonas putida CBB5 mCherry-NdmA/NdmB complex - static 手法: SAXS/SANS SASDFF7: Pseudomonas putida CBB5 NdmA hexamer (Methylxanthine N1-demethylase NdmA) 手法: SAXS/SANS SASDFG7: Pseudomonas putida CBB5 NdmB hexamer (Methylxanthine N3-demethylase NdmB) 手法: SAXS/SANS SASDFH7: Pseudomonas putida CBB5 NdmAB complex (Methylxanthine N1-demethylase NdmA + Methylxanthine N3-demethylase NdmB) 手法: SAXS/SANS SASDFJ7: Pseudomonas putida CBB5 mCherry-NdmA/ECFP-NdmB complex - static 手法: SAXS/SANS PDB-6ick: Pseudomonas putida CBB5 NdmA 手法: X-RAY DIFFRACTION / 解像度: 1.952 Å PDB-6icl: Pseudomonas putida CBB5 NdmB 手法: X-RAY DIFFRACTION / 解像度: 2.1 Å PDB-6icm: Pseudomonas putida CBB5 NdmA with ferredoxin domain of NdmD 手法: X-RAY DIFFRACTION / 解像度: 2.961 Å PDB-6icn: Pseudomonas putida CBB5 NdmA with caffeine 手法: X-RAY DIFFRACTION / 解像度: 1.65 Å PDB-6ico: Pseudomonas putida CBB5 NdmA with theophylline 手法: X-RAY DIFFRACTION / 解像度: 1.85 Å PDB-6icp: Pseudomonas putida CBB5 NdmA QL mutant with caffeine 手法: X-RAY DIFFRACTION / 解像度: 2.2 Å PDB-6icq: Pseudomonas putida CBB5 NdmA QL mutant with theobromine 手法: X-RAY DIFFRACTION / 解像度: 1.9 Å
化合物	ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER ChemComp-FE: Unknown entry ChemComp-HOH: WATER ChemComp-PG4: TETRAETHYLENE GLYCOL / テトラエチレングリコ-ル / 沈殿剤YM ChemComp-CO: Unknown entry ChemComp-CFF: CAFFEINE / カフェイン / 薬剤YM ChemComp-TEP: THEOPHYLLINE / テオフィリン ChemComp-37T: THEOBROMINE / テオブロミン / alkaloid*YM
由来	pseudomonas putida (バクテリア)
キーワード	METAL BINDING PROTEIN / N-demethylase / Rieske oxygenase / non-heme iron center / caffeine degradation / METAL BINDING PROTEIN/OXIDOREDUCTASE / reductase plant type ferredoxin / METAL BINDING PROTEIN-OXIDOREDUCTASE complex