- EMDB-30808: Cryo-EM structure of DgpB-C at 2.85 angstrom resolution -
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基本情報
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データベース: EMDB / ID: EMD-30808
タイトル
Cryo-EM structure of DgpB-C at 2.85 angstrom resolution
マップデータ
試料
複合体: DgpB-C
機能・相同性
Domain of unknown function DUF6379 / Domain of unknown function (DUF6379) / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / metal ion binding / DUF6379 domain-containing protein / Xylose isomerase-like TIM barrel domain-containing protein
Japan Agency for Medical Research and Development (AMED)
JP20am0101071
日本
引用
ジャーナル: Nat Commun / 年: 2021 タイトル: C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes. 著者: Takahiro Mori / Takuto Kumano / Haibing He / Satomi Watanabe / Miki Senda / Toshio Moriya / Naruhiko Adachi / Sanae Hori / Yuzu Terashita / Masato Kawasaki / Yoshiteru Hashimoto / Takayoshi ...著者: Takahiro Mori / Takuto Kumano / Haibing He / Satomi Watanabe / Miki Senda / Toshio Moriya / Naruhiko Adachi / Sanae Hori / Yuzu Terashita / Masato Kawasaki / Yoshiteru Hashimoto / Takayoshi Awakawa / Toshiya Senda / Ikuro Abe / Michihiko Kobayashi / 要旨: C-Glycosides, in which a sugar moiety is linked via a carbon-carbon (C-C) bond to a non-sugar moiety (aglycone), are found in our food and medicine. The C-C bond is cleaved by intestinal microbes and ...C-Glycosides, in which a sugar moiety is linked via a carbon-carbon (C-C) bond to a non-sugar moiety (aglycone), are found in our food and medicine. The C-C bond is cleaved by intestinal microbes and the resulting aglycones exert various bioactivities. Although the enzymes responsible for the reactions have been identified, their catalytic mechanisms and the generality of the reactions in nature remain to be explored. Here, we present the identification and structural basis for the activation of xenobiotic C-glycosides by heterocomplex C-deglycosylation enzymes from intestinal and soil bacteria. They are found to be metal-dependent enzymes exhibiting broad substrate specificity toward C-glycosides. X-ray crystallographic and cryo-electron microscopic analyses, as well as structure-based mutagenesis, reveal the structural details of these enzymes and the detailed catalytic mechanisms of their remarkable C-C bond cleavage reactions. Furthermore, bioinformatic and biochemical analyses suggest that the C-deglycosylation enzymes are widely distributed in the gut, soil, and marine bacteria.
EMPIAR-11124 (タイトル: Cryo-EM structure of DgpB-C at 2.85 angstrom resolution Data size: 1.9 TB Data #1: Cryo-EM structure of DgpB-C at 2.85 angstrom resolution [micrographs - multiframe])
モデルのタイプ: OTHER 詳細: An ab initio model was generated using RELION3's own implementation of Stochastic Gradient Descent (SGD) algorithm and low-pass filtered to 25.03 A for use as an initial model for 3D classification.