+Open data
-Basic information
Entry | Database: PDB / ID: 7drd | ||||||
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Title | Cryo-EM structure of DgpB-C at 2.85 angstrom resolution | ||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / C-deglycosylase / sugar-isomerase-like | ||||||
Function / homology | 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 Function and homology information | ||||||
Biological species | human intestinal bacterium PUE (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å | ||||||
Authors | Mori, T. / Moriya, T. / Adachi, N. / Senda, T. / Abe, I. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes. Authors: Takahiro Mori / Takuto Kumano / Haibing He / Satomi Watanabe / Miki Senda / Toshio Moriya / Naruhiko Adachi / Sanae Hori / Yuzu Terashita / Masato Kawasaki / Yoshiteru Hashimoto / Takayoshi ...Authors: 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 / Abstract: 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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7drd.cif.gz | 281.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7drd.ent.gz | 228.7 KB | Display | PDB format |
PDBx/mmJSON format | 7drd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7drd_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7drd_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7drd_validation.xml.gz | 61.1 KB | Display | |
Data in CIF | 7drd_validation.cif.gz | 92.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/7drd ftp://data.pdbj.org/pub/pdb/validation_reports/dr/7drd | HTTPS FTP |
-Related structure data
Related structure data | 30808MC 7bvrC 7bvsC 7dreC 7exbC 7exzC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-11124 (Title: 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]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 38457.039 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) human intestinal bacterium PUE (bacteria) Gene: dgpC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q9WXL1 #2: Protein | Mass: 16062.067 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) human intestinal bacterium PUE (bacteria) Gene: dgpB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q9WUX0 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DgpB and DgpC / Type: COMPLEX / Details: heterodimer complex of DgpB and DgpC / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.21 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: human intestinal bacterium PUE (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono-disperse. | |||||||||||||||
Specimen support | Details: The grid was washed by acetone prior to use. / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K / Details: Blotting time was 20 second (blot force 0) |
-Electron microscopy imaging
Microscopy | Model: TFS TALOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 54.23 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2122 |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 857817 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56924 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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