[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleC-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 6294, Year 2021
Publish dateNov 2, 2021
AuthorsTakahiro 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 /
PubMed AbstractC-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.
External linksNat Commun / PubMed:34728636 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.4 - 2.85 Å
Structure data

30808

7drd

EMDB-30808, PDB-7drd:
Cryo-EM structure of DgpB-C at 2.85 angstrom resolution
Method: EM (single particle) / Resolution: 2.85 Å

30809

7dre

EMDB-30809, PDB-7dre:
Cryo-EM structure of DfgA-B at 2.54 angstrom resolution
Method: EM (single particle) / Resolution: 2.54 Å

PDB-7bvr:
DgpB-DgpC complex apo
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-7bvs:
DfgA-DfgB complex apo
Method: X-RAY DIFFRACTION / Resolution: 2.85 Å

PDB-7exb:
DfgA-DfgB complex apo 2.4 angstrom
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-7exz:
DgpB-DgpC complex apo 2.5 angstrom
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

Chemicals

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-MN:
Unknown entry

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM / HEPES

ChemComp-HOH:
WATER / Water

ChemComp-SO4:
SULFATE ION / Sulfate

Source
  • human intestinal bacterium pue (bacteria)
  • Eubacterium cellulosolvens (bacteria)
  • [Eubacterium] cellulosolvens (bacteria)
  • [eubacterium] cellulosolvens 6 (bacteria)
KeywordsLYASE / C-deglycosylation / sugar phosphate isomerase/epimerase / BIOSYNTHETIC PROTEIN / C-deglycosylase / sugar-isomerase-like

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more