[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

TitleActive and stable alcohol dehydrogenase-assembled hydrogels via synergistic bridging of triazoles and metal ions.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 2117, Year 2023
Publish dateApr 13, 2023
AuthorsQiang Chen / Ge Qu / Xu Li / Mingjian Feng / Fan Yang / Yanjie Li / Jincheng Li / Feifei Tong / Shiyi Song / Yujun Wang / Zhoutong Sun / Guangsheng Luo /
PubMed AbstractBiocatalysis is increasingly replacing traditional methods of manufacturing fine chemicals due to its green, mild, and highly selective nature, but biocatalysts, such as enzymes, are generally ...Biocatalysis is increasingly replacing traditional methods of manufacturing fine chemicals due to its green, mild, and highly selective nature, but biocatalysts, such as enzymes, are generally costly, fragile, and difficult to recycle. Immobilization provides protection for the enzyme and enables its convenient reuse, which makes immobilized enzymes promising heterogeneous biocatalysts; however, their industrial applications are limited by the low specific activity and poor stability. Herein, we report a feasible strategy utilizing the synergistic bridging of triazoles and metal ions to induce the formation of porous enzyme-assembled hydrogels with increased activity. The catalytic efficiency of the prepared enzyme-assembled hydrogels toward acetophenone reduction is 6.3 times higher than that of the free enzyme, and the reusability is confirmed by the high residual catalytic activity after 12 cycles of use. A near-atomic resolution (2.1 Å) structure of the hydrogel enzyme is successfully analyzed via cryogenic electron microscopy, which indicates a structure-property relationship for the enhanced performance. In addition, the possible mechanism of gel formation is elucidated, revealing the indispensability of triazoles and metal ions, which guides the use of two other enzymes to prepare enzyme-assembled hydrogels capable of good reusability. The described strategy can pave the way for the development of practical catalytic biomaterials and immobilized biocatalysts.
External linksNat Commun / PubMed:37055470 / PubMed Central
MethodsEM (single particle)
Resolution2.12 Å
Structure data

33514

7xy9

EMDB-33514, PDB-7xy9:
Cryo-EM structure of secondary alcohol dehydrogenases TbSADH after carrier-free immobilization based on weak intermolecular interactions
Method: EM (single particle) / Resolution: 2.12 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

Source
  • thermoanaerobacter brockii (bacteria)
KeywordsOXIDOREDUCTASE / Coordination complex / Activity / Stability / Enzyme Immobilization

+
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