[English] 日本語
Yorodumi
- EMDB-50545: Alcohol dehydrogenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50545
TitleAlcohol dehydrogenase
Map dataRelion blush map
Sample
  • Complex: PDEN_2367
    • Protein or peptide: alcohol dehydrogenase
  • Ligand: ZINC ION
  • Ligand: water
KeywordsAlcohol dehydrogenase / tetramer / OXIDOREDUCTASE
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
alcohol dehydrogenase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLamers MH / Schada von Borzyskowski L / Ren M
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Scholarship CouncilCSC202207720003 China
CitationJournal: Nat Commun / Year: 2025
Title: NAD-dependent dehydrogenases enable efficient growth of Paracoccus denitrificans on the PET monomer ethylene glycol.
Authors: Minrui Ren / Danni Li / Holly Addison / Willem E M Noteborn / Elisabeth H Andeweg / Timo Glatter / Johannes H de Winde / Johannes G Rebelein / Meindert H Lamers / Lennart Schada von Borzyskowski /
Abstract: Ethylene glycol is a monomer of the plastic polyethylene terephthalate (PET) and an environmental pollutant of increasing concern. Although it is generally accepted that bacteria use ethylene glycol ...Ethylene glycol is a monomer of the plastic polyethylene terephthalate (PET) and an environmental pollutant of increasing concern. Although it is generally accepted that bacteria use ethylene glycol as growth substrate, not all involved enzymes are well understood. Here, we show that Paracoccus denitrificans assimilates ethylene glycol solely via NAD-dependent alcohol and aldehyde dehydrogenases. Using comparative proteomics, we identify a gene cluster that is strongly expressed in the presence of ethylene glycol. We report the functional and structural characterization of EtgB and EtgA, key enzymes encoded by this etg gene cluster. We furthermore show that the transcriptional activator EtgR controls expression of the gene cluster. Adaptive laboratory evolution on ethylene glycol results in faster growth, enabled by increased production of EtgB and EtgA. Bioinformatic analysis reveals that the etg gene cluster is widely distributed among bacteria, suggesting a common role of NAD-dependent dehydrogenases in microbial ethylene glycol assimilation.
History
DepositionJun 5, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50545.png

Downloads & links

-
Map

FileDownload / File: emd_50545.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRelion blush map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.037335843 - 0.07029121
Average (Standard dev.)0.00009998322 (±0.001873382)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.016 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map 1

Fileemd_50545_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_50545_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PDEN_2367

EntireName: PDEN_2367
Components
  • Complex: PDEN_2367
    • Protein or peptide: alcohol dehydrogenase
  • Ligand: ZINC ION
  • Ligand: water

-
Supramolecule #1: PDEN_2367

SupramoleculeName: PDEN_2367 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Paracoccus denitrificans (bacteria)

-
Macromolecule #1: alcohol dehydrogenase

MacromoleculeName: alcohol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: alcohol dehydrogenase
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Molecular weightTheoretical: 38.696234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH HHSSGHIEGR HNMAKTMKAA VVREFGKPLT IDEVPVPEPG PGMIQVRIQA SGVCHTDLHA AEGDWPVKPN PPFIPGHEG VGFVSAVGAG VKHVKEGDRV GVPWLYTACG HCRHCLGGWE TLCESQLNTG YSVNGGFADY VVADPNYVGH L PKNVDFLD ...String:
MGHHHHHHHH HHSSGHIEGR HNMAKTMKAA VVREFGKPLT IDEVPVPEPG PGMIQVRIQA SGVCHTDLHA AEGDWPVKPN PPFIPGHEG VGFVSAVGAG VKHVKEGDRV GVPWLYTACG HCRHCLGGWE TLCESQLNTG YSVNGGFADY VVADPNYVGH L PKNVDFLD IAPVLCAGVT VYKGLKVTDT KPGDWVVISG IGGLGHMAVQ YAKAMGMNVA AVDIDDEKLA LARKLGATVT VN AATEPDP AAAIRKQTDG GAQGVLVTAV GRKAFEQAIG MVARGGTVAL NGLPPGDFPL DIFGMVLNGI TVRGSIVGTR LDL QESLDF AGDGKVKATV HKAKLEDINN IFGQMHKGQI EGRMVLDMAG

UniProtKB: alcohol dehydrogenase

-
Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 206685
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

+
About Yorodumi

-
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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more