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- EMDB-50550: Aldehyde dehydrogenase -

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Basic information

Entry
Database: EMDB / ID: EMD-50550
TitleAldehyde dehydrogenase
Map datarelion blush map
Sample
  • Complex: PDEN_2366
    • Protein or peptide: Aldehyde dehydrogenase
  • Ligand: POTASSIUM ION
KeywordsAldehyde dehydrogenase / tetramer / oxidoreductase
Function / homology
Function and homology information


acetaldehyde dehydrogenase (NAD+) activity / aldehyde dehydrogenase (NAD+)
Similarity search - Function
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Aldehyde dehydrogenase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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

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Structure visualization

Supplemental images

emd_50550.png

Downloads & links

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Map

FileDownload / File: emd_50550.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: 0.0122
Minimum - Maximum-0.033219367 - 0.06613168
Average (Standard dev.)0.00017563082 (±0.0018829866)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_50550_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50550_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PDEN_2366

EntireName: PDEN_2366
Components
  • Complex: PDEN_2366
    • Protein or peptide: Aldehyde dehydrogenase
  • Ligand: POTASSIUM ION

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Supramolecule #1: PDEN_2366

SupramoleculeName: PDEN_2366 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Paracoccus denitrificans (bacteria)

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Macromolecule #1: Aldehyde dehydrogenase

MacromoleculeName: Aldehyde dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: aldehyde dehydrogenase (NAD+)
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Molecular weightTheoretical: 58.316895 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH HHSSGHIEGR HMPNDQTHPF RGVNALPFEE RYDNFIGGEW VAPVSGRYFT NTTPITGAEI GQIARSEAGD IELALDAAH AAKEKWGATS PAERANIMLK IADRMERNLE LLATAETWDN GKPIRETMAA DLPLAIDHFR YFAGVLRAQE G SISQIDDD ...String:
MGHHHHHHHH HHSSGHIEGR HMPNDQTHPF RGVNALPFEE RYDNFIGGEW VAPVSGRYFT NTTPITGAEI GQIARSEAGD IELALDAAH AAKEKWGATS PAERANIMLK IADRMERNLE LLATAETWDN GKPIRETMAA DLPLAIDHFR YFAGVLRAQE G SISQIDDD TVAYHFHEPL GVVGQIIPWN FPLLMACWKL APAIAAGNCV VLKPAEQTPA GIMVWANLIG DLLPPGVLNI VN GFGLEAG KPLASSNRIA KIAFTGETTT GRLIMQYASE NLIPVTLELG GKSPNIFFAD VAREDDDFFD KALEGFTMFA LNQ GEVCTC PSRVLIQESI YDKFMERAVQ RVQAIKQGDP RESDTMIGAQ ASSEQKEKIL SYLDIGKKEG AEVLTGGKAA DLGG ELSGG YYIEPTIFRG NNKMRIFQEE IFGPVVSVTT FKDQAEALEI ANDTLYGLGA GVWSRDANTC YRMGRGIKAG RVWTN CYHA YPAHAAFGGY KQSGIGRETH KMMLDHYQQT KNMLVSYSPK KLGFF

UniProtKB: Aldehyde dehydrogenase

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

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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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185597
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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