9FM9 | pdb_00009fm9

Aldehyde dehydrogenase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

NAD-dependent dehydrogenases enable efficient growth of Paracoccus denitrificans on the PET monomer ethylene glycol.

Ren, M.Li, D.Addison, H.Noteborn, W.E.M.Andeweg, E.H.Glatter, T.de Winde, J.H.Rebelein, J.G.Lamers, M.H.Schada von Borzyskowski, L.

(2025) Nat Commun 16: 5845-5845

  • DOI: https://doi.org/10.1038/s41467-025-61056-x
  • Primary Citation of Related Structures:  
    9FLZ, 9FM9

  • PubMed 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 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.


  • Organizational Affiliation
    • Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde dehydrogenase
A, B, C, D
529Paracoccus denitrificansMutation(s): 0 
Gene Names: adhPden_2366
EC: 1.2.1.3
UniProt
Find proteins for A1B4L2 (Paracoccus denitrificans (strain Pd 1222))
Explore A1B4L2 
Go to UniProtKB:  A1B4L2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1B4L2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Scholarship CouncilChinaCSC202207720003

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection
  • Version 1.2: 2026-02-04
    Changes: Data collection, Database references