9C4O | pdb_00009c4o

Cryo-EM structure of PqqU with ligand PQQ


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

High-affinity PQQ import is widespread in Gram-negative bacteria.

Munder, F.Voutsinos, M.Hantke, K.Venugopal, H.Grinter, R.

(2025) Sci Adv 11: eadr2753-eadr2753

  • DOI: https://doi.org/10.1126/sciadv.adr2753
  • Primary Citation of Related Structures:  
    9C4O

  • PubMed Abstract: 

    Pyrroloquinoline quinone (PQQ) is a soluble redox cofactor used by diverse bacteria. Many Gram-negative bacteria that encode PQQ-dependent enzymes do not produce it and instead obtain it from the environment. To achieve this, Escherichia coli uses the TonB-dependent transporter PqqU as a high-affinity PQQ importer. Here, we show that PqqU binds PQQ with high affinity and determine the high-resolution structure of the PqqU-PQQ complex, revealing that PqqU undergoes conformational changes in PQQ binding to capture the cofactor in an internal cavity. We show that these conformational changes preclude the binding of a bacteriophage, which targets PqqU as a cell surface receptor. Guided by the PqqU-PQQ structure, we identify amino acids essential for PQQ import and leverage this information to map the presence of PqqU across Gram-negative bacteria. This reveals that PqqU is encoded by Gram-negative bacteria from at least 22 phyla occupying diverse habitats, indicating that PQQ is an important cofactor for bacteria that adopt diverse lifestyles and metabolic strategies.


  • Organizational Affiliation
    • Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrroloquinoline quinone transporter707Escherichia coli BW25113Mutation(s): 0 
Gene Names: pqqUyncDb1451JW1446
Membrane Entity: Yes 
UniProt
Find proteins for P76115 (Escherichia coli (strain K12))
Explore P76115 
Go to UniProtKB:  P76115
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76115
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.99 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
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1197376
Australian Research Council (ARC)AustraliaDP230102150
Australian Research Council (ARC)AustraliaLE200100045
Australian Research Council (ARC)AustraliaLE120100090

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-05-28
    Changes: Data collection
  • Version 1.3: 2025-06-11
    Changes: Data collection, Database references
  • Version 1.4: 2025-08-13
    Changes: Data collection