7BWL

Structure of antibiotic sequester from Pseudomonas aerurinosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the Pseudomonas aeruginosa PA0423 protein and its functional implication in antibiotic sequestration.

Lee, C.Kim, M.I.Park, J.Kim, J.Oh, H.Cho, Y.Son, J.Jeon, B.Y.Ka, H.Hong, M.

(2020) Biochem Biophys Res Commun 528: 85-91

  • DOI: https://doi.org/10.1016/j.bbrc.2020.05.023
  • Primary Citation of Related Structures:  
    7BWL

  • PubMed Abstract: 

    Pseudomonas aeruginosa is a widely found opportunistic pathogen. The emergence of multidrug-resistant strains and persistent chronic infections have increased. The protein encoded by the pa0423 gene in P. aeruginosa is proposed to be critical for pathogenesis and could be a virulence-promoting protease or a bacterial lipocalin that binds a lipid-like antibiotic for drug resistance. Although two functions of proteolysis and antibiotic resistance are mutually related to bacterial survival in the host, it is very unusual for a single-domain protein to target unrelated ligand molecules such as protein substrates and lipid-like antibiotics. To clearly address the biological role of the PA0423 protein, we performed structural and biochemical studies. We found that PA0423 adopts a single-domain β-barrel structure and belongs to the lipocalin family. The PA0423 structure houses an internal tubular cavity, which accommodates a ubiquinone-8 molecule. Furthermore, we reveal that PA0423 can directly interact with the polymyxin B antibiotic using the internal cavity, suggesting that PA0423 has a physiological function in the antibiotic resistance of P. aeruginosa.


  • Organizational Affiliation

    Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0312 protein PA0423191Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA0423
UniProt
Find proteins for Q9I690 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I690 
Go to UniProtKB:  Q9I690
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I690
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UQ8 (Subject of Investigation/LOI)
Query on UQ8

Download Ideal Coordinates CCD File 
B [auth A]Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.338α = 90
b = 53.338β = 90
c = 134.639γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2020-12-02 
  • Deposition Author(s): Hong, M.

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Democratic People's Republic Of2018R1A2B6001619

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description