6UEG

Pseudomonas aeruginosa LpxA Complex Structure with Ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of dual-activity small-molecule ligands of Pseudomonas aeruginosa LpxA and LpxD using SPR and X-ray crystallography.

Kroeck, K.G.Sacco, M.D.Smith, E.W.Zhang, X.Shoun, D.Akhtar, A.Darch, S.E.Cohen, F.Andrews, L.D.Knox, J.E.Chen, Y.

(2019) Sci Rep 9: 15450-15450

  • DOI: https://doi.org/10.1038/s41598-019-51844-z
  • Primary Citation of Related Structures:  
    6UEC, 6UED, 6UEE, 6UEG

  • PubMed Abstract: 

    The lipid A biosynthesis pathway is essential in Pseudomonas aeruginosa. LpxA and LpxD are the first and third enzymes in this pathway respectively, and are regarded as promising antibiotic targets. The unique structural similarities between these two enzymes make them suitable targets for dual-binding inhibitors, a characteristic that would decrease the likelihood of mutational resistance and increase cell-based activity. We report the discovery of multiple small molecule ligands that bind to P. aeruginosa LpxA and LpxD, including dual-binding ligands. Binding poses were determined for select compounds by X-ray crystallography. The new structures reveal a previously uncharacterized magnesium ion residing at the core of the LpxD trimer. In addition, ligand binding in the LpxD active site resulted in conformational changes in the distal C-terminal helix-bundle, which forms extensive contacts with acyl carrier protein (ACP) during catalysis. These ligand-dependent conformational changes suggest a potential allosteric influence of reaction intermediates on ACP binding, and vice versa. Taken together, the novel small molecule ligands and their crystal structures provide new chemical scaffolds for ligand discovery targeting lipid A biosynthesis, while revealing structural features of interest for future investigation of LpxD function.


  • Organizational Affiliation

    Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
A, B, C, D, E
A, B, C, D, E, F
258Pseudomonas aeruginosa PA7Mutation(s): 0 
Gene Names: lpxAPSPA7_1495
EC: 2.3.1.129
UniProt
Find proteins for A6V1E4 (Pseudomonas aeruginosa (strain PA7))
Explore A6V1E4 
Go to UniProtKB:  A6V1E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6V1E4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q5G (Subject of Investigation/LOI)
Query on Q5G

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
J [auth C]
K [auth D]
L [auth E]
G [auth A],
H [auth A],
J [auth C],
K [auth D],
L [auth E],
M [auth F]
3-({2-[(2R)-2-carbamoyl-2,3-dihydro-4H-1,4-benzoxazin-4-yl]-2-oxoethyl}sulfanyl)propanoic acid
C14 H16 N2 O5 S
SDNYVGUVTOZEQL-LLVKDONJSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
I [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.39α = 90
b = 82.52β = 90
c = 224.02γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references