5DG3

Structure of Pseudomonas aeruginosa LpxA in complex with UDP-3-O-(R-3-hydroxydecanoyl)-GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structures of Pseudomonas aeruginosa LpxA Reveal the Basis for Its Substrate Selectivity.

Smith, E.W.Zhang, X.Behzadi, C.Andrews, L.D.Cohen, F.Chen, Y.

(2015) Biochemistry 54: 5937-5948

  • DOI: https://doi.org/10.1021/acs.biochem.5b00720
  • Primary Citation of Related Structures:  
    5DEM, 5DEP, 5DG3

  • PubMed Abstract: 

    In Gram-negative bacteria, the first step of lipid A biosynthesis is catalyzed by UDP-N-acetylglucosamine acyltransferase (LpxA) through the transfer of a R-3-hydroxyacyl chain from the acyl carrier protein (ACP) to the 3-hydroxyl group of UDP-GlcNAc. Previous studies suggest that LpxA is a critical determinant of the acyl chain length found in lipid A, which varies among species of bacteria. In Escherichia coli and Leptospira interrogans, LpxA prefers to incorporate longer R-3-hydroxyacyl chains (C14 and C12, respectively), whereas in Pseudomonas aeruginosa, the enzyme is selective for R-3-hydroxydecanoyl, a 10-hydrocarbon long acyl chain. We now report three P. aeruginosa LpxA crystal structures: apo protein, substrate complex with UDP-GlcNAc, and product complex with UDP-3-O-(R-3-hydroxydecanoyl)-GlcNAc. A comparison between the apo form and complexes identifies key residues that position UDP-GlcNAc appropriately for catalysis and supports the role of catalytic His121 in activating the UDP-GlcNAc 3-hydroxyl group for nucleophilic attack during the reaction. The product-complex structure, for the first time, offers structural insights into how Met169 serves to constrain the length of the acyl chain and thus functions as the so-called hydrocarbon ruler. Furthermore, compared with ortholog LpxA structures, the purported oxyanion hole, formed by the backbone amide group of Gly139, displays a different conformation in P. aeruginosa LpxA, which suggests flexibility of this structural feature important for catalysis and the potential need for substrate-induced conformational change in catalysis. Taken together, the three structures provide valuable insights into P. aeruginosa LpxA catalysis and substrate specificity as well as templates for future inhibitor discovery.


  • 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.963α = 90
b = 83.328β = 90
c = 220.369γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Derived calculations
  • Version 1.2: 2015-09-30
    Changes: Database references
  • Version 1.3: 2015-10-14
    Changes: Database references
  • Version 1.4: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-03-06
    Changes: Data collection, Database references, Refinement description, Structure summary