6P86

E.coli LpxD in complex with compound 4.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and biological basis of small molecule inhibition of Escherichia coli LpxD acyltransferase essential for lipopolysaccharide biosynthesis.

Ma, X.Prathapam, R.Wartchow, C.Chie Leon, B.Ho, C.M.de Vicente, J.Han, W.Li, M.Lu, Y.Ramurthy, S.Shia, S.Steffek, M.Uehara, T.

(2019) Acs Infect Dis. --: --

  • DOI: 10.1021/acsinfecdis.9b00127
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • LpxD, acyl-ACP-dependent <i>N </i>-acyltransferase, is the third enzyme of lipid A biosynthesis in Gram-negative bacteria. A recent probe-based screen identified several compounds, including 6359-0284 (compound <b>1 </b>), that inhibit the enzymati ...

    LpxD, acyl-ACP-dependent N -acyltransferase, is the third enzyme of lipid A biosynthesis in Gram-negative bacteria. A recent probe-based screen identified several compounds, including 6359-0284 (compound 1 ), that inhibit the enzymatic activity of Escherichia coli ( E. coli ) LpxD. Here, we use these inhibitors to chemically validate LpxD as an attractive antibacterial target. We first found that compound 1 was oxidized in solution to the more stable aromatized tetrahydro-pyrazolo-quinolinone compound 1o . From the Escherichia coli strain deficient in efflux, we isolated a mutant that was less susceptible to compound 1o and had an lpxD missense mutation (Gly268Cys), supporting the cellular on-target activity. Using surface plasma resonance, we showed direct binding to E. coli LpxD for compound 1o and other reported LpxD inhibitors in vitro . Furthermore, we determined eight cocrystal structures of E. coli LpxD/inhibitor complexes. These costructures pinpointed the 4'-phosphopantetheine binding site as the common ligand binding hotspot, where hydrogen bonds to Gly269 and/or Gly287 were important for inhibitor binding. In addition, the LpxD/compound 1o costructure rationalized the reduced activity of compound 1o in the LpxD Gly268Cys mutant. Moreover, we obtained the LpxD structure in complex with a previously reported LpxA/LpxD dual targeting peptide inhibitor, RJPXD33, providing structural rationale for the unique dual targeting properties of this peptide. Given that the active site residues of LpxD are conserved in multidrug resistant Enterobacteriaceae, this work paves the way for future LpxD drug discovery efforts combating these Gram-negative pathogens.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
A, B, C
343Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: lpxD (firA, omsA)
EC: 2.3.1.191
Find proteins for P21645 (Escherichia coli (strain K12))
Go to UniProtKB:  P21645
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
O4S
Query on O4S

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Download CCD File 
A
N-[(4-ethylphenyl)methyl]-2-[(6aR)-6-oxo-3-(pyrrolidine-1-carbonyl)-6,6a,7,8,9,10-hexahydro-5H-pyrido[1,2-a]quinoxalin-5-yl]acetamide
C28 H34 N4 O3
HPKMORZWWWMLAR-XMMPIXPASA-N
 Ligand Interaction
O3V
Query on O3V

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Download CCD File 
B, C
3-hydroxy-7,7-dimethyl-2-phenyl-4-(thiophen-2-yl)-2,6,7,8-tetrahydro-5H-pyrazolo[3,4-b]quinolin-5-one
C22 H19 N3 O2 S
UAVKPYTVCWRHPL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.617α = 90.00
b = 97.617β = 90.00
c = 216.638γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-06-06 
  • Released Date: 2019-08-28 
  • Deposition Author(s): Ma, X., Shia, S.

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release