6P9T

E.coli LpxA in complex with UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc and Compound 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Two Distinct Mechanisms of Inhibition of LpxA Acyltransferase Essential for Lipopolysaccharide Biosynthesis.

Han, W.Ma, X.Balibar, C.J.Baxter Rath, C.M.Benton, B.Bermingham, A.Casey, F.Chie-Leon, B.Cho, M.K.Frank, A.O.Frommlet, A.Ho, C.M.Lee, P.S.Li, M.Lingel, A.Ma, S.Merritt, H.Ornelas, E.De Pascale, G.Prathapam, R.Prosen, K.R.Rasper, D.Ruzin, A.Sawyer, W.S.Shaul, J.Shen, X.Shia, S.Steffek, M.Subramanian, S.Vo, J.Wang, F.Wartchow, C.Uehara, T.

(2020) J Am Chem Soc 142: 4445-4455

  • DOI: 10.1021/jacs.9b13530
  • Primary Citation of Related Structures:  
    6P9P, 6P9R, 6P9Q, 6P9T, 6P9S

  • PubMed Abstract: 
  • The lipopolysaccharide biosynthesis pathway is considered an attractive drug target against the rising threat of multi-drug-resistant Gram-negative bacteria. Here, we report two novel small-molecule inhibitors (compounds 1 and 2 ) of the acyltransferase LpxA, the first enzyme in the lipopolysaccharide biosynthesis pathway ...

    The lipopolysaccharide biosynthesis pathway is considered an attractive drug target against the rising threat of multi-drug-resistant Gram-negative bacteria. Here, we report two novel small-molecule inhibitors (compounds 1 and 2 ) of the acyltransferase LpxA, the first enzyme in the lipopolysaccharide biosynthesis pathway. We show genetically that the antibacterial activities of the compounds against efflux-deficient Escherichia coli are mediated by LpxA inhibition. Consistently, the compounds inhibited the LpxA enzymatic reaction in vitro. Intriguingly, using biochemical, biophysical, and structural characterization, we reveal two distinct mechanisms of LpxA inhibition; compound 1 is a substrate-competitive inhibitor targeting apo LpxA, and compound 2 is an uncompetitive inhibitor targeting the LpxA/product complex. Compound 2 exhibited more favorable biological and physicochemical properties than compound 1 and was optimized using structural information to achieve improved antibacterial activity against wild-type E. coli . These results show that LpxA is a promising antibacterial target and imply the advantages of targeting enzyme/product complexes in drug discovery.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferaseA268Escherichia coliMutation(s): 0 
Gene Names: lpxAEC958_0327
EC: 2.3.1.129
UniProt
Find proteins for P0A722 (Escherichia coli (strain K12))
Explore P0A722 
Go to UniProtKB:  P0A722
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U20
Query on U20

Download Ideal Coordinates CCD File 
B [auth A]uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-N-acetyl-D-glucosamine
C31 H53 N3 O19 P2
TZSJGZGYQDNRRX-MPLCHSTDSA-N
 Ligand Interaction
O5D
Query on O5D

Download Ideal Coordinates CCD File 
H [auth A][3-(5-amino-4-methylpyridin-2-yl)-1H-pyrazol-5-yl]{(3R)-3-[(2-chloro-6-methoxyphenyl)methyl]morpholin-4-yl}methanone
C22 H24 Cl N5 O3
ZAPLCZOOCDRDCZ-CQSZACIVSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.793α = 90
b = 95.793β = 90
c = 95.793γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references, Refinement description