2JF2

Nucleotide substrate binding by UDP-N-acetylglucosamine acyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Nucleotide Substrate Recognition by Udp-N-Acetylglucosamine Acyltransferase (Lpxa) in the First Step of Lipid a Biosynthesis.

Ulaganathan, V.Buetow, L.Hunter, W.N.

(2007) J.Mol.Biol. 369: 305

  • DOI: 10.1016/j.jmb.2007.03.039
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lipid A is an integral component of the lipopolysaccharide (LPS) that forms the selective and protective outer monolayer of Gram-negative bacteria, and is essential for bacterial growth and viability. UDP-N-acetylglucosamine acyltransferase (LpxA) in ...

    Lipid A is an integral component of the lipopolysaccharide (LPS) that forms the selective and protective outer monolayer of Gram-negative bacteria, and is essential for bacterial growth and viability. UDP-N-acetylglucosamine acyltransferase (LpxA) initiates lipid A biosynthesis by catalyzing the transfer of R-3-hydroxymyristic acid from acyl carrier protein to the 3'-hydroxyl group of UDP-GlcNAc. The enzyme is a homotrimer, and previous studies suggested that the active site lies within a positively charged cleft formed at the subunit-subunit interface. The crystal structure of Escherichia coli LpxA in complex with UDP-GlcNAc reveals details of the substrate-binding site, with prominent hydrophilic interactions between highly conserved clusters of residues (Asn198, Glu200, Arg204 and Arg205) with UDP, and (Asp74, His125, His144 and Gln161) with the GlcNAc moiety. These interactions serve to bind and orient the substrate for catalysis. The crystallographic model supports previous results, which suggest that acylation occurs via nucleophilic attack of deprotonated UDP-GlcNAc on the acyl donor in a general base-catalyzed mechanism involving a catalytic dyad of His125 and Asp126. His125, the general base, interacts with the 3'-hydroxyl group of UDP-GlcNAc to generate the nucleophile. The Asp126 side-chain accepts a hydrogen bond from His125 and helps orient the general base to participate in catalysis. Comparisons with an LpxA:peptide inhibitor complex indicate that the peptide competes with both nucleotide and acyl carrier protein substrates.


    Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE
A
264Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: lpxA
EC: 2.3.1.129
Find proteins for P0A722 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A722
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.163 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 95.402α = 90.00
b = 95.402β = 90.00
c = 95.402γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2013-12-04
    Type: Derived calculations, Other, Source and taxonomy, Version format compliance