1P42

Crystal structure of Aquifex aeolicus LpxC Deacetylase (Zinc-Inhibited Form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of LpxC, a Zinc-Dependent Deacetylase Essential for Endotoxin Biosynthesis

Whittington, D.A.Rusche, K.M.Shin, H.Fierke, C.A.Christianson, D.W.

(2003) Proc Natl Acad Sci U S A 100: 8146-8150

  • DOI: 10.1073/pnas.1432990100
  • Primary Citation of Related Structures:  
    1P42

  • PubMed Abstract: 
  • The outer leaflet of the outer membrane of the Gram-negative bacterium serves as a permeability barrier and is composed of lipopolysaccharide, also known as endotoxin. The membrane anchor of lipopolysaccharide is lipid A, the biosynthesis of which is ...

    The outer leaflet of the outer membrane of the Gram-negative bacterium serves as a permeability barrier and is composed of lipopolysaccharide, also known as endotoxin. The membrane anchor of lipopolysaccharide is lipid A, the biosynthesis of which is essential for cell viability. The first committed step in lipid A biosynthesis is catalyzed by UDP-(3-O-(R-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase (LpxC), a zinc-dependent deacetylase. Here we report the crystal structure of LpxC from Aquifex aeolicus, which reveals a new alpha+beta fold reflecting primordial gene duplication and fusion, as well as a new zinc-binding motif. The catalytic zinc ion resides at the base of an active-site cleft and adjacent to a hydrophobic tunnel occupied by a fatty acid. This tunnel accounts for the specificity of LpxC toward substrates and inhibitors bearing appropriately positioned 3-O-fatty acid substituents. Notably, simple inhibitors designed to target interactions in the hydrophobic tunnel bind with micromolar affinity, thereby representing a step toward the structure-based design of a potent, broad-spectrum antibacterial drug.


    Organizational Affiliation

    Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseAB270Aquifex aeolicusMutation(s): 1 
Gene Names: LPXC OR ENVA OR AQ_1772
EC: 3.5.1 (PDB Primary Data), 3.5.1.108 (UniProt)
Find proteins for O67648 (Aquifex aeolicus (strain VF5))
Explore O67648 
Go to UniProtKB:  O67648
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download CCD File 
A, B
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.66α = 90
b = 101.66β = 90
c = 125.1γ = 120
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description