5KNK

Lipid A secondary acyltransferase LpxM from Acinetobacter baumannii with catalytic residue substitution (E127A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-guided enzymology of the lipid A acyltransferase LpxM reveals a dual activity mechanism.

Dovala, D.Rath, C.M.Hu, Q.Sawyer, W.S.Shia, S.Elling, R.A.Knapp, M.S.Metzger, L.E.

(2016) Proc.Natl.Acad.Sci.USA 113: E6064-E6071

  • DOI: 10.1073/pnas.1610746113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gram-negative bacteria possess a characteristic outer membrane, of which the lipid A constituent elicits a strong host immune response through the Toll-like receptor 4 complex, and acts as a component of the permeability barrier to prevent uptake of ...

    Gram-negative bacteria possess a characteristic outer membrane, of which the lipid A constituent elicits a strong host immune response through the Toll-like receptor 4 complex, and acts as a component of the permeability barrier to prevent uptake of bactericidal compounds. Lipid A species comprise the bulk of the outer leaflet of the outer membrane and are produced through a multistep biosynthetic pathway conserved in most Gram-negative bacteria. The final steps in this pathway involve the secondary acylation of lipid A precursors. These are catalyzed by members of a superfamily of enzymes known as lysophospholipid acyltransferases (LPLATs), which are present in all domains of life and play important roles in diverse biological processes. To date, characterization of this clinically important class of enzymes has been limited by a lack of structural information and the availability of only low-throughput biochemical assays. In this work, we present the structure of the bacterial LPLAT protein LpxM, and we describe a high-throughput, label-free mass spectrometric assay to characterize acyltransferase enzymatic activity. Using our structure and assay, we identify an LPLAT thioesterase activity, and we provide experimental evidence to support an ordered-binding and "reset" mechanistic model for LpxM function. This work enables the interrogation of other bacterial acyltransferases' structure-mechanism relationships, and the assay described herein provides a foundation for quantitatively characterizing the enzymology of any number of clinically relevant LPLAT proteins.


    Organizational Affiliation

    Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, CA 94608.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipid A biosynthesis lauroyl acyltransferase
B
333Acinetobacter baumannii NIPH 410Mutations: A133E
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Acyltransferases
Protein: 
LpxM lipid A acyltransferase
Find proteins for S3TFW2 (Acinetobacter baumannii NIPH 410)
Go to UniProtKB:  S3TFW2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

Download SDF File 
Download CCD File 
B
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
11A
Query on 11A

Download SDF File 
Download CCD File 
B
UNDECANOIC ACID
C11 H22 O2
ZDPHROOEEOARMN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.225 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 59.300α = 90.00
b = 145.470β = 90.00
c = 87.610γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references
  • Version 1.2: 2016-10-19
    Type: Database references
  • Version 1.3: 2016-10-26
    Type: Database references