5IXM

The LPS Transporter LptDE from Yersinia pestis, core complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.746 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens.

Botos, I.Majdalani, N.Mayclin, S.J.McCarthy, J.G.Lundquist, K.Wojtowicz, D.Barnard, T.J.Gumbart, J.C.Buchanan, S.K.

(2016) Structure 24: 965-976

  • DOI: 10.1016/j.str.2016.03.026
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Incorporation of lipopolysaccharide (LPS) into the outer membrane of Gram-negative bacteria is essential for viability, and is accomplished by a two-protein complex called LptDE. We solved crystal structures of the core LptDE complexes from Yersinia ...

    Incorporation of lipopolysaccharide (LPS) into the outer membrane of Gram-negative bacteria is essential for viability, and is accomplished by a two-protein complex called LptDE. We solved crystal structures of the core LptDE complexes from Yersinia pestis, Klebsiella pneumoniae, Pseudomonas aeruginosa, and a full-length structure of the K. pneumoniae LptDE complex. Our structures adopt the same plug and 26-strand β-barrel architecture found recently for the Shigella flexneri and Salmonella typhimurium LptDE structures, illustrating a conserved fold across the family. A comparison of the only two full-length structures, SfLptDE and our KpLptDE, reveals a 21° rotation of the LptD N-terminal domain that may impart flexibility on the trans-envelope LptCAD scaffold. Utilizing mutagenesis coupled to an in vivo functional assay and molecular dynamics simulations, we demonstrate the critical role of Pro231 and Pro246 in the function of the LptD lateral gate that allows partitioning of LPS into the outer membrane.


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20892 USA.,Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LPS-assembly protein LptD
A, C, E, G
577Yersinia pestisMutation(s): 0 
Gene Names: lptD (imp, ostA)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Lipopolysaccharide (LPS) Transport Proteins
Protein: 
LptD-LptE lipopolysaccharide transport complex
Find proteins for Q8ZIK3 (Yersinia pestis)
Go to UniProtKB:  Q8ZIK3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LPS-assembly lipoprotein LptE
B, D, F, H
198Yersinia pestisMutation(s): 0 
Gene Names: lptE (rlpB)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Lipopolysaccharide (LPS) Transport Proteins
Protein: 
LptD-LptE lipopolysaccharide transport complex
Find proteins for Q7CJV2 (Yersinia pestis)
Go to UniProtKB:  Q7CJV2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E

Download SDF File 
Download CCD File 
A, C, E, G
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.746 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.892α = 90.00
b = 176.354β = 96.11
c = 143.848γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Database references
  • Version 1.2: 2016-06-15
    Type: Database references