5NNW

NLPPya in complex with glucosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Eudicot plant-specific sphingolipids determine host selectivity of microbial NLP cytolysins.

Lenarcic, T.Albert, I.Bohm, H.Hodnik, V.Pirc, K.Zavec, A.B.Podobnik, M.Pahovnik, D.Zagar, E.Pruitt, R.Greimel, P.Yamaji-Hasegawa, A.Kobayashi, T.Zienkiewicz, A.Gomann, J.Mortimer, J.C.Fang, L.Mamode-Cassim, A.Deleu, M.Lins, L.Oecking, C.Feussner, I.Mongrand, S.Anderluh, G.Nurnberger, T.

(2017) Science 358: 1431-1434

  • DOI: 10.1126/science.aan6874
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Necrosis and ethylene-inducing peptide 1-like (NLP) proteins constitute a superfamily of proteins produced by plant pathogenic bacteria, fungi, and oomycetes. Many NLPs are cytotoxins that facilitate microbial infection of eudicot, but not of monocot ...

    Necrosis and ethylene-inducing peptide 1-like (NLP) proteins constitute a superfamily of proteins produced by plant pathogenic bacteria, fungi, and oomycetes. Many NLPs are cytotoxins that facilitate microbial infection of eudicot, but not of monocot plants. Here, we report glycosylinositol phosphorylceramide (GIPC) sphingolipids as NLP toxin receptors. Plant mutants with altered GIPC composition were more resistant to NLP toxins. Binding studies and x-ray crystallography showed that NLPs form complexes with terminal monomeric hexose moieties of GIPCs that result in conformational changes within the toxin. Insensitivity to NLP cytolysins of monocot plants may be explained by the length of the GIPC head group and the architecture of the NLP sugar-binding site. We unveil early steps in NLP cytolysin action that determine plant clade-specific toxin selectivity.


    Organizational Affiliation

    Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
25 kDa protein elicitor
A, B, C, D
219Pythium aphanidermatumMutation(s): 0 
Gene Names: SD21-1
Find proteins for Q9SPD4 (Pythium aphanidermatum)
Go to UniProtKB:  Q9SPD4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCS
Query on GCS

Download SDF File 
Download CCD File 
D
D-GLUCOSAMINE
2-AMINO-2-DEOXY-D-GLUCOSE
C6 H13 N O5
MSWZFWKMSRAUBD-QZABAPFNSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 114.996α = 90.00
b = 122.285β = 90.00
c = 121.099γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySloveniaJ1-7515
Slovenian Research AgencySloveniaP1-0391

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release