7BAX

Crystal structure of LYS11 ectodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Kinetic proofreading of lipochitooligosaccharides determines signal activation of symbiotic plant receptors.

Gysel, K.Laursen, M.Thygesen, M.B.Lironi, D.Bozsoki, Z.Hjuler, C.T.Maolanon, N.N.Cheng, J.Bjork, P.K.Vinther, M.Madsen, L.H.Rubsam, H.Muszynski, A.Ghodrati, A.Azadi, P.Sullivan, J.T.Ronson, C.W.Jensen, K.J.Blaise, M.Radutoiu, S.Stougaard, J.Andersen, K.R.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2111031118
  • Primary Citation of Related Structures:  
    7AU7, 7BAX

  • PubMed Abstract: 

    Plants and animals use cell surface receptors to sense and interpret environmental signals. In legume symbiosis with nitrogen-fixing bacteria, the specific recognition of bacterial lipochitooligosaccharide (LCO) signals by single-pass transmembrane receptor kinases determines compatibility. Here, we determine the structural basis for LCO perception from the crystal structures of two lysin motif receptor ectodomains and identify a hydrophobic patch in the binding site essential for LCO recognition and symbiotic function. We show that the receptor monitors the composition of the amphiphilic LCO molecules and uses kinetic proofreading to control receptor activation and signaling specificity. We demonstrate engineering of the LCO binding site to fine-tune ligand selectivity and correct binding kinetics required for activation of symbiotic signaling in plants. Finally, the hydrophobic patch is found to be a conserved structural signature in this class of LCO receptors across legumes that can be used for in silico predictions. Our results provide insights into the mechanism of cell-surface receptor activation by kinetic proofreading of ligands and highlight the potential in receptor engineering to capture benefits in plant-microbe interactions.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University 8000 Aarhus C, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LysM type receptor kinase268Lotus japonicusMutation(s): 0 
Gene Names: LYS11
UniProt
Find proteins for D3KTZ8 (Lotus japonicus)
Explore D3KTZ8 
Go to UniProtKB:  D3KTZ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3KTZ8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.94α = 90
b = 114.94β = 90
c = 59.15γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata processing
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates Foundation--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description