8PEH

Crystal structure of Lotus japonicus SYMRK kinase domain D738N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Phosphorylation of the alpha-I motif in SYMRK drives root nodule organogenesis.

Abel, N.B.Norgaard, M.M.M.Hansen, S.B.Gysel, K.Diez, I.A.Jensen, O.N.Stougaard, J.Andersen, K.R.

(2024) Proc Natl Acad Sci U S A 121: e2311522121-e2311522121

  • DOI: https://doi.org/10.1073/pnas.2311522121
  • Primary Citation of Related Structures:  
    8PEH

  • PubMed Abstract: 

    Symbiosis receptor-like kinase SYMRK is required for root nodule symbiosis between legume plants and nitrogen-fixing bacteria. To understand symbiotic signaling from SYMRK, we determined the crystal structure to 1.95 Å and mapped the phosphorylation sites onto the intracellular domain. We identified four serine residues in a conserved "alpha-I" motif, located on the border between the kinase core domain and the flexible C-terminal tail, that, when phosphorylated, drives organogenesis. Substituting the four serines with alanines abolished symbiotic signaling, while substituting them with phosphorylation-mimicking aspartates induced the formation of spontaneous nodules in the absence of bacteria. These findings show that the signaling pathway controlling root nodule organogenesis is mediated by SYMRK phosphorylation, which may help when engineering this trait into non-legume plants.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-like kinase SYMRKA [auth B],
B [auth C],
C [auth A]
300Lotus japonicusMutation(s): 1 
UniProt
Find proteins for Q8LKX1 (Lotus japonicus)
Explore Q8LKX1 
Go to UniProtKB:  Q8LKX1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8LKX1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth B]
E [auth B]
F [auth B]
G [auth B]
H [auth B]
D [auth B],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
N [auth C],
O [auth C],
P [auth C],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
L [auth B]
M [auth B]
Q [auth C]
R [auth C]
AA [auth A],
L [auth B],
M [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A [auth B],
B [auth C],
C [auth A]
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.87α = 90
b = 77.96β = 90.15
c = 101.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF19SA0059362
Bill & Melinda Gates FoundationUnited StatesOPP11772165

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references