9HEH | pdb_00009heh

Structure of the ligand binding domain of the chemoreceptor MkcA (DSOMK10_RS0100305) of Dickeya solani MK10 in complex with choline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.202 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

Acetylcholine chemotaxis in global bacterial plant pathogens.

Gavira, J.A.Gilabert, M.J.Santamaria-Hernando, S.Molina-Ollero, A.Rico-Jimenez, M.Cabrera, J.J.Lopez-Solanilla, E.Matilla, M.A.

(2025) Microbiol Res 300: 128294-128294

  • DOI: https://doi.org/10.1016/j.micres.2025.128294
  • Primary Citation of Related Structures:  
    9HEH

  • PubMed Abstract: 

    Interactions within the plant holobiont involve a wide diversity of plant- and microbial-derived signals. Bacterial perception of these signals allows directed movement along chemical gradients through chemotaxis, a process that is an important determinant for plant colonization and infection. The quaternary amine acetylcholine is primarily known for its function as a neurotransmitter in mammalian nervous systems, but is emerging as a signal molecule that regulates plant growth, development, and stress resistance. Here, we report that plant pathogenic bacteria of the genera Agrobacterium and Dickeya exhibit strong chemotaxis to acetylcholine. These responses are mediated in Agrobacterium fabrum, Dickeya solani, and Dickeya dadantii by the dCache_1-type ligand binding domain (LBD) containing chemoreceptors AtuA, MkcA, and DdaA, respectively, which recognize acetylcholine with affinities between 19 and 91 µM. These chemoreceptors also recognize additional quaternary amines such as choline, L-carnitine, and betaine. The high-resolution structure of MkcA-LBD of D. solani was solved in complex with choline, which allowed the identification of the molecular determinants of choline and acetylcholine recognition in this chemoreceptor. Functionally, DdaA was found to contribute to competitive colonization fitness in planta. Acetylcholine serves as a nutritional source for A. fabrum, but not for D. solani and D. dadantii, and provides osmoprotective effects in all three phytopathogenic species. Plant-associated bacteria exhibit chemotaxis toward a diversity of key plant signals, and their ability to sense acetylcholine may represent an adaptive strategy to ensure efficient plant infection and manage osmotic stress. Our findings suggest potential co-evolutionary interactions between plants and their associated microbiomes.


  • Organizational Affiliation
    • Laboratory of Crystallographic Studies, IACT (CSIC), Armilla, Spain.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-accepting chemotaxis protein306Dickeya solani MK10Mutation(s): 0 
Gene Names: trg_19FGLHLNJM_03480HAT90_03954I2625_07850O0557_07220
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHT (Subject of Investigation/LOI)
Query on CHT

Download Ideal Coordinates CCD File 
B [auth A]CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.202 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.714α = 90
b = 67.185β = 97.6
c = 53.824γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2019-103972GA-I00
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2020-116261GB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references