4JHI

Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with N6-benzyladenine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The landscape of cytokinin binding by a plant nodulin.

Ruszkowski, M.Szpotkowski, K.Sikorski, M.Jaskolski, M.

(2013) Acta Crystallogr D Biol Crystallogr 69: 2365-2380

  • DOI: 10.1107/S0907444913021975
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Nodulation is an extraordinary symbiotic interaction between leguminous plants and nitrogen-fixing bacteria (rhizobia) that assimilate atmospheric nitrogen (in root nodules) and convert it into compounds suitable for the plant host. A class of plant ...

    Nodulation is an extraordinary symbiotic interaction between leguminous plants and nitrogen-fixing bacteria (rhizobia) that assimilate atmospheric nitrogen (in root nodules) and convert it into compounds suitable for the plant host. A class of plant hormones called cytokinins are involved in the nodulation process. In the model legume Medicago truncatula, nodulin 13 (MtN13), which belongs to the pathogenesis-related proteins of class 10 (PR-10), is expressed in the outer cortex of the nodules. In general, PR-10 proteins are small and monomeric and have a characteristic fold with an internal hydrophobic cavity formed between a seven-stranded antiparallel β-sheet and a C-terminal α-helix. Previously, some PR-10 proteins not related to nodulation were found to bind cytokinins such as trans-zeatin. Here, four crystal structures of the MtN13 protein are reported in complexes with several cytokinins, namely trans-zeatin, N6-isopentenyladenine, kinetin and N6-benzyladenine. All four phytohormones are bound in the hydrophobic cavity in the same manner and have excellent definition in the electron-density maps. The binding of the cytokinins appears to be strong and specific and is reinforced by several hydrogen bonds. Although the binding stoichiometry is 1:1, the complex is actually dimeric, with a cytokinin molecule bound in each subunit. The ligand-binding site in each cavity is formed with the participation of a loop element from the other subunit, which plugs the only entrance to the cavity. Interestingly, a homodimer of MtN13 is also formed in solution, as confirmed by small-angle X-ray scattering (SAXS).


    Related Citations: 
    • Structural and functional aspects of PR-10 proteins.
      Fernandes, H., Michalska, K., Sikorski, M., Jaskolski, M.
      (2013) FEBS J 280: 1169
    • Lupinus luteus pathogenesis-related protein as a reservoir for cytokinin.
      Fernandes, H., Pasternak, O., Bujacz, G., Bujacz, A., Sikorski, M.M., Jaskolski, M.
      (2008) J Mol Biol 378: 1040
    • Cytokinin-induced structural adaptability of a Lupinus luteus PR-10 protein.
      Fernandes, H., Bujacz, A., Bujacz, G., Jelen, F., Jasinski, M., Kachlicki, P., Otlewski, J., Sikorski, M.M., Jaskolski, M.
      (2009) FEBS J 276: 1596
    • Crystal structure of Vigna radiata cytokinin-specific binding protein in complex with zeatin.
      Pasternak, O., Bujacz, G.D., Fujimoto, Y., Hashimoto, Y., Jelen, F., Otlewski, J., Sikorski, M.M., Jaskolski, M.
      (2006) Plant Cell 18: 2622
    • Symbiosis-specific expression of two Medicago truncatula nodulin genes, MtN1 and MtN13, encoding products homologous to plant defense proteins.
      Gamas, P., de Billy, F., Truchet, G.
      (1998) Mol Plant Microbe Interact 11: 393

    Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MtN13 proteinA167Medicago truncatulaMutation(s): 0 
Gene Names: MtN13N13
Find proteins for P93330 (Medicago truncatula)
Explore P93330 
Go to UniProtKB:  P93330
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EMU
Query on EMU

Download CCD File 
A
N-BENZYL-9H-PURIN-6-AMINE
C12 H11 N5
NWBJYWHLCVSVIJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.175 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.086α = 90
b = 96.086β = 90
c = 113.584γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2014-01-08
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Advisory, Data collection, Refinement description