4JHH

Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with kinetin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.,Sect.D 69: 2365-2380

  • DOI: 10.1107/S0907444913021975
  • Primary Citation of Related Structures:  
  • Also Cited By: 5I8F, 5MXW, 5MXB, 4PSB, 4Q0K

  • 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: 
    • 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
    • Structural and functional aspects of PR-10 proteins.
      Fernandes, H.,Michalska, K.,Sikorski, M.,Jaskolski, M.
      (2013) Febs J. 280: 1169
    • 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
    • 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
    • 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


    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 protein
A
168Medicago truncatulaMutation(s): 0 
Gene Names: N13
Find proteins for P93330 (Medicago truncatula)
Go to UniProtKB:  P93330
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MLI
Query on MLI

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Download CCD File 
A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
H35
Query on H35

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Download CCD File 
A
N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE
C10 H9 N5 O
QANMHLXAZMSUEX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.186 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 96.415α = 90.00
b = 96.415β = 90.00
c = 113.407γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
MxCuBEdata collection
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2014-01-08
    Type: Database references