4GY9

Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with N6-isopentenyladenine (2iP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/10.1107/S0907444913021975
  • Primary Citation of Related Structures:  
    4GY9, 4JHG, 4JHH, 4JHI

  • 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 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).


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MtN13 protein168Medicago truncatulaMutation(s): 0 
Gene Names: MtN13
UniProt
Find proteins for P93330 (Medicago truncatula)
Explore P93330 
Go to UniProtKB:  P93330
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP93330
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZIP
Query on ZIP

Download Ideal Coordinates CCD File 
B [auth A]N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE
C10 H13 N5
HYVABZIGRDEKCD-UHFFFAOYSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
I [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.596α = 90
b = 96.596β = 90
c = 112.031γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-12-04
    Changes: Database references
  • Version 1.2: 2014-01-08
    Changes: Database references
  • Version 1.3: 2014-12-03
    Changes: Data collection
  • Version 1.4: 2018-03-07
    Changes: Data collection
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description