4PSB

Crystal Structure of Phytohormone Binding Protein from Vigna radiata in complex with gibberellic acid (GA3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Specific binding of gibberellic acid by Cytokinin-Specific Binding Proteins: a new aspect of plant hormone-binding proteins with the PR-10 fold.

Ruszkowski, M.Sliwiak, J.Ciesielska, A.Barciszewski, J.Sikorski, M.Jaskolski, M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2032-2041

  • DOI: 10.1107/S1399004714010578
  • Primary Citation of Related Structures:  
    4Q0K, 4PSB

  • PubMed Abstract: 
  • Pathogenesis-related proteins of class 10 (PR-10) are a family of plant proteins with the same fold characterized by a large hydrophobic cavity that allows them to bind various ligands, such as phytohormones. A subfamily with only ~20% sequence ident ...

    Pathogenesis-related proteins of class 10 (PR-10) are a family of plant proteins with the same fold characterized by a large hydrophobic cavity that allows them to bind various ligands, such as phytohormones. A subfamily with only ~20% sequence identity but with a conserved canonical PR-10 fold have previously been recognized as Cytokinin-Specific Binding Proteins (CSBPs), although structurally the binding mode of trans-zeatin (a cytokinin phytohormone) was found to be quite diversified. Here, it is shown that two CSBP orthologues from Medicago truncatula and Vigna radiata bind gibberellic acid (GA3), which is an entirely different phytohormone, in a conserved and highly specific manner. In both cases a single GA3 molecule is found in the internal cavity of the protein. The structural data derived from high-resolution crystal structures are corroborated by isothermal titration calorimetry (ITC), which reveals a much stronger interaction with GA3 than with trans-zeatin and pH dependence of the binding profile. As a conclusion, it is postulated that the CSBP subfamily of plant PR-10 proteins should be more properly linked with general phytohormone-binding properties and termed phytohormone-binding proteins (PhBP).


    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
    • Crystal structures of two homologous pathogenesis-related proteins from yellow lupine.
      Biesiadka, J., Bujacz, G., Sikorski, M.M., Jaskolski, M.
      (2002) J Mol Biol 319: 1223
    • 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
    • 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
    • Structural and functional aspects of PR-10 proteins.
      Fernandes, H., Michalska, K., Sikorski, M., Jaskolski, M.
      (2013) FEBS J 280: 1169

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytokinin-specific binding proteinA155Vigna radiataMutation(s): 0 
Gene Names: vrphbp
Find proteins for A0A1S3THR8 (Vigna radiata var. radiata)
Explore A0A1S3THR8 
Go to UniProtKB:  A0A1S3THR8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GA3
Query on GA3

Download CCD File 
A
GIBBERELLIN A3
C19 H22 O6
IXORZMNAPKEEDV-OBDJNFEBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GA3Kd:  23000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.38α = 90
b = 54.29β = 98.7
c = 71.09γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Data collection