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 

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.,Sect.D 70: 2032-2041

  • DOI: 10.1107/S1399004714010578
  • Primary Citation of Related Structures:  
  • Also Cited By: 5I8F, 5MXW, 5MXB

  • 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: 
    • 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
    • The landscape of cytokinin binding by a plant nodulin.
      Ruszkowski, M.,Szpotkowski, K.,Sikorski, M.,Jaskolski, M.
      (2013) Acta Crystallogr.,Sect.D 69: 2365
    • Structural and functional aspects of PR-10 proteins.
      Fernandes, H.,Michalska, K.,Sikorski, M.,Jaskolski, M.
      (2013) Febs J. 280: 1169
    • 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


    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
Cytokinin-specific binding protein
A
155Vigna radiata var. radiataMutation(s): 0 
Gene Names: CSBP
Find proteins for A0A1S3THR8 (Vigna radiata var. radiata)
Go to UniProtKB:  A0A1S3THR8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GA3
Query on GA3

Download SDF File 
Download CCD File 
A
GIBBERELLIN A3
(1S,2S,4aR,4bR,7S,9aS,10S,10aR)-2,7-dihydroxy-1-methyl-8-methylidene-13-oxo-1,2,4b,5,6,7,8,9,10,10a-decahydro-4a,1-(epoxymethano)-7,9a-methanobenzo[a]azulene-10-carboxylic acid
C19 H22 O6
IXORZMNAPKEEDV-OBDJNFEBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GA3Kd: 23000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.152 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 34.380α = 90.00
b = 54.290β = 98.70
c = 71.090γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
MxCuBEdata collection
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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