2FLH

Crystal structure of cytokinin-specific binding protein from mung bean in complex with cytokinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 2622-2634

  • DOI: 10.1105/tpc.105.037119
  • Also Cited By: 5I8F, 5MXW, 5MXB, 4PSB, 4GY9, 4Q0K, 4JHI, 4JHH, 4JHG, 3US7, 3RWS, 3IE5, 3E85, 3C0V, 2QIM

  • PubMed Abstract: 
  • The cytosolic fraction of Vigna radiata contains a 17-kD protein that binds plant hormones from the cytokinin group, such as zeatin. Using recombinant protein and isothermal titration calorimetry as well as fluorescence measurements coupled with liga ...

    The cytosolic fraction of Vigna radiata contains a 17-kD protein that binds plant hormones from the cytokinin group, such as zeatin. Using recombinant protein and isothermal titration calorimetry as well as fluorescence measurements coupled with ligand displacement, we have reexamined the K(d) values and show them to range from approximately 10(-6) M (for 4PU30) to 10(-4) M (for zeatin) for 1:1 stoichiometry complexes. In addition, we have crystallized this cytokinin-specific binding protein (Vr CSBP) in complex with zeatin and refined the structure to 1.2 A resolution. Structurally, Vr CSBP is similar to plant pathogenesis-related class 10 (PR-10) proteins, despite low sequence identity (<20%). This unusual fold conservation reinforces the notion that classic PR-10 proteins have evolved to bind small-molecule ligands. The fold consists of an antiparallel beta-sheet wrapped around a C-terminal alpha-helix, with two short alpha-helices closing a cavity formed within the protein core. In each of the four independent CSBP molecules, there is a zeatin ligand located deep in the cavity with conserved conformation and protein-ligand interactions. In three cases, an additional zeatin molecule is found in variable orientation but with excellent definition in electron density, which plugs the entrance to the binding pocket, sealing the inner molecule from contact with bulk solvent.


    Related Citations: 
    • Purification and cDNA cloning of cytokinin-specific binding protein from mung bean (Vigna radiata)
      Fujimoto, Y.,Nagata, R.,Fukasawa, H.,Yano, K.,Azuma, M.,Iida, A.,Sugimoto, S.,Shudo, K.,Hashimoto, Y.
      (1998) Eur.J.Biochem. 258: 794
    • X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy.
      Gajhede, M.,Osmark, P.,Poulsen, F.M.,Ipsen, H.,Larsen, J.N.,van Neerven, R.J.J.,Schou, C.,Lowenstein, H.,Spangford, M.D.
      (1996) Nat.Struct.Mol.Biol. 3: 1040
    • Crystallization and preliminary crystallographic studies of mung bean cytokinin-specific binding protein
      Bujacz, G.,Pasternak, O.,Fujimoto, Y.,Hashimoto, Y.,Sikorski, M.M.,Jaskolski, M.
      (2003) Acta Crystallogr.,Sect.D 59: 522
    • 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
    • Structure of a yellow lupine pathogenesis-related PR-10 protein belonging to a novel subclass
      Pasternak, O.,Biesiadka, J.,Dolot, R.,Handschuh, L.,Bujacz, G.,Sikorski, M.M.,Jaskolski, M.
      (2005) Acta Crystallogr.,Sect.D 61: 99


    Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61704 Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cytokinin-specific binding protein
A, B, C, D
155Vigna radiata var. radiataMutation(s): 0 
Gene Names: CSBP
Find proteins for A0A1S3THR8 (Vigna radiata var. radiata)
Go to UniProtKB:  A0A1S3THR8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ZEA
Query on ZEA

Download SDF File 
Download CCD File 
A, B, C, D
(2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol
TRANS-ZEATIN
C10 H13 N5 O
UZKQTCBAMSWPJD-FARCUNLSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZEAKd: 148000 nM BINDINGMOAD
ZEAKd: 106000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.190 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 113.790α = 90.00
b = 113.790β = 90.00
c = 86.980γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance