2QIM

Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Cytokinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 1040-1051

  • DOI: 10.1016/j.jmb.2008.03.027
  • Also Cited By: 5I8F, 5MXW, 5MXB, 4PSB, 4GY9, 4Q0K, 4JHI, 4JHH, 4JHG, 3RWS, 3IE5, 3E85

  • PubMed Abstract: 
  • Plant pathogenesis-related (PR) proteins of class 10 (PR-10) are small and cytosolic. The main feature of their three-dimensional structure is a large cavity between a seven-stranded antiparallel beta-sheet and a long C-terminal alpha-helix. Although ...

    Plant pathogenesis-related (PR) proteins of class 10 (PR-10) are small and cytosolic. The main feature of their three-dimensional structure is a large cavity between a seven-stranded antiparallel beta-sheet and a long C-terminal alpha-helix. Although PR-10 proteins are abundant in plants, their physiological role remains unknown. Recent data have indicated ligand binding as their possible biological function. The article describes the structure of a complex between a classic PR-10 protein (yellow lupine LlPR-10.2B) and the plant hormone, trans-zeatin. Previously, trans-zeatin binding has been reported in a structurally related cytokinin-specific binding protein, which has a distant sequence relation with classic PR-10 proteins. In the present 1.35 A resolution crystallographic model, three perfectly ordered zeatin molecules are found in the binding cavity of the protein. The fact that three zeatin molecules are bound by the protein when only a fourfold molar excess of the ligand was used indicates an unusual type of affinity for this ligand and suggests that LlPR-10.2B, and perhaps other PR-10 proteins as well, acts as a reservoir of cytokinin molecules in the aqueous environment of the cell.


    Related Citations: 
    • Crystal structure of a hypoallergenic isoform of the major birch pollen allergen Bet v 1 and its likely biological function as a plant steroid carrier.
      Markovic-Housley, Z.,Degano, M.,Lamba, D.,von Roepenack-Lahaye, E.,Clemens, S.,Susani, M.,Ferreira, F.,Scheiner, O.,Breiteneder, H.
      (2003) J.Mol.Biol. 325: 123
    • Structure of a yellow lupin 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
    • 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.,Joost van Neerven, R.J.,Schou, C.,Lowenstein, H.,Spangfort, M.D.
      (1996) Nat.Struct.Mol.Biol. 3: 1040
    • 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, 61-704 Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PR10.2B
A
158Lupinus luteusMutation(s): 0 
Gene Names: PR10.2B
EC: 3.1.27.-
Find proteins for Q9LLQ2 (Lupinus luteus)
Go to UniProtKB:  Q9LLQ2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
ZEA
Query on ZEA

Download SDF File 
Download CCD File 
A
(2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol
TRANS-ZEATIN
C10 H13 N5 O
UZKQTCBAMSWPJD-FARCUNLSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.147 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 73.822α = 90.00
b = 73.822β = 90.00
c = 67.212γ = 120.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance