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 
  • R-Value Observed: 0.148 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    2QIM

  • 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 PR-10 proteins are abundant in plants, their physiological role remains unknown ...

    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: 
    • 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 D Biol Crystallogr 61: 99
    • 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
    • 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
    • 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 Biol 3: 1040
    • 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

    Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PR10.2BA158Lupinus luteusMutation(s): 0 
Gene Names: PR10.2BYpr10.2b
EC: 3.1.27
UniProt
Find proteins for Q9LLQ2 (Lupinus luteus)
Explore Q9LLQ2 
Go to UniProtKB:  Q9LLQ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LLQ2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZEA
Query on ZEA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
(2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol
C10 H13 N5 O
UZKQTCBAMSWPJD-FARCUNLSSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-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 
  • R-Value Observed: 0.148 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.822α = 90
b = 73.822β = 90
c = 67.212γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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