1IFV

CRYSTAL STRUCTURE OF PATHOGENESIS-RELATED PROTEIN LLPR10.1B FROM YELLOW LUPINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 1223-1234

  • DOI: 10.1016/S0022-2836(02)00385-6
  • Primary Citation of Related Structures:  
    1ICX, 1IFV

  • PubMed Abstract: 
  • Pathogenesis-related class 10 (PR10) proteins are restricted to the plant kingdom where they are coded by multigene families and occur at high levels. In spite of their abundance, their physiological role is obscure although members of a distantly re ...

    Pathogenesis-related class 10 (PR10) proteins are restricted to the plant kingdom where they are coded by multigene families and occur at high levels. In spite of their abundance, their physiological role is obscure although members of a distantly related subclass (cytokinin-specific binding proteins) are known to bind plant hormones. PR10 proteins are of special significance in legume plants where their expression patterns are related to infection by the symbiotic, nitrogen-fixing bacteria. Here we present the first crystal structures of classic PR10 proteins representing two homologues from one subclass in yellow lupine. The general fold is similar and, as in a birch pollen allergen, consists of a seven-stranded beta-sheet wrapped around a long C-terminal helix. The mouth of a large pocket formed between the beta-sheet and the helix seems a likely site for ligand binding. The shape of the pocket varies because, in variance with the rigid beta-sheet, the helix shows unusual conformational variability consisting in bending, disorder, and axial shifting. A surface loop, proximal to the entrance to the internal cavity, shows an unusual structural conservation and rigidity in contrast to the high glycine content in its sequence. The loop is different from the so-called glycine-rich P-loops that bind phosphate groups of nucleotides, but it is very likely that it does play a role in ligand binding in PR10 proteins.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Structure Determination of Lupinus Luteus Pr10 Protein
      Biesiadka, J., Sikorski, M.M., Bujacz, G., Jaskolski, M.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 1925
    • Expression of Genes Encoding Pr10 Class Pathogenesis-Related Proteins is Inhibited in Yellow Lupine Root Nodules
      Sikorski, M.M., Biesiadka, J., Kasperska, A.E., Kopcinska, J., Lotocka, B., Golinowski, W., Legocki, A.B.
      (1999) Plant Sci 149: 125
    • 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

    Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN LLR18BAB155Lupinus luteusMutation(s): 0 
Gene Names: LLR18B
EC: 3.1.27
Find proteins for P52779 (Lupinus luteus)
Explore P52779 
Go to UniProtKB:  P52779
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.88α = 90
b = 107.445β = 90
c = 46.879γ = 90
Software Package:
Software NamePurpose
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance