1XDF

Crystal structure of pathogenesis-related protein LlPR-10.2A from yellow lupine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 99-107

  • DOI: 10.1107/S0907444904028173
  • Also Cited By: 5MXW, 5MXB, 3US7, 3IE5, 3E85, 2QIM, 2FLH

  • PubMed Abstract: 
  • Pathogenesis-related (PR) proteins of class 10 are abundant in higher plants. Some of these proteins are induced under stress conditions as part of the plant defence mechanism. Other homologues are developmentally regulated and their expression varie ...

    Pathogenesis-related (PR) proteins of class 10 are abundant in higher plants. Some of these proteins are induced under stress conditions as part of the plant defence mechanism. Other homologues are developmentally regulated and their expression varies in different plant organs. The PR-10 proteins are encoded by multigene families, have a weight of about 17 kDa and are found in the cytosol. In yellow lupin, nine different homologues have been identified and divided into two subclasses, LlPR-10.1 and LlPR-10.2. Within each subclass the sequence identity is about 75-91%, while across the subclasses it is only 59-60%. Here, the crystal structure of a yellow lupin PR-10 protein from the second subclass, LlPR-10.2A, is presented. The structure was solved by molecular replacement and refined to R = 0.205 using 1.9 A resolution data. The general fold of LlPR-10.2A resembles that of the other PR-10 proteins and consists of a long C-terminal alpha-helix surrounded by a seven-stranded antiparallel beta-sheet, with two shorter alpha-helices located between strands beta1 and beta2. The most variable part of the structure, the C-terminal helix, is strongly kinked towards the beta-sheet core in both LlPR-10.2A molecules present in the asymmetric unit. This unexpected feature reduces the size of the hydrophobic cavity observed in other PR-10 proteins that is reported to be the ligand-binding site. As in other PR-10 structures, a surface loop located near the entrance to the cavity shows very high structural conservation and stability despite the high glycine content in its sequence.


    Related Citations: 
    • 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
    • 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.,Spangfort, M.D.
      (1996) Nat.Struct.Mol.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
    • Crystallization and preliminary x-ray structure determination of Lupinus luteus PR10 protein
      Biesiadka, J.,Sikorski, M.M.,Bujacz, G.,Jaskolski, M.
      (1999) ACTA CRYSTALLOGR.,SECT.D 55: 1925


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PR10.2A
A, B
157Lupinus luteusMutation(s): 0 
Gene Names: PR10.2A
EC: 3.1.27.-
Find proteins for Q9LLQ3 (Lupinus luteus)
Go to UniProtKB:  Q9LLQ3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.956α = 90.00
b = 69.243β = 90.00
c = 112.918γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance