4C9C

Crystal Structure of the Strawberry Pathogenesis-Related 10 (PR-10) Fra a 1E protein (Form A)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The Strawberry Pathogenesis-Related 10 (Pr-10) Fra a Proteins Control Flavonoid Biosynthesis by Binding to Metabolic Intermediates.

Casanal, A., Zander, U., Munoz, C., Dupeux, F., Luque, I., Botella, M.A., Schwab, W., Valpuesta, V., Marquez, J.A.

(2013) J Biol Chem 288: 35322

  • DOI: 10.1074/jbc.M113.501528
  • Primary Citation of Related Structures:  
    4C94, 4C9C, 4C9I

  • PubMed Abstract: 

    • Pathogenesis-related 10 (PR-10) proteins are involved in many aspects of plant biology but their molecular function is still unclear. They are related by sequence and structural homology to mammalian lipid transport and plant abscisic acid receptor proteins and are predicted to have cavities for ligand binding ...

    Pathogenesis-related 10 (PR-10) proteins are involved in many aspects of plant biology but their molecular function is still unclear. They are related by sequence and structural homology to mammalian lipid transport and plant abscisic acid receptor proteins and are predicted to have cavities for ligand binding. Recently, three new members of the PR-10 family, the Fra a proteins, have been identified in strawberry, where they are required for the activity of the flavonoid biosynthesis pathway, which is essential for the development of color and flavor in fruits. Here, we show that Fra a proteins bind natural flavonoids with different selectivity and affinities in the low μm range. The structural analysis of Fra a 1 E and a Fra a 3-catechin complex indicates that loops L3, L5, and L7 surrounding the ligand-binding cavity show significant flexibility in the apo forms but close over the ligand in the Fra a 3-catechin complex. Our findings provide mechanistic insight on the function of Fra a proteins and suggest that PR-10 proteins, which are widespread in plants, may play a role in the control of secondary metabolic pathways by binding to metabolic intermediates.

    Related Citations: 
    • Purification, Crystallization and Preliminary X-Ray Analysis of the Strawberry Allergens Fra a 1E and Fra a 3 in the Presence of Catechin.
      Casanal, A., Zander, U., Dupeux, F., Valpuesta, V., Marquez, J.A.
      (2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 510
    Organizational Affiliation: 

    From the Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-Consejo Superior de Investigaciones Científicas), Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, 29071 Málaga, Spain.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MAJOR STRAWBERRY ALLERGEN FRA A 1-EA, B162Fragaria x ananassaMutation(s): 0 
Gene Names: FRAA1E.1, FRAA1E.2
UniProt
Find proteins for Q256S2 (Fragaria ananassa)
Explore Q256S2 
Go to UniProtKB:  Q256S2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ256S2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth B],
F [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.02α = 90
b = 74.42β = 90
c = 84.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references
  • Version 1.2: 2013-10-30
    Changes: Database references
  • Version 1.3: 2013-12-25
    Changes: Database references