4C94

Crystal Structure of the Strawberry Pathogenesis-Related 10 (PR-10) Fra a 3 protein in complex with Catechin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.5 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:  

  • 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 p ...

    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 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FRA A 3 ALLERGEN
A, B, C, D, E
161Fragaria ananassaMutation(s): 0 
Gene Names: FRAA3
Find proteins for D0E0C7 (Fragaria ananassa)
Go to UniProtKB:  D0E0C7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KXN
Query on KXN

Download SDF File 
Download CCD File 
A, B, C, D, E
(2R,3S)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol
C15 H14 O6
PFTAWBLQPZVEMU-DZGCQCFKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KXNKd: 8900 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.178 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 137.899α = 90.00
b = 206.594β = 90.00
c = 174.691γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-10-23
    Type: Database references
  • Version 1.2: 2013-10-30
    Type: Database references
  • Version 1.3: 2013-11-06
    Type: Atomic model
  • Version 1.4: 2013-12-25
    Type: Database references
  • Version 1.5: 2017-08-09
    Type: Data collection