3CQN

Crystal Structure of the Lipocalin domain of Violaxanthin de-epoxidase (VDE) at pH7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A structural basis for the pH-dependent xanthophyll cycle in Arabidopsis thaliana.

Arnoux, P.Morosinotto, T.Saga, G.Bassi, R.Pignol, D.

(2009) Plant Cell 21: 2036-2044

  • DOI: 10.1105/tpc.109.068007
  • Primary Citation of Related Structures:  
    3CQN, 3CQR

  • PubMed Abstract: 
  • Plants adjust their photosynthetic activity to changing light conditions. A central regulation of photosynthesis depends on the xanthophyll cycle, in which the carotenoid violaxanthin is converted into zeaxanthin in strong light, thus activating the dissipation of the excess absorbed energy as heat and the scavenging of reactive oxygen species ...

    Plants adjust their photosynthetic activity to changing light conditions. A central regulation of photosynthesis depends on the xanthophyll cycle, in which the carotenoid violaxanthin is converted into zeaxanthin in strong light, thus activating the dissipation of the excess absorbed energy as heat and the scavenging of reactive oxygen species. Violaxanthin deepoxidase (VDE), the enzyme responsible for zeaxanthin synthesis, is activated by the acidification of the thylakoid lumen when photosynthetic electron transport exceeds the capacity of assimilatory reactions: at neutral pH, VDE is a soluble and inactive enzyme, whereas at acidic pH, it attaches to the thylakoid membrane where it binds its violaxanthin substrate. VDE also uses ascorbate as a cosubstrate with a pH-dependent Km that may reflect a preference for ascorbic acid. We determined the structures of the central lipocalin domain of VDE (VDEcd) at acidic and neutral pH. At neutral pH, VDEcd is monomeric with its active site occluded within a lipocalin barrel. Upon acidification, the barrel opens up and the enzyme appears as a dimer. A channel linking the two active sites of the dimer can harbor the entire carotenoid substrate and thus may permit the parallel deepoxidation of the two violaxanthin beta-ionone rings, making VDE an elegant example of the adaptation of an asymmetric enzyme to its symmetric substrate.


    Organizational Affiliation

    Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie Environementale et de Biotechnologie, Laboratoire de Bioénergétique Cellulaire, Saint-Paul-lez-Durance, F-13108, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Violaxanthin de-epoxidase, chloroplastA, B185Arabidopsis thalianaMutation(s): 0 
Gene Names: VDE1AVDE1NPQ1VXDEAt1g08550F22O13.3T27G7.23
EC: 1.10.99.3 (PDB Primary Data), 1.23.5.1 (UniProt)
UniProt
Find proteins for Q39249 (Arabidopsis thaliana)
Explore Q39249 
Go to UniProtKB:  Q39249
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.634α = 82.52
b = 52.458β = 75.99
c = 54.605γ = 74.54
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-26
    Changes: Database references