5A3V

Crystal structure of the chloroplastic gamma-ketol reductase from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of the Chloroplastic Oxoene Reductase ceQORH from Arabidopsis thaliana.

Mas Y Mas, S.Curien, G.Giustini, C.Rolland, N.Ferrer, J.L.Cobessi, D.

(2017) Front Plant Sci 8: 329-329

  • DOI: https://doi.org/10.3389/fpls.2017.00329
  • Primary Citation of Related Structures:  
    5A3J, 5A3V, 5A4D

  • PubMed Abstract: 

    Enzymatic and non-enzymatic peroxidation of polyunsaturated fatty acids give rise to accumulation of aldehydes, ketones, and α,β-unsaturated carbonyls of various lengths, known as oxylipins. Oxylipins with α,β-unsaturated carbonyls are reactive electrophile species and are toxic. Cells have evolved several mechanisms to scavenge reactive electrophile oxylipins and decrease their reactivity such as by coupling with glutathione, or by reduction using NAD(P)H-dependent reductases and dehydrogenases of various substrate specificities. Plant cell chloroplasts produce reactive electrophile oxylipins named γ-ketols downstream of enzymatic lipid peroxidation. The chloroplast envelope quinone oxidoreductase homolog (ceQORH) from Arabidopsis thaliana was previously shown to reduce the reactive double bond of γ-ketols. In marked difference with its cytosolic homolog alkenal reductase (AtAER) that displays a high activity toward the ketodiene 13-oxo-9(Z),11(E)-octadecadienoic acid (13-KODE) and the ketotriene 13-oxo-9(Z), 11(E), 15(Z)-octadecatrienoic acid (13-KOTE), ceQORH binds, but does not reduce, 13-KODE and 13-KOTE. Crystal structures of apo-ceQORH and ceQORH bound to 13-KOTE or to NADP + and 13-KOTE have been solved showing a large ligand binding site, also observed in the structure of the cytosolic alkenal/one reductase. Positioning of the α,β-unsaturated carbonyl of 13-KOTE in ceQORH-NADP + -13-KOTE, far away from the NADP + nicotinamide ring, provides a rational for the absence of activity with the ketodienes and ketotrienes. ceQORH is a monomeric enzyme in solution whereas other enzymes from the quinone oxidoreductase family are stable dimers and a structural explanation of this difference is proposed. A possible in vivo role of ketodienes and ketotrienes binding to ceQORH is also discussed.


  • Organizational Affiliation

    Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, Centre National de la Recherche Scientifique (CNRS) Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
A, B
329Arabidopsis thalianaMutation(s): 0 
EC: 1 (PDB Primary Data), 1.3.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q9SV68 (Arabidopsis thaliana)
Explore Q9SV68 
Go to UniProtKB:  Q9SV68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SV68
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.72α = 90
b = 142.65β = 90
c = 209.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references
  • Version 1.2: 2017-04-05
    Changes: Database references
  • Version 1.3: 2017-08-09
    Changes: Data collection
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Other