Crystal structure of 12-oxophytodienoate reductase 3 (OPR3) from tomato

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.225 

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Crystal structure of 12-oxophytodienoate reductase 3 from tomato: Self-inhibition by dimerization.

Breithaupt, C.Kurzbauer, R.Lilie, H.Schaller, A.Strassner, J.Huber, R.Macheroux, P.Clausen, T.

(2006) Proc Natl Acad Sci U S A 103: 14337-14342

  • DOI: https://doi.org/10.1073/pnas.0606603103
  • Primary Citation of Related Structures:  
    2HS6, 2HS8, 2HSA

  • PubMed Abstract: 

    12-Oxophytodienoate reductase (OPR) 3, a homologue of old yellow enzyme (OYE), catalyzes the reduction of 9S,13S-12-oxophytodienoate to the corresponding cyclopentanone, which is subsequently converted to the plant hormone jasmonic acid (JA). JA and JA derivatives, as well as 12-oxophytodienoate and related cyclopentenones, are known to regulate gene expression in plant development and defense. Together with other oxygenated fatty acid derivatives, they form the oxylipin signature in plants, which resembles the pool of prostaglandins in animals. Here, we report the crystal structure of OPR3 from tomato and of two OPR3 mutants. Although the catalytic residues of OPR3 and related OYEs are highly conserved, several characteristic differences can be discerned in the substrate-binding regions, explaining the remarkable substrate stereoselectivity of OPR isozymes. Interestingly, OPR3 crystallized as an extraordinary self-inhibited dimer. Mutagenesis studies and biochemical analysis confirmed a weak dimerization of OPR3 in vitro, which correlated with a loss of enzymatic activity. Based on structural data of OPR3, a putative mechanism for a strong and reversible dimerization of OPR3 in vivo that involves phosphorylation of OPR3 is suggested. This mechanism could contribute to the shaping of the oxylipin signature, which is critical for fine-tuning gene expression in plants.

  • Organizational Affiliation

    Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, 82152 Martinsried, Germany. constanze.breithaupt@sbg.ac.at

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
12-oxophytodienoate reductase 3A [auth B],
B [auth A]
402Solanum lycopersicumMutation(s): 0 
Gene Names: OPR3
Find proteins for Q9FEW9 (Solanum lycopersicum)
Explore Q9FEW9 
Go to UniProtKB:  Q9FEW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FEW9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.904α = 90
b = 89.677β = 109.46
c = 81.378γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations