2G5W

X-ray crystal structure of Arabidopsis thaliana 12-oxophytodienoate reductase isoform 3 (AtOPR3) in complex with 8-iso prostaglandin A1 and its cofactor, flavin mononucleotide.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history. 


Literature

Crystal structure of Arabidopsis thaliana 12-oxophytodienoate reductase isoform 3 in complex with 8-iso prostaglandin A(1).

Han, B.W., Malone, T.E., Kim, D.J., Bingman, C.A., Kim, H.J., Fox, B.G., Phillips, G.N.

(2011) Proteins 79: 3236-3241

  • DOI: https://doi.org/10.1002/prot.23153
  • Primary Citation of Related Structures:  
    2G5W

  • PubMed Abstract: 

    12-Oxophytodienoate reductase 3 (OPR3), one of the enzymes involved in the biosynthesis of the plant hormone jasmonic acid (JA), catalyzes the reduction of the cyclopentenone ring of (9 S ,13 S )-12-oxophytodienoate [(9 S ,13 S )-OPDA]. However, there has been no structural information about the interaction between OPRs and the physiologically relevant (9 S ,13 S )-OPDA. Here we report the crystal structure of Arabidopsis thaliana OPR3 in complex with 8- iso prostaglandin A1 (8- iso PGA 1 ) which has the same stereochemistry in the cyclopentenone ring as in the physiologically relevant 9 S ,13 S -OPDA. This structure reveals a new binding mode for substrate that likely contributes to the relaxed stereospecificity observed for AtOPR3.

    • Organizational Affiliation: 

    Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea. [email protected]


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
12-oxophytodienoate reductase 3
A, B
391Arabidopsis thalianaMutation(s): 0 
Gene Names: At2g06050
EC: 1.3.1.42
UniProt
Find proteins for Q9FUP0 (Arabidopsis thaliana)
Explore Q9FUP0 
Go to UniProtKB:  Q9FUP0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FUP0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.702α = 90
b = 86.608β = 90
c = 123.583γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-04
    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: 2012-10-24
    Changes: Database references
  • Version 1.4: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description