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.

• PDB DOI: https://doi.org/10.2210/pdb2G5W/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-02-23 Released: 2006-04-04 
• Deposition Author(s): Han, B.W., Malone, T.E., Bingman, C.A., Wesenberg, G.E., Phillips Jr., G.N., Fox, B.G., Center for Eukaryotic Structural Genomics (CESG)

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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 

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

• PubMed: 21915915 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 87.07 kDa 
• Atom Count: 5,845 
• Modelled Residue Count: 729 
• Deposited Residue Count: 782 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
12-oxophytodienoate reductase 3	A, B	391	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At2g06050 EC: 1.3.1.42
UniProt
Find proteins for Q9FUP0 (Arabidopsis thaliana) Explore Q9FUP0  Go to UniProtKB:  Q9FUP0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], E [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
8PG	D [auth A], F [auth B]	(8S,12S)-15S-HYDROXY-9-OXOPROSTA-10Z,13E-DIEN-1-OIC ACID C20 H32 O4 BGKHCLZFGPIKKU-DRSVPBQLSA-N

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 = 79.702	α = 90
b = 86.608	β = 90
c = 123.583	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-04 
Deposition Author(s): Han, B.W., Malone, T.E., Bingman, C.A., Wesenberg, G.E., Phillips Jr., G.N., Fox, B.G., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• 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