1ICQ

CRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO COMPLEXED WITH 9R,13R-OPDA

• PDB DOI:  https://doi.org/10.2210/pdb1ICQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Solanum lycopersicum
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2001-04-02 Released: 2001-05-16 
• Deposition Author(s): Breithaupt, C., Strassner, J., Breitinger, U., Huber, R., Macheroux, P., Schaller, A., Clausen, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.198 

Literature

X-ray structure of 12-oxophytodienoate reductase 1 provides structural insight into substrate binding and specificity within the family of OYE.

Breithaupt, C., Strassner, J., Breitinger, U., Huber, R., Macheroux, P., Schaller, A., Clausen, T.

(2001) Structure 9: 419-429

• PubMed: 11377202 
• DOI: https://doi.org/10.1016/s0969-2126(01)00602-5
• Primary Citation of Related Structures:  
  1ICP, 1ICQ, 1ICS


• PubMed Abstract: 
  

12-Oxophytodienoate reductase (OPR) is a flavin mononucleotide (FMN)-dependent oxidoreductase in plants that belongs to the family of Old Yellow Enzyme (OYE). It was initially characterized as an enzyme involved in the biosynthesis of the plant hormone jasmonic acid, where it catalyzes the reduction of the cyclic fatty acid derivative 9S,13S-12-oxophytodienoate (9S,13S-OPDA) to 1S,2S-3-oxo-2(2'[Z]-pentenyl)-cyclopentane-1-octanoate. Several isozymes of OPR are now known that show different stereoselectivities with regard to the four stereoisomers of OPDA.

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152, Martinsried, Germany. [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: 86.38 kDa 
• Atom Count: 5,973 
• Modelled Residue Count: 704 
• Deposited Residue Count: 752 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
12-OXOPHYTODIENOATE REDUCTASE 1	A, B	376	Solanum lycopersicum	Mutation(s): 1  Gene Names: OPR1 EC: 1.3.1.42
UniProt
Find proteins for Q9XG54 (Solanum lycopersicum) Explore Q9XG54  Go to UniProtKB:  Q9XG54

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
OPD	D [auth A], F [auth B]	9R,13R-12-OXOPHYTODIENOIC ACID C18 H28 O3 PMTMAFAPLCGXGK-HZPDHXFCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.198 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.583	α = 62.42
b = 72.759	β = 85.19
c = 72.616	γ = 79.96

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-05-16 
Deposition Author(s): Breithaupt, C., Strassner, J., Breitinger, U., Huber, R., Macheroux, P., Schaller, A., Clausen, T.

Revision History  

• Version 1.0: 2001-05-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-09
  Changes: Data collection, Refinement description