1JNQ

LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH EPIGALLOCATHECHIN (EGC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of lipoxygenase by (-)-epigallocatechin gallate: X-ray analysis at 2.1 A reveals degradation of EGCG and shows soybean LOX-3 complex with EGC instead.

Skrzypczak-Jankun, E.Zhou, K.Jankun, J.

(2003) INT.J.MOL.MED. 12: 415-420


  • PubMed Abstract: 
  • Lipoxygenases (LOXs) are non-heme iron containing enzymes ubiquitous in nature and participating in the metabolism of the polyunsaturated fatty acids (PUFA). They are capable of combining their dioxygenase activity with its co-oxidative activity mani ...

    Lipoxygenases (LOXs) are non-heme iron containing enzymes ubiquitous in nature and participating in the metabolism of the polyunsaturated fatty acids (PUFA). They are capable of combining their dioxygenase activity with its co-oxidative activity manifesting itself in biotransformation reactions catalyzed by LOXs for other than PUFA small molecules. LOXs involvement in inflammatory diseases and cancer have been well documented. Catechins are the natural flavonoids of known inhibitory activity toward dioxygenases with a potential to be utilized in disease prevention and treatment. This work presents results obtained from an X-ray analysis of (-)-epigallocatechin gallate (EGCG) interacting with soybean lipoxygenase-3. The 3D structure of the resulting complex reveals the inhibitor depicting (-)-epigallo-catechin that lacks galloyl moiety. The A-ring is near the iron co-factor, attached by the hydrogen bond to the C-terminus of the enzyme, and the B-ring hydroxyl groups participate in the hydrogen bonds and the van der Waals interactions formed by the surrounding amino acids and water molecules.


    Related Citations: 
    • Why Drinking Green Tea Could Prevent Cancer
      Jankun, J.,Selman, S.H.,Swiercz, R.,Skrzypczak-Jankun, E.
      (1997) Nature 387: 561
    • Structural and Thermochemical Characterization of Lipoxygenase-Catechol Complexes
      Pham, C.,Jankun, J.,Skrzypczak_Jankun, E.,Flowers II, R.A.,Funk Jr., M.O.
      (1998) Biochemistry 37: 17952
    • Position 713 is Critical for Catalysis But not Iron Binding in Soybean Lipoxygenase 3
      Kramer, J.A.,Johnson, K.R.,Dunham, W.R.,Sands, R.H.,Funk Jr., M.O.
      (1994) Biochemistry 33: 15017
    • Structure of Soybean Lipoxygenase L3 and a Comparison with its L1 Isoenzyme
      Skrzypczak-Jankun, E.,Amzel, L.M.,Kroa, B.A.,Funk Jr., M.O.
      (1997) Proteins: Struct.,Funct.,Genet. 29: 15


    Organizational Affiliation

    Urology Research Center, Medical College of Ohio, Toledo, OH 43614-5807, USA. eskrzypczak@mco.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
lipoxygenase-3
A
857Glycine maxGene Names: LOX1.3 (LOX3)
EC: 1.13.11.58
Find proteins for P09186 (Glycine max)
Go to UniProtKB:  P09186
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EGT
Query on EGT

Download SDF File 
Download CCD File 
A
2-(3,4,5-TRIHYDROXY-PHENYL)-CHROMAN-3,5,7-TRIOL
EPIGALLOCATECHIN
C15 H14 O7
XMOCLSLCDHWDHP-IUODEOHRSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.730α = 90.00
b = 137.270β = 95.53
c = 61.880γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
SCALEPACKdata scaling
DENZOdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance