1IK3

LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH 13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Three-dimensional structure of a purple lipoxygenase.

Skrzypczak-Jankun, E.Bross, R.A.Carroll, R.T.Dunham, W.R.Funk, M.O.

(2001) J.Am.Chem.Soc. 123: 10814-10820


  • PubMed Abstract: 
  • Polyunsaturated fatty acid metabolism is governed primarily by two enzymes, prostaglandin H synthase and lipoxygenase. The crystal structure of the metastable product-oxidized purple form of soybean lipoxygenase-3 was determined at 2.0 A resolution. ...

    Polyunsaturated fatty acid metabolism is governed primarily by two enzymes, prostaglandin H synthase and lipoxygenase. The crystal structure of the metastable product-oxidized purple form of soybean lipoxygenase-3 was determined at 2.0 A resolution. The data reveal that the chromophore corresponds to an iron-peroxide complex, a potential intermediate in the catalyzed reaction. A significant alteration of the iron site accompanies the formation of the complex. The structure, the first for a fatty acid-lipoxygenase complex, also reveals an unexpected mode of binding, and identifies amino acid residues that may play significant roles in catalysis, regio- and stereoselectivity.


    Related Citations: 
    • 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
    • Curcumin Inhibits Lipoxygenase by Binding to its Central Cavity: Theoretical and X-Ray Evidence.
      Skrzypczak-Jankun, E.,Mccabe, N.P.,Selman, S.H.,Jankun, J.
      (2000) INT.J.MOL.MED. 6: 521
    • 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 29: 15


    Organizational Affiliation

    Department of Chemistry, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA. ejankun@protein.wo.utoledo.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LIPOXYGENASE-3
A
857Glycine maxMutation(s): 0 
Gene Names: LOX1.3 (LOX3)
EC: 1.13.11.58
Find proteins for P09186 (Glycine max)
Go to UniProtKB:  P09186
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9OH
Query on 9OH

Download SDF File 
Download CCD File 
A
(TRANS-12,13-EPOXY)-9-HYDROXY-10(E)-OCTADECENOIC ACID
C18 H32 O4
WCCLYKMJXGYGEN-WFZKJPOOSA-N
 Ligand Interaction
13S
Query on 13S

Download SDF File 
Download CCD File 
A
13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID
C18 H32 O4
JDSRHVWSAMTSSN-IRQZEAMPSA-N
 Ligand Interaction
13R
Query on 13R

Download SDF File 
Download CCD File 
A
13(R)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID
C18 H32 O4
JDSRHVWSAMTSSN-PIHGWCCBSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
11O
Query on 11O

Download SDF File 
Download CCD File 
A
(TRANS-12,13-EPOXY)-11-HYDROXY-9(Z)-OCTADECENOIC ACID
C18 H32 O4
UZCLYICSWADYGM-RXWDXHPSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.650α = 90.00
b = 137.280β = 95.56
c = 61.890γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Advisory, Refinement description