1LNH

LIPOXYGENASE-3(SOYBEAN) NON-HEME FE(II) METALLOPROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 15-31


  • PubMed Abstract: 
  • Soybean lipoxygenase isoenzyme L3 represents a second example (after L1) of the X-ray structure (R = 17% at 2.6 A resolution) for a member of the large family of lipoxygenases. L1 and L3 have different characteristics in catalysis, although they shar ...

    Soybean lipoxygenase isoenzyme L3 represents a second example (after L1) of the X-ray structure (R = 17% at 2.6 A resolution) for a member of the large family of lipoxygenases. L1 and L3 have different characteristics in catalysis, although they share 72% sequence identity (the changes impact 255 amino acids) and similar folding (average C alpha rms deviation of 1 A). The critical nonheme iron site has the same features as for L1:3O and 3N in pseudo C3v orientation, with two oxygen atoms (from Asn713 and water) at a nonbinding distance. Asn713 and His518 are strategically located at the junction of three cavities connecting the iron site with the molecule surface. The most visible differences between L1 and L3 isoenzymes occur in and near these cavities, affecting their accessibility and volume. Among the L1/L3 substitutions Glu256/ Thr274, Tyr409/His429, and Ser747/Asp766 affect the salt bridges (L1: Glu256...His248 and Asp490...Arg707) that in L1 restrict the access to the iron site from two opposite directions. The L3 molecule has a passage going through the whole length of the helical domain, starting at the interface with the Nt-domain (near 25-27 and 254-278) and going to the opposite end of the Ct-domain (near 367, 749). The substrate binding and the role of His513, His266, His776 (and other residues nearby) are illustrated and discussed by using models of linoleic acid binding. These hypotheses provide a possible explanation for a stringent stereo-specificity of catalytic products in L1 (that produces predominantly 13-hydroperoxide) versus the lack of such specificity in L3 (that turns out a mixture of 9- and 13-hydroperoxides and their diastereoisomers).


    Related Citations: 
    • Lipoxygenase-A Molecular Complex with a Non-Heme Iron
      Skrzypczak-Jankun, E.,Funk Junior, M.O.,Boyington, J.C.,Amzel, L.M.
      (1996) J.Mol.Struct. 374: 47
    • 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 Junior, M.O.
      (1994) Biochemistry 33: 15017
    • Crystallization and Preliminary X-Ray Characterization of a Soybean Seed Lipoxygenase
      Stallings, W.C.,Kroa, B.A.,Carroll, R.T.,Metzger, A.L.,Funk, M.O.
      (1990) J.Mol.Biol. 211: 685


    Organizational Affiliation

    Department of Chemistry, University of Toledo, Ohio 43606, USA. ejankun@uoft02.utoledo.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
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Lipoxygenases
Protein: 
Lipoxygenase-L3 from soybeans
Find proteins for P09186 (Glycine max)
Go to UniProtKB:  P09186
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 2.6 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.800α = 90.00
b = 137.400β = 95.50
c = 61.850γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
MSCdata reduction
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-02-02
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance