1YGE

LIPOXYGENASE-1 (SOYBEAN) AT 100K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of soybean lipoxygenase L-1 at 1.4 A resolution.

Minor, W.Steczko, J.Stec, B.Otwinowski, Z.Bolin, J.T.Walter, R.Axelrod, B.

(1996) Biochemistry 35: 10687-10701

  • DOI: 10.1021/bi960576u
  • Also Cited By: 3PZW

  • PubMed Abstract: 
  • Lipoxygenases, which are widely distributed among plant and animal species, are Fe-containing dioxygenases that act on lipids containing (Z,Z)-pentadiene moieties in the synthesis of compounds with a variety of functions. Utilizing an improved strate ...

    Lipoxygenases, which are widely distributed among plant and animal species, are Fe-containing dioxygenases that act on lipids containing (Z,Z)-pentadiene moieties in the synthesis of compounds with a variety of functions. Utilizing an improved strategy of data collection, low temperature, and synchrotron radiation of short wavelength, the structure of ferrous soybean lipoxygenase L-1, a single chain protein of 839 amino acid residues, has been determined by X-ray crystallography to a resolution of 1.4 A. The R-factor for the refined model is 19.7%. General features of the protein structure were found to be consistent with the results of prior crystallographic studies at lower (2.6 A) resolution. In contrast to the prior studies, the binding of a water molecule to the active site Fe was established. The octahedral coordination sphere of the Fe also includes the side chains of His499, His504, His690, and Asn694 as well as the terminal carboxylate of Ile839, which binds as a monodentate ligand. Asn694 is involved in a number of labile polar interactions with other protein groups, including an amide-aromatic hydrogen bond, and appears to be a weak ligand. Several possible access routes for dioxygen and fatty acids to the internal active site and substrate binding cavity are described. The protein structure restricts access to the Fe site such that the formation of an organo-Fe intermediate seems improbable. Structural restrictions pertinent to other proposed reaction intermediates, such as planar pentadienyl and nonplanar allyl radicals, are also discussed.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Investigation of Lipoxygenase 1 from Soybeans
      Steczko, J.,Muchmore, C.R.,Smith, J.L.,Axelrod, B.
      (1990) J.Biol.Chem. 265: 11352
    • Conserved Histidine Residues in Soybean Lipoxygenase: Functional Consequences of Their Replacement
      Steczko, J.,Donoho, G.P.,Clemens, J.C.,Dixon, J.E.,Axelrod, B.
      (1992) Biochemistry 31: 4053
    • Spectroscopic Studies of the Non-Heme Ferric Active Site in Soybean Lipoxygenase: Magnetic Circular Dichroism as a Probe of Electronic and Geometric Structure. Ligand-Field Origin of Zero-Field
      Zhang, Y.,Gebhard, M.S.,Solomon, E.I.
      (1991) J.Am.Chem.Soc. 113: 5162
    • The Structure and Function of Lipoxygenase
      Nelson, M.J.,Seitz, S.P.
      (1994) Curr.Opin.Struct.Biol. 4: 878
    • Structural Characterization of Alkyl and Peroxyl Radicals in Solutions of Purple Lipoxygenase
      Nelson, M.J.,Cowling, R.A.,Seitz, S.P.
      (1994) Biochemistry 33: 4966
    • X-Ray Spectroscopy of the Iron Site in Soybean Lipoxygenase-1: Changes in Coordination Upon Oxidation or Addition of Methanol
      Scarrow, R.C.,Trimitsis, M.G.,Buck, C.P.,Grove, G.N.,Cowling, R.A.,Nelson, M.J.
      (1994) Biochemistry 33: 15023
    • Position 713 is Critical for Catalysis But not Iron Binding in Soybean Lipoxygenase
      Kramer, J.A.,Johnson, K.R.,Dunham, W.R.,Sands, R.H.,Funk Junior, M.O.
      (1994) Biochemistry 33: 15017
    • The Three-Dimensional Structure of an Arachidonic Acid 15-Lipoxygenase
      Boyington, J.C.,Gaffney, B.J.,Amzel, L.M.
      (1993) Science 260: 1482
    • Crystallographic Determination of the Active Site Iron and its Ligands in Soybean Lipoxygenase L-1
      Minor, W.,Steczko, J.,Bolin, J.T.,Otwinowski, Z.,Axelrod, B.
      (1993) Biochemistry 32: 6320


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LIPOXYGENASE-1
A
839Glycine maxGene Names: LOX1.1 (LOX1)
EC: 1.13.11.12
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Lipoxygenases
Protein: 
Lipoxygenase-L1 from soybeans
Find proteins for P08170 (Glycine max)
Go to UniProtKB:  P08170
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 94.900α = 90.00
b = 94.000β = 90.10
c = 49.900γ = 90.00
Software Package:
Software NamePurpose
HKLdata reduction
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance