2IUK

Crystal structure of Soybean Lipoxygenase-D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of Vegetative Soybean Lipoxygenase Vlx-B and Vlx-D, and Comparisons with Seed Isoforms Lox-1 and Lox-3.

Youn, B.Sellhorn, G.E.Mirchel, R.J.Gaffney, B.J.Grimes, H.D.Kang, C.

(2006) Proteins 65: 1008

  • DOI: 10.1002/prot.21182
  • Primary Citation of Related Structures:  
    2IUJ, 2IUK

  • PubMed Abstract: 
  • The lipoxygenase family of lipid-peroxidizing, nonheme iron dioxygenases form products that are precursors for diverse physiological processes in both plants and animals. In soybean (Glycine max), five vegetative isoforms, VLX-A, VLX-B, VLX-C, VLX-D, VLX-E, and four seed isoforms LOX-1, LOX-2, LOX-3a, LOX-3b have been identified ...

    The lipoxygenase family of lipid-peroxidizing, nonheme iron dioxygenases form products that are precursors for diverse physiological processes in both plants and animals. In soybean (Glycine max), five vegetative isoforms, VLX-A, VLX-B, VLX-C, VLX-D, VLX-E, and four seed isoforms LOX-1, LOX-2, LOX-3a, LOX-3b have been identified. In this study, we determined the crystal structures of the substrate-free forms of two major vegetative isoforms, with distinct enzymatic characteristics, VLX-B and VLX-D. Their structures are similar to the two seed isoforms, LOX-1 and LOX-3, having two domains with similar secondary structural elements: a beta-barrel N-terminal domain containing highly flexible loops and an alpha-helix-rich C-terminal catalytic domain. Detailed comparison of the structures of these two vegetative isoforms with the structures of LOX-1 and LOX-3 reveals important differences that help explain distinct aspects of the activity and positional specificity of these enzymes. In particular, the shape of the three branches of the internal subcavity, corresponding to substrate-binding and O(2) access, differs among the isoforms in a manner that reflects the differences in positional specificities.


    Organizational Affiliation

    School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SEED LIPOXYGENASEA, B864Glycine maxMutation(s): 0 
Gene Names: LOX1.4SC514
EC: 1.13.11.12 (PDB Primary Data), 1.13.11.58 (UniProt)
UniProt
Find proteins for P24095 (Glycine max)
Explore P24095 
Go to UniProtKB:  P24095
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24095
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.76α = 90
b = 115.1β = 112.34
c = 120.22γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-11
    Type: Initial release
  • Version 1.1: 2011-12-28
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2022-05-04
    Changes: Database references, Derived calculations