3RDE

Crystal structure of the catalytic domain of porcine leukocyte 12-lipoxygenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of 12-lipoxygenase catalytic-domain-inhibitor complex identifies a substrate-binding channel for catalysis.

Xu, S.Mueser, T.C.Marnett, L.J.Funk, M.O.

(2012) Structure 20: 1490-1497

  • DOI: 10.1016/j.str.2012.06.003
  • Primary Citation of Related Structures:  
    3RDE

  • PubMed Abstract: 
  • Lipoxygenases are critical enzymes in the biosynthesis of families of bioactive lipids including compounds with important roles in the initiation and resolution of inflammation and in associated diseases such as diabetes, cardiovascular disease, and ...

    Lipoxygenases are critical enzymes in the biosynthesis of families of bioactive lipids including compounds with important roles in the initiation and resolution of inflammation and in associated diseases such as diabetes, cardiovascular disease, and cancer. Crystals diffracting to high resolution (1.9 Å) were obtained for a complex between the catalytic domain of leukocyte 12-lipoxygenase and the isoform-specific inhibitor, 4-(2-oxapentadeca-4-yne)phenylpropanoic acid (OPP). In the three-dimensional structure of the complex, the inhibitor occupied a new U-shaped channel open at one end to the surface of the protein and extending past the redox-active iron site that is essential for catalysis. In models, the channel accommodated arachidonic acid, defining the binding site for the substrate of the catalyzed reaction. There was a void adjacent to the OPP binding site connecting to the surface of the enzyme and providing a plausible access channel for the other substrate, oxygen.


    Organizational Affiliation

    Department of Chemistry, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arachidonate 12-lipoxygenase, 12S-typeABCD573Sus scrofaMutation(s): 3 
Gene Names: ALOX12ALOX15
EC: 1.13.11.31 (PDB Primary Data), 1.13.11.33 (UniProt), 1.13.11 (UniProt), 1.13.11.12 (UniProt)
Find proteins for P16469 (Sus scrofa)
Explore P16469 
Go to UniProtKB:  P16469
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OYP
Query on OYP

Download CCD File 
A, B, C, D
3-{4-[(tridec-2-yn-1-yloxy)methyl]phenyl}propanoic acid
C23 H34 O3
RYRHYCDBTFUGMI-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download CCD File 
A, B, C, D
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OYPIC50 :  35   nM  PDBBind
OYPIC50:  35   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.45α = 90
b = 181.54β = 92.86
c = 91.61γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-06-20
    Changes: Database references
  • Version 1.2: 2012-08-01
    Changes: Database references
  • Version 1.3: 2012-09-26
    Changes: Database references