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 

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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 cancer ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arachidonate 12-lipoxygenase, 12S-typeA, B, C, D573Sus scrofaMutation(s): 3 
Gene Names: ALOX12, ALOX15
EC: 1.13.11.31 (PDB Primary Data), 1.13.11.33 (UniProt), 1.13.11 (UniProt), 1.13.11.12 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P16469 (Sus scrofa)
Explore P16469 
Go to UniProtKB:  P16469
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
OYP PDBBind:  3RDE IC50: 35 (nM) from 1 assay(s)
BindingDB:  3RDE IC50: 35 (nM) from 1 assay(s)
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  (Full details and data files)

  • 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