2P0M

Revised structure of rabbit reticulocyte 15S-lipoxygenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:1LOX


Literature

Conformational flexibility in mammalian 15S-lipoxygenase: Reinterpretation of the crystallographic data.

Choi, J.Chon, J.K.Kim, S.Shin, W.

(2008) Proteins 70: 1023-1032

  • DOI: 10.1002/prot.21590
  • Primary Citation of Related Structures:  
    2P0M

  • PubMed Abstract: 
  • Lipoxygenases (LOXs) are a family of nonheme iron dioxygenases that catalyze the regioselective and stereospecific hydroperoxidation of polyunsaturated fatty acids, and are involved in a variety of inflammatory diseases and cancers. The crystal struc ...

    Lipoxygenases (LOXs) are a family of nonheme iron dioxygenases that catalyze the regioselective and stereospecific hydroperoxidation of polyunsaturated fatty acids, and are involved in a variety of inflammatory diseases and cancers. The crystal structure of rabbit 15S-LOX1 that was reported by Gillmor et al. in 1997 has played key roles for understanding the properties of mammalian LOXs. In this structure, three segments, including 12 residues in the superficial alpha2 helix, are absent and have usually been described as "disordered." By reinterpreting the original crystallographic data we were able to elucidate two different conformations of the molecule, both having well ordered alpha2 helices. Surprisingly, one molecule contained an inhibitor and the other did not, thereby adopting a closed and an open form, respectively. They differed in the conformation of the segments that were absent in the original structure, which is highlighted by a 12 A movement of alpha2. Consequently, they showed a difference in the size and shape of the substrate-binding cavity. The new model should provide new insight into the catalytic mechanism involving induced conformational change of the binding pocket. It may also be helpful for the structure-based design of LOX inhibitors.


    Related Citations: 
    • The structure of mammalian 15-lipoxygenase reveals similarity to the lipases and the determinants of substrate specificity
      Gillmor, S.A., Villasenor, A., Fletterick, R., Sigal, E., Browner, M.F.
      (1997) Nat Struct Biol 4: 1003

    Organizational Affiliation

    Department of Chemistry, Seoul National University, Seoul, Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arachidonate 15-lipoxygenaseAB662Oryctolagus cuniculusMutation(s): 0 
Gene Names: ALOX15
EC: 1.13.11.33 (PDB Primary Data), 1.13.11.31 (UniProt), 1.13.11 (UniProt), 1.13.11.12 (UniProt)
Find proteins for P12530 (Oryctolagus cuniculus)
Explore P12530 
Go to UniProtKB:  P12530
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RS7
Query on RS7

Download CCD File 
B
(2E)-3-(2-OCT-1-YN-1-YLPHENYL)ACRYLIC ACID
C17 H20 O2
KRDSGPLHVQJFLM-BUHFOSPRSA-N
 Ligand Interaction
FE2
Query on FE2

Download CCD File 
A, B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 198.9α = 90
b = 198.9β = 90
c = 136.1γ = 120
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2011-09-28
    Changes: Other