5EK8

Crystal structure of a 9R-lipoxygenase from Cyanothece PCC8801 at 2.7 Angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a lipoxygenase from Cyanothece sp. may reveal novel features for substrate acquisition.

Newie, J.Andreou, A.Neumann, P.Einsle, O.Feussner, I.Ficner, R.

(2016) J.Lipid Res. 57: 276-287

  • DOI: 10.1194/jlr.M064980

  • PubMed Abstract: 
  • In eukaryotes, oxidized PUFAs, so-called oxylipins, are vital signaling molecules. The first step in their biosynthesis may be catalyzed by a lipoxygenase (LOX), which forms hydroperoxides by introducing dioxygen into PUFAs. Here we characterized Csp ...

    In eukaryotes, oxidized PUFAs, so-called oxylipins, are vital signaling molecules. The first step in their biosynthesis may be catalyzed by a lipoxygenase (LOX), which forms hydroperoxides by introducing dioxygen into PUFAs. Here we characterized CspLOX1, a phylogenetically distant LOX family member from Cyanothece sp. PCC 8801 and determined its crystal structure. In addition to the classical two domains found in plant, animal, and coral LOXs, we identified an N-terminal helical extension, reminiscent of the long α-helical insertion in Pseudomonas aeruginosa LOX. In liposome flotation studies, this helical extension, rather than the β-barrel domain, was crucial for a membrane binding function. Additionally, CspLOX1 could oxygenate 1,2-diarachidonyl-sn-glycero-3-phosphocholine, suggesting that the enzyme may act directly on membranes and that fatty acids bind to the active site in a tail-first orientation. This binding mode is further supported by the fact that CspLOX1 catalyzed oxygenation at the n-10 position of both linoleic and arachidonic acid, resulting in 9R- and 11R-hydroperoxides, respectively. Together these results reveal unifying structural features of LOXs and their function. While the core of the active site is important for lipoxygenation and thus highly conserved, peripheral domains functioning in membrane and substrate binding are more variable.


    Organizational Affiliation

    Albrecht-von-Haller Institute for Plant Sciences, Department of Plant Biochemistry, Georg-August-University Goettingen, 37077 Goettingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipoxygenase
A
668Cyanothece sp. (strain PCC 8801)Mutation(s): 0 
Find proteins for B7K2Q5 (Cyanothece sp. (strain PCC 8801))
Go to UniProtKB:  B7K2Q5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 121.166α = 90.00
b = 121.166β = 90.00
c = 234.673γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
ARPmodel building
XDSdata reduction
PHENIXrefinement
autoSHARPphasing
PDB_EXTRACTdata extraction
SHELXCDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
International Research Training Group (IRTG) 1422Germany--
Fonds of the Chemical Industry (FCI)Germany--
Goettingen Graduate School of Neurosciences and Molecular Biology (GGNB)Germany--

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-01-13
    Type: Database references
  • Version 1.2: 2016-02-10
    Type: Database references