5MED

Cyanothece lipoxygenase 2 (CspLOX2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Lipoxygenase 2 from Cyanothece sp. controls dioxygen insertion by steric shielding and substrate fixation.

Newie, J.Neumann, P.Werner, M.Mata, R.A.Ficner, R.Feussner, I.

(2017) Sci Rep 7: 2069-2069

  • DOI: 10.1038/s41598-017-02153-w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The biological function of lipoxygenases depends on the regio and stereo specific formation of fatty acid-derived hydroperoxides and different concepts exist to explain the mechanism that directs dioxygen to a specific carbon atom within the substrat ...

    The biological function of lipoxygenases depends on the regio and stereo specific formation of fatty acid-derived hydroperoxides and different concepts exist to explain the mechanism that directs dioxygen to a specific carbon atom within the substrate. Here, we report the 1.8 Å resolution crystal structure of a cyanobacterial lipoxygenase that produces bis-allylic hydroperoxides (CspLOX2). Site directed mutagenesis experiments combined with computational approaches reveal that residues around the active site direct dioxygen to a preferred carbon atom and stereo configuration in the substrate fatty acid. Modulating the cavity volume around the pentadiene system of linoleic acid shifted the product formation towards 9S-, 9R-, 13S- or 13R-hydroperoxides in correlation with the site of mutation, thus decreasing the amount of the bis-allylic 11R-hydroperoxide. Decreasing the channel size of a 9R-lipoxygenase (CspLOX1) on the other hand could in turn induce formation of the bis-allylic 11R-hydroperoxide. Together this study suggests that an active site clamp fixing the pentadiene system of the substrate together with steric shielding controls the stereo and regio specific positioning of dioxygen at all positions of the reacting pentadiene system of substrate fatty acids.


    Organizational Affiliation

    University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany. ifeussn@uni-goettingen.de.,University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.,University of Goettingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Plant Biochemistry, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany. ifeussn@uni-goettingen.de.,University of Goettingen, Institute for Physical Chemistry, Tammannstr. 6, 37077, Goettingen, Germany.,University of Goettingen, Institute of Microbiology and Genetics, Department of Molecular Structural Biology, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.,University of Goettingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Plant Biochemistry, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arachidonate 15-lipoxygenase
A, B
569Rippkaea orientalis (strain PCC 8801)Mutation(s): 0 
EC: 1.13.11.33
Find proteins for B7JX99 (Rippkaea orientalis (strain PCC 8801))
Go to UniProtKB:  B7JX99
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POL
Query on POL

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A, B
N-PROPANOL
1-PROPONOL
C3 H8 O
BDERNNFJNOPAEC-UHFFFAOYSA-N
 Ligand Interaction
HEZ
Query on HEZ

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A
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
BU1
Query on BU1

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A, B
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PGR
Query on PGR

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A, B
R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N
 Ligand Interaction
1BO
Query on 1BO

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B
1-BUTANOL
BUTAN-1-OL
C4 H10 O
LRHPLDYGYMQRHN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
PDO
Query on PDO

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B
1,3-PROPANDIOL
C3 H8 O2
YPFDHNVEDLHUCE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.500α = 90.00
b = 165.400β = 90.00
c = 166.210γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release