5LC8

Crystal Structure of specific mutant from Pseudomonas aeruginosa Lipoxygenase at 1.8A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of Pseudomonas aeruginosa lipoxygenase Ala420Gly mutant explains the improved oxygen affinity and the altered reaction specificity.

Kalms, J.Banthiya, S.Galemou Yoga, E.Hamberg, M.Holzhutter, H.G.Kuhn, H.Scheerer, P.

(2017) Biochim. Biophys. Acta 1862: 463-473

  • DOI: 10.1016/j.bbalip.2017.01.003

  • PubMed Abstract: 
  • Secreted LOX from Pseudomonas aeruginosa (PA-LOX) has previously been identified as arachidonic acid 15S-lipoxygenating enzyme. Here we report that the substitution of Ala420Gly in PA-LOX leads to an enzyme variant with pronounced dual specificity fa ...

    Secreted LOX from Pseudomonas aeruginosa (PA-LOX) has previously been identified as arachidonic acid 15S-lipoxygenating enzyme. Here we report that the substitution of Ala420Gly in PA-LOX leads to an enzyme variant with pronounced dual specificity favoring arachidonic acid 11R-oxygenation. When compared with other LOX-isoforms the molecular oxygen affinity of wild-type PA-LOX is 1-2 orders of magnitude lower (Km O 2 of 0.4mM) but Ala420Gly exchange improved the molecular oxygen affinity (Km O 2 of 0.2mM). Experiments with stereo-specifically deuterated linoleic acid indicated that the formation of both 13S- and 9R-HpODE involves abstraction of the proS-hydrogen from C11 of the fatty acid backbone. To explore the structural basis for the observed functional changes (altered specificity, improved molecular oxygen affinity) we solved the crystal structure of the Ala420Gly mutant of PA-LOX at 1.8Å resolution and compared it with the wild-type enzyme. Modeling of fatty acid alignment at the catalytic center suggested that in the wild-type enzyme dioxygen is directed to C15 of arachidonic acid by a protein tunnel, which interconnects the catalytic center with the protein surface. Ala420Gly exchange redirects intra-enzyme O 2 diffusion by bifurcating this tunnel so that C11 of arachidonic acid also becomes accessible for O 2 insertion.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.,Institute of Medical Physics and Biophysics (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charité - University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany.,Institute for Biochemistry (CC2), Charité - University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany.,Institute of Medical Physics and Biophysics (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charité - University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany. Electronic address: patrick.scheerer@charite.de.,Institute for Biochemistry (CC2), Charité - University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany. Electronic address: hartmut.kuehn@charite.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arachidonate 15-lipoxygenase
A
667Pseudomonas aeruginosaMutation(s): 0 
Gene Names: lox
EC: 1.13.11.12, 1.13.11.58
Find proteins for Q8RNT4 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q8RNT4
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZPE
Query on ZPE

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Download CCD File 
A
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradec-5-enoyloxy)propyl (11Z)-octadec-11-enoate
C37 H70 N O8 P
SWNDXEVFPWKPGK-SPZKJSGBSA-N
 Ligand Interaction
GOL
Query on GOL

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

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

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A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.139 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 84.332α = 90.00
b = 97.416β = 90.00
c = 155.599γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyUnicat - Research Field
German Research FoundationGermanyKu961/11-1
German Research FoundationGermanyGRK1673
German Research FoundationGermanySFB740-B6
German Research FoundationGermanySFB1078-B6

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Derived calculations