3FG4

Crystal structure of Delta413-417:GS I805A LOX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 1.85 A structure of an 8R-lipoxygenase suggests a general model for lipoxygenase product specificity.

Neau, D.B.Gilbert, N.C.Bartlett, S.G.Boeglin, W.Brash, A.R.Newcomer, M.E.

(2009) Biochemistry 48: 7906-7915

  • DOI: 10.1021/bi900084m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lipoxygenases (LOX) play pivotal roles in the biosynthesis of leukotrienes and other biologically active eicosanoids derived from arachidonic acid. A mechanistic understanding of substrate recognition, when lipoxygenases that recognize the same subst ...

    Lipoxygenases (LOX) play pivotal roles in the biosynthesis of leukotrienes and other biologically active eicosanoids derived from arachidonic acid. A mechanistic understanding of substrate recognition, when lipoxygenases that recognize the same substrate generate different products, can be used to help guide the design of enzyme-specific inhibitors. We report here the 1.85 A resolution structure of an 8R-lipoxygenase from Plexaura homomalla, an enzyme with a sequence approximately 40% identical to that of human 5-LOX. The structure reveals a U-shaped channel, defined by invariant amino acids, that would allow substrate access to the catalytic iron. We demonstrate that mutations within the channel significantly impact enzyme activity and propose a novel model for substrate binding potentially applicable to other members of this enzyme family.


    Related Citations: 
    • Improving protein crystal quality by selective removal of a Ca(2+)-dependent membrane-insertion loop.
      Neau, D.B.,Gilbert, N.C.,Bartlett, S.G.,Dassey, A.,Newcomer, M.E.
      (2007) Acta Crystallogr.,Sect.F 63: 972


    Organizational Affiliation

    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Allene oxide synthase-lipoxygenase protein
A, B, C, D
696Plexaura homomallaMutation(s): 3 
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Lipoxygenases
Protein: 
8R-Lipoxygenase from coral
Find proteins for O16025 (Plexaura homomalla)
Go to UniProtKB:  O16025
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACD
Query on ACD

Download SDF File 
Download CCD File 
A, B, C, D
ARACHIDONIC ACID
C20 H32 O2
YZXBAPSDXZZRGB-DOFZRALJSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B, C, D
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A, B, C, D
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 104.361α = 90.00
b = 170.382β = 95.51
c = 104.900γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description