3FG1

Crystal structure of Delta413-417:GS LOX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    3FG1, 3FG3, 3FG4

  • 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 substrate generate different products, can be used to help guide the design of enzyme-specific inhibitors ...

    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 Struct Biol Cryst Commun 63: 972

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Allene oxide synthase-lipoxygenase proteinA, B, C, D696Plexaura homomallaMutation(s): 2 
EC: 1.13.11.40 (PDB Primary Data), 4.2.1 (UniProt)
UniProt
Find proteins for O16025 (Plexaura homomalla)
Explore O16025 
Go to UniProtKB:  O16025
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO16025
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth C],
BB [auth C],
IA [auth B],
JA [auth B],
KA [auth B],
AB [auth C],
BB [auth C],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MB [auth D],
NB [auth D],
OB [auth D],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
WA [auth C],
X [auth A],
XA [auth C],
Y [auth A],
YA [auth C],
ZA [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
EA [auth B],
FA [auth B],
FB [auth D],
GA [auth B],
H [auth A],
EA [auth B],
FA [auth B],
FB [auth D],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IB [auth D],
J [auth A],
JB [auth D],
K [auth A],
KB [auth D],
L [auth A],
LB [auth D],
M [auth A],
N [auth A],
O [auth A],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C],
UA [auth C],
VA [auth C]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
CA [auth B],
E [auth A],
GB [auth D],
NA [auth C]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth A],
DA [auth B],
EB [auth C],
F [auth A],
G [auth A],
BA [auth A],
DA [auth B],
EB [auth C],
F [auth A],
G [auth A],
HB [auth D],
OA [auth C],
PA [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth A],
CB [auth C],
DB [auth C],
MA [auth B],
PB [auth D],
AA [auth A],
CB [auth C],
DB [auth C],
MA [auth B],
PB [auth D],
Z [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.982α = 90
b = 170.224β = 95.88
c = 104.497γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Advisory, Refinement description
  • Version 1.3: 2021-10-20
    Changes: Advisory, Database references, Derived calculations