1N8Q

LIPOXYGENASE IN COMPLEX WITH PROTOCATECHUIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Lipoxygenase interactions with natural flavonoid, quercetin, reveal a complex with protocatechuic acid in its X-ray structure at 2.1 A resolution.

Borbulevych, O.Y.Jankun, J.Selman, S.H.Skrzypczak-Jankun, E.

(2004) PROTEINS: STRUCT.,FUNCT.,GENET. 54: 13-19

  • DOI: 10.1002/prot.10579

  • PubMed Abstract: 
  • PUFA metabolites have a profound effect on inflammatory diseases and cancer progression. Blocking their production by inhibiting PUFA metabolizing enzymes (dioxygenases: cyclooxygenases and LOXs) might be a successful way to control and relieve such ...

    PUFA metabolites have a profound effect on inflammatory diseases and cancer progression. Blocking their production by inhibiting PUFA metabolizing enzymes (dioxygenases: cyclooxygenases and LOXs) might be a successful way to control and relieve such problems, if we learn to better understand their actions at a molecular level. Compounds with strong antioxidative and free radical scavenging properties, such as polyphenols, could be effective in blocking PUFA activities, and natural flavonoids possess such qualities. Quercetin belongs to the group of natural catecholic compounds and is known as a potent, competitive inhibitor of LOX. Structural analysis reveals that quercetin entrapped within LOX undergoes degradation, and the resulting compound has been identified by X-ray analysis as protocatechuic acid (3,4-dihydroxybenzoic acid) positioned near the iron site. Its C3-OH group points toward His523, C4-OH forms a hydrogen bond with O=C from the enzyme's C-terminus, and the carboxylic group is incorporated into the hydrogen bonding network of the active-site neighborhood via Gln514. This unexpected result, together with our previous observations concerning other polyphenols, yields new evidence about the metabolism of natural flavonoids. These compounds might be vulnerable to the co-oxidase activity of LOX, leading to enzyme-stimulated oxidative degradation, which results in an inhibitor of a lower molecular weight.


    Related Citations: 
    • Curcumin inhibits lipoxygenase by binding to its central cavity: Theoretical and X-ray evidence
      Skrzypczak-Jankun, E.,McCabe, N.P.,Selman, S.H.,Jankun, J.
      (2000) Int.J.Mol.Med. 6: 521
    • Structural and thermochemical characterization of lipoxygenase-catechol complexes
      Pham, C.H.,Jankun, J.,Skrzypczak-Jankun, E.,Flowers II, R.A.,Funk Jr., M.O.
      (1998) Biochemistry 37: 17952


    Organizational Affiliation

    Medical College of Ohio, Urology Research Center, Department of Urology, Toledo, Ohio 43614, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
lipoxygenase-3
A
857Glycine maxGene Names: LOX1.3 (LOX3)
EC: 1.13.11.58
Find proteins for P09186 (Glycine max)
Go to UniProtKB:  P09186
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DHB
Query on DHB

Download SDF File 
Download CCD File 
A
3,4-DIHYDROXYBENZOIC ACID
C7 H6 O4
YQUVCSBJEUQKSH-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: 2.1 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.645α = 90.00
b = 136.961β = 95.48
c = 61.799γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CCP4phasing
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description
  • Version 1.4: 2018-01-24
    Type: Database references