NMR solution structure of lipocalin-type prostaglandin D synthase: evidence for partial overlapping of catalytic pocket and retinoic acid-binding pocket within the central cavity

J Biol Chem. 2007 Oct 26;282(43):31373-9. doi: 10.1074/jbc.M700123200. Epub 2007 Aug 22.


Lipocalin-type prostaglandin (PG) D synthase (L-PGDS) catalyzes the isomerization of PGH(2), a common precursor of various prostanoids, to produce PGD(2), an endogenous somnogen and nociceptive modulator, in the brain. L-PGDS is a member of the lipocalin superfamily and binds lipophilic substances, such as retinoids and bile pigments, suggesting that L-PGDS is a dual functional protein acting as a PGD(2)-synthesizing enzyme and a transporter for lipophilic ligands. In this study we determined by NMR the three-dimensional structure of recombinant mouse L-PGDS with the catalytic residue Cys-65. The structure of L-PGDS exhibited the typical lipocalin fold, consisting of an eight-stranded, antiparallel beta-barrel and a long alpha-helix associated with the outer surface of the barrel. The interior of the barrel formed a hydrophobic cavity opening to the upper end of the barrel, the size of which was larger than those of other lipocalins, and the cavity contained two pockets. Molecular docking studies, based on the result of NMR titration experiments with retinoic acid and PGH(2) analog, revealed that PGH(2) almost fully occupied the hydrophilic pocket 1, in which Cys-65 was located and all-trans-retinoic acid occupied the hydrophobic pocket 2, in which amino acid residues important for retinoid binding in other lipocalins were well conserved. Mutational and kinetic studies provide the direct evidence for the PGH(2) binding mode. These results indicated that the two binding sites for PGH(2) and retinoic acid in the large cavity of L-PGDS were responsible for the broad ligand specificity of L-PGDS and the non-competitive inhibition of L-PGDS activity by retinoic acid.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Catalysis
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Intramolecular Oxidoreductases / chemistry*
  • Intramolecular Oxidoreductases / genetics
  • Intramolecular Oxidoreductases / metabolism*
  • Kinetics
  • Ligands
  • Lipocalins / chemistry*
  • Lipocalins / genetics
  • Lipocalins / metabolism*
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Nitrogen Isotopes / metabolism
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Protein Binding
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Secondary
  • Protons
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • Titrimetry
  • Tretinoin / chemistry*


  • Ligands
  • Lipocalins
  • Nitrogen Isotopes
  • Protons
  • Recombinant Proteins
  • Tretinoin
  • Intramolecular Oxidoreductases
  • prostaglandin R2 D-isomerase

Associated data

  • PDB/2E4J