2CZU

lipocalin-type prostaglandin D synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase.

Kumasaka, T.Aritake, K.Ago, H.Irikura, D.Tsurumura, T.Yamamoto, M.Miyano, M.Urade, Y.Hayaishi, O.

(2009) J Biol Chem 284: 22344-22352

  • DOI: 10.1074/jbc.M109.018341
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Lipocalin type prostaglandin D synthase (L-PGDS) is a multifunctional protein acting as a somnogen (PGD2)-producing enzyme, an extracellular transporter of various lipophilic ligands, and an amyloid-beta chaperone in human cerebrospinal fluid. In thi ...

    Lipocalin type prostaglandin D synthase (L-PGDS) is a multifunctional protein acting as a somnogen (PGD2)-producing enzyme, an extracellular transporter of various lipophilic ligands, and an amyloid-beta chaperone in human cerebrospinal fluid. In this study, we determined the crystal structures of two different conformers of mouse L-PGDS, one with an open cavity of the beta-barrel and the other with a closed cavity due to the movement of the flexible E-F loop. The upper compartment of the central large cavity contains the catalytically essential Cys65 residue and its network of hydrogen bonds with the polar residues Ser45, Thr67, and Ser81, whereas the lower compartment is composed of hydrophobic amino acid residues that are highly conserved among other lipocalins. SH titration analysis combined with site-directed mutagenesis revealed that the Cys65 residue is activated by its interaction with Ser45 and Thr67 and that the S45A/T67A/S81A mutant showed less than 10% of the L-PGDS activity. The conformational change between the open and closed states of the cavity indicates that the mobile calyx contributes to the multiligand binding ability of L-PGDS.


    Related Citations: 
    • Cloning, expression, crystallization, and preliminary X-ray analysis of recombinant mouse lipocalin-type prostaglandin D synthase, a somnogen-producing enzyme
      Irikura, D., Kumasaka, T., Yamamoto, M., Ago, H., Miyano, M., Kubata, K.B., Sakai, H., Hayaishi, O., Urade, Y.
      (2003) J Biochem 133: 29
    • Lack of tactile pain (allodynia) in lipocalin-type prostaglandin D synthase-deficient mice
      Eguchi, N., Minami, T., Shirafuji, N., Kanaoka, Y., Tanaka, T., Nagata, A., Yoshida, N., Urade, Y., Ito, S., Hayaishi, O.
      (1999) Proc Natl Acad Sci U S A 96: 726

    Organizational Affiliation

    Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, Kouto, Sayo, Hyogo 679-5148, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prostaglandin-H2 D-isomerase
A, B
167Mus musculusMutation(s): 1 
Gene Names: Ptgds
EC: 5.3.99.2
Find proteins for O09114 (Mus musculus)
Go to UniProtKB:  O09114
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.2α = 90
b = 66.8β = 90
c = 105.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance