1PD2

CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPLEX WITH GLUTATHIONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Cloning and crystal structure of hematopoietic prostaglandin D synthase.

Kanaoka, Y.Ago, H.Inagaki, E.Nanayama, T.Miyano, M.Kikuno, R.Fujii, Y.Eguchi, N.Toh, H.Urade, Y.Hayaishi, O.

(1997) Cell 90: 1085-1095


  • PubMed Abstract: 
  • Hematopoietic prostaglandin (PG) D synthase is the key enzyme for production of the D and J series of prostanoids in the immune system and mast cells. We isolated a cDNA for the rat enzyme, crystallized the recombinant enzyme, and determined the thre ...

    Hematopoietic prostaglandin (PG) D synthase is the key enzyme for production of the D and J series of prostanoids in the immune system and mast cells. We isolated a cDNA for the rat enzyme, crystallized the recombinant enzyme, and determined the three-dimensional structure of the enzyme complexed with glutathione at 2.3 A resolution. The enzyme is the first member of the sigma class glutathione S-transferase (GST) from vertebrates and possesses a prominent cleft as the active site, which is never seen among other members of the GST family. The unique 3-D architecture of the cleft leads to the putative substrate binding mode and its catalytic mechanism, responsible for the specific isomerization from PGH2 to PGD2.


    Related Citations: 
    • Erratum. Cloning and Crystal Structure of Hematopoietic Prostaglandin D Synthase
      Kanaoka, Y.,Ago, H.,Inagaki, E.,Nanayama, T.,Miyano, M.,Kikuno, R.,Fujii, Y.,Eguchi, N.,Toh, H.,Urade, Y.,Hayaishi, O.
      (1999) Cell 96: 449


    Organizational Affiliation

    Department of Molecular Behavioral Biology, Osaka Bioscience Institute, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
1, 2
199Rattus norvegicusGene Names: Hpgds (Gsts, Pgds, Ptgds2)
EC: 5.3.99.2, 2.5.1.18
Find proteins for O35543 (Rattus norvegicus)
Go to UniProtKB:  O35543
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSH
Query on GSH

Download SDF File 
Download CCD File 
1, 2
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.204 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 56.500α = 90.00
b = 56.500β = 90.00
c = 233.400γ = 120.00
Software Package:
Software NamePurpose
WEISdata scaling
PHASESphasing
WEISdata reduction
X-PLORrefinement
ROTAVATAdata scaling
CCP4data scaling
ROTAVATAdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-12-14 
  • Released Date: 1999-10-13 
  • Deposition Author(s): Miyano, M., Ago, H.

Revision History 

  • Version 1.0: 1999-10-13
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-12-14
    Type: Non-polymer description
  • Version 1.4: 2017-10-04
    Type: Refinement description