PDBsum entry 2czu

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protein Protein-protein interface(s) links
Isomerase PDB id
Protein chains
153 a.a. *
Waters ×106
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Lipocalin-type prostaglandin d synthase
Structure: Prostaglandin-h2 d-isomerase. Chain: a, b. Synonym: lipocalin-type prostaglandin-d synthase, glutathio independent pgd synthetase, prostaglandin-h2 d-isomerase, p synthase, ptgds, pgds. Engineered: yes. Mutation: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562
2.10Å     R-factor:   0.245     R-free:   0.279
Authors: T.Kumasaka,D.Irikura,H.Ago,K.Aritake,M.Yamamoto,T.Inoue,M.Mi Y.Urade,O.Hayaishi,Riken Structural Genomics/proteomics Ini (Rsgi)
Key ref:
T.Kumasaka et al. (2009). Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase. J Biol Chem, 284, 22344-22352. PubMed id: 19546224 DOI: 10.1074/jbc.M109.018341
17-Jul-05     Release date:   03-Oct-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O09114  (PTGDS_MOUSE) -  Prostaglandin-H2 D-isomerase
189 a.a.
153 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Prostaglandin-D synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (5Z,13E,15S)-9-alpha,11-alpha-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E,15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
= (5Z,13E,15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
      Cofactor: Glutathione
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   11 terms 
  Biological process     negative regulation of male germ cell proliferation   9 terms 
  Biochemical function     transporter activity     6 terms  


    Added reference    
DOI no: 10.1074/jbc.M109.018341 J Biol Chem 284:22344-22352 (2009)
PubMed id: 19546224  
Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase.
T.Kumasaka, K.Aritake, H.Ago, D.Irikura, T.Tsurumura, M.Yamamoto, M.Miyano, Y.Urade, O.Hayaishi.
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.
  Selected figure(s)  
Figure 4.
Superimposed models of the crystal structures of Δ^1–24-C65A L-PGDS with the NMR structures of the Δ^1–24-C89A/C186A L-PGDS (A) and with the SAXS molecular envelope of mouse L-PGDS (B). The crystal structures of the open (pink) and closed (sky blue) forms of Δ^1–24-C65A l-pgds in schematic models are superimposed on 15 NMR structures of the Δ^1–24-C89A/C186A l-pgds in hair ribbon models (PDB code 2E4J) (43) or a transparent surface model of mouse apo-l-pgds by SAXS (44). Phe^34, Trp^54, Pro^110, and Cys^89–Cys^186 residues are represented by stick models with transparent spheres in A. (Color codes are the same as in Fig. 1A).
Figure 5.
Docking model of PGH[2] to the catalytic pocket of L-PGDS (A) and the proposed catalytic mechanism of L-PGDS (B). See “Discussion” for detailed description.
  The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2009, 284, 22344-22352) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21482803 M.Griesser, T.Suzuki, N.Tejera, S.Mont, W.E.Boeglin, A.Pozzi, and C.Schneider (2011).
Biosynthesis of hemiketal eicosanoids by cross-over of the 5-lipoxygenase and cyclooxygenase-2 pathways.
  Proc Natl Acad Sci U S A, 108, 6945-6950.  
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