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5.3.99.2: Prostaglandin-D synthase

This is an abbreviated version!
For detailed information about Prostaglandin-D synthase, go to the full flat file.

Word Map on EC 5.3.99.2

Reaction

(5Z,13E,15S)-9alpha,11alpha-epidioxy-15-hydroxyprosta-5,13-dienoate
=
(5Z,13E,15S)-9alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate

Synonyms

beta-Trace, Beta-trace protein, betaTP, glutathione dependent prostaglandine D2 synthase, Glutathione-dependent PGD synthetase, glutathione-dependent prostaglandin D2 synthase, Glutathione-independent PGD synthetase, H-PGDS, haematopoietic PGD synthase, haematopoietic prostaglandin D synthase, Hematopoietic prostaglandin D synthase, hematopoietic prostaglandin D2 synthase, HPGDS, Isomerase, prostaglanin R2 D-, L-PGDS, L-prostaglandin D synthase, L-type prostaglandin synthase, lipocalin prostaglandin D synthase, lipocalin type prostaglandin D synthase, lipocalin-prostaglandin D synthase, lipocalin-type PG D synthase, lipocalin-type PGD synthase, lipocalin-type Pgds, lipocalin-type prostaglandin d synthase, lipocalin-type prostaglandin D2 synthase, lipocaline-type prostaglandin D synthase, PGD synthase, PGD-S, PGD2 synthase, PGD2 synthetase, PGDS, PGDS2, PGH-PGD isomerase, PGH2 D-isomerase, Prostaglandin D synthase, Prostaglandin D2 synthase, prostaglandin D2 synthetase, prostaglandin synthase, Prostaglandin-D synthase, Prostaglandin-H2 D-isomerase, Prostaglandin-R-prostaglandin D isomerase, PTGDS

ECTree

     5 Isomerases
         5.3 Intramolecular oxidoreductases
             5.3.99 Other intramolecular oxidoreductases
                5.3.99.2 Prostaglandin-D synthase

Crystallization

Crystallization on EC 5.3.99.2 - Prostaglandin-D synthase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals of H-PGDS are first grown by hanging-drop vapor diffusion method with PEG6000 as the precipitant at 20°C in the presence of 5 mM Mg2+ and the native crystals are then soaked in the precipitant solution with a saturating concentration of 2-(2'-benzothiazolyl)-5-styryl-3-(4'-phthalhydrazyl) tetrazolium chloride for 2 weeks. Structure of the enzyme complexed with 2-(2'-benzothiazolyl)-5-styryl-3-(4'-phthalhydrazyl) tetrazolium chloride at 1.9 A resolution in the presence of Mg2+. The styryl group of the inhibitor penetrates to the bottom of the active site cleft, and the tetrazole ring is stabilized by the stacking interaction with TRp104, inducing large movement around the alpha5-helix, which causes the space group of the complex crystal to change from P2(1) to P1 upon binding of 2-(2'-benzothiazolyl)-5-styryl-3-(4'-phthalhydrazyl) tetrazolium chloride
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H-PGDS is crystallized in a microgravity environment at 20°C, using 30% (w/v) PEG 6000, 10 mM dithiothreitol, 10 mM glutathione, 1% (v/v) dioxane and 1 mM magnesium chloride in 50 mM Tris-HCl pH 8.4
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hanging drop vapor diffusion method, using 0.1 M MES/NaOH at pH 6.5, 0.005 M MgCl2 and 24% (w/v) PEG 3350
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macro-seeding using a solution containing 14% polyethylene glycol 6000, 50 mM Tris-HCl, pH 8.4, 5 mM reduced glutathione, 5 mM dithiothreitol, 2.5 mM CaCl2 or MgCl2 and 1% dioxane, structure resolution at 1.8 A
mutant C65A in complex with oleic acid and palmitoleic acid, hanging drop vapor diffusion method, using 0.1 M citric acid (pH 4.0) and 1.7 M ammonium sulfate
mutant enzymes C65A/K59A, C65A, C65A/W54F, C65A/W112F and C65A/W54F/W112F hanging drop vapor diffusion method, using 0.2 M ammonium sulfate, 30% (w/v) PEG 4000
purified His-tagged recombinant enzyme, in complex with 9,11-epoxymethano prostaglandin H2, hanging drop vapor diffusion method, condition A: 0.1 M potassium thiocyanate and 30% PEG-MME 2000 in 1:1 protein-reservoir ratio, 5 days, 4°C, condition B: 1.4 M tri-sodium citrate, pH 6.5, using a similar method except in 2:1 protein-reservoir ratio. Micro-crystals from condition A are used to seed crystallization of ligand-free L-PGDS in the same condition but in the absence of SA U44069. Cryoprotection of condition A crystals using reservoir with 25% glycerol added, while crystals from condition B are cryo-protected with 1.6 M tri-sodium citrate solution. X-ray diffraction structure analysis at 1.88-2.09 A resolution
the structure of H-PGDS in complex with GSH and nocodazole is solved to a resolution of 1.9 A
mutant DELTA1-24_C65A L-PGDS is crystallized in two different crystal forms representing the conformational change between the open and closed states of the cavity of the beta-barrel, the structures are determined to resolutions of 2.1 and 2.0 A
NMR solution structure, enzyme consists 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 forms a hydrophobic cavity containing two pockets. Prostaglandin H2 almost fully occupies hydrophilic pocket 1, in which C65 is located, and all-trans retinoic acid occupies hydrophilic pocket 2
in complex with glutathione, sitting drop vapor diffusion method, using 0.1 M Tris-HCl, pH 8.0, 28% (w/v) PEG4000
recombinant enzyme
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