Literature summary for 5.3.99.2 extracted from

Lim, S.M.; Chen, D.; Teo, H.; Roos, A.; Jansson, A.E.; Nyman, T.; Tresaugues, L.; Pervushin, K.; Nordlund, P.
Structural and dynamic insights into substrate binding and catalysis of human lipocalin prostaglandin D synthase (2013), J. Lipid Res., 54, 1630-1643.

Cloned(Commentary)

Cloned (Comment)	Organism
expression of C-terminally His6-tagged enzyme in Escherichia coli strain Rosetta BL21(DE3)	Homo sapiens

Crystallization (Commentary)

Crystallization (Comment)	Organism
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	Homo sapiens

Crystallization (Comment)

Organism

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

Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
(5Z,13E,15S)-9alpha,11alpha-epidioxy-15-hydroxyprosta-5,13-dienoate	Homo sapiens	-	(5Z,13E,15S)-9alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate	-	?

Organism

Organism	UniProt	Comment	Textmining
Homo sapiens	P41222	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant C-terminally His6-tagged enzyme from Escherichia coli strain Rosetta BL21(DE3) by nickel affinity chromatography and gel filtration	Homo sapiens

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
(5Z,13E,15S)-9alpha,11alpha-epidioxy-15-hydroxyprosta-5,13-dienoate	-	Homo sapiens	(5Z,13E,15S)-9alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate	-	?
(5Z,13E,15S)-9alpha,11alpha-epidioxy-15-hydroxyprosta-5,13-dienoate	i.e. prostaglandin H2, PGH2	Homo sapiens	(5Z,13E,15S)-9alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate	i.e. prostaglandin D2, PGD2	?
9,11-epoxymethano-prostaglandin H2	substrate analogue U44069	Homo sapiens	9,11-epoxymethano-prostaglandin D2	product analogue 12415	?

Subunits

Subunits	Comment	Organism
More	analysis of enzyme structure in complex with substrate analogue U44069, 9,11-epoxymethano-PGH2, and in ligand-free form, NMR analysis, overview. The enzyme overall structure shows the classical lipocalin fold comprising an eight-stranded beta-barrel with two alpha-helices. The ligand-bound and the ligand-free structures differ only in the Omega loop conformationss	Homo sapiens

Synonyms

Synonyms	Comment	Organism
L-PGDS	-	Homo sapiens
lipocalin prostaglandin D synthase	-	Homo sapiens

General Information

General Information	Comment	Organism
additional information	analysis of enzyme structure in complex with substrate analogue U44069, 9,11-epoxymethano-PGH2, and in ligand-free form. The catalytic Cys 65 thiol group occurs in two different conformations, each making a distinct hydrogen bond network to neighboring residues, mechanism of the cysteine nucleophile activation, and modelling of dynamics of protein-substrate and protein-product interactions, overview	Homo sapiens
physiological function	lipocalin prostaglandin D synthase regulates synthesis of an important inflammatory and signaling mediator, prostaglandin D2	Homo sapiens