BRENDA - Enzyme Database show

Structural and dynamic insights into substrate binding and catalysis of human lipocalin prostaglandin D synthase

Lim, S.M.; Chen, D.; Teo, H.; Roos, A.; Jansson, A.E.; Nyman, T.; Tresaugues, L.; Pervushin, K.; Nordlund, P.; J. Lipid Res. 54, 1630-1643 (2013)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
5.3.99.2
expression of C-terminally His6-tagged enzyme in Escherichia coli strain Rosetta BL21(DE3)
Homo sapiens
Crystallization (Commentary)
EC Number
Crystallization
Organism
5.3.99.2
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, 4C, 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)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
5.3.99.2
(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
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
5.3.99.2
Homo sapiens
P41222
-
-
Purification (Commentary)
EC Number
Commentary
Organism
5.3.99.2
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)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
5.3.99.2
(5Z,13E,15S)-9alpha,11alpha-epidioxy-15-hydroxyprosta-5,13-dienoate
-
728090
Homo sapiens
(5Z,13E,15S)-9alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
-
-
-
?
5.3.99.2
(5Z,13E,15S)-9alpha,11alpha-epidioxy-15-hydroxyprosta-5,13-dienoate
i.e. prostaglandin H2, PGH2
728090
Homo sapiens
(5Z,13E,15S)-9alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
i.e. prostaglandin D2, PGD2
-
-
?
5.3.99.2
9,11-epoxymethano-prostaglandin H2
substrate analogue U44069
728090
Homo sapiens
9,11-epoxymethano-prostaglandin D2
product analogue 12415
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
5.3.99.2
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
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
5.3.99.2
expression of C-terminally His6-tagged enzyme in Escherichia coli strain Rosetta BL21(DE3)
Homo sapiens
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
5.3.99.2
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, 4C, 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) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
5.3.99.2
(5Z,13E,15S)-9alpha,11alpha-epidioxy-15-hydroxyprosta-5,13-dienoate
Homo sapiens
-
(5Z,13E,15S)-9alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
5.3.99.2
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) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
5.3.99.2
(5Z,13E,15S)-9alpha,11alpha-epidioxy-15-hydroxyprosta-5,13-dienoate
-
728090
Homo sapiens
(5Z,13E,15S)-9alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
-
-
-
?
5.3.99.2
(5Z,13E,15S)-9alpha,11alpha-epidioxy-15-hydroxyprosta-5,13-dienoate
i.e. prostaglandin H2, PGH2
728090
Homo sapiens
(5Z,13E,15S)-9alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
i.e. prostaglandin D2, PGD2
-
-
?
5.3.99.2
9,11-epoxymethano-prostaglandin H2
substrate analogue U44069
728090
Homo sapiens
9,11-epoxymethano-prostaglandin D2
product analogue 12415
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
5.3.99.2
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
General Information
EC Number
General Information
Commentary
Organism
5.3.99.2
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
5.3.99.2
physiological function
lipocalin prostaglandin D synthase regulates synthesis of an important inflammatory and signaling mediator, prostaglandin D2
Homo sapiens
General Information (protein specific)
EC Number
General Information
Commentary
Organism
5.3.99.2
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
5.3.99.2
physiological function
lipocalin prostaglandin D synthase regulates synthesis of an important inflammatory and signaling mediator, prostaglandin D2
Homo sapiens