Literature summary 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)
EC Number |
Cloned (Comment) |
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 (Comment) |
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, 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)
EC Number |
Natural Substrates |
Organism |
Comment (Nat. Sub.) |
Natural Products |
Comment (Nat. Pro.) |
Rev. |
Reac. |
---|
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 |
UniProt |
Comment |
Textmining |
---|
5.3.99.2 |
Homo sapiens |
P41222 |
- |
- |
Purification (Commentary)
EC Number |
Purification (Comment) |
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 |
Comment Substrates |
Organism |
Products |
Comment (Products) |
Rev. |
Reac. |
---|
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 |
- |
? |
|
5.3.99.2 |
(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 |
? |
|
5.3.99.2 |
9,11-epoxymethano-prostaglandin H2 |
substrate analogue U44069 |
Homo sapiens |
9,11-epoxymethano-prostaglandin D2 |
product analogue 12415 |
? |
|
Subunits
EC Number |
Subunits |
Comment |
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 |
Synonyms
EC Number |
Synonyms |
Comment |
Organism |
---|
5.3.99.2 |
L-PGDS |
- |
Homo sapiens |
5.3.99.2 |
lipocalin prostaglandin D synthase |
- |
Homo sapiens |
General Information
EC Number |
General Information |
Comment |
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 |