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Catalytic Site Atlas

CSA LITERATURE entry for 1pd2

E.C. nameglutathione transferase
SpeciesRattus norvegicus (Rat)
E.C. Number (IntEnz) 2.5.1.18
CSA Homologues of 1pd2
CSA Entries With UniProtID O35543
CSA Entries With EC Number 2.5.1.18
PDBe Entry 1pd2
PDBSum Entry 1pd2
MACiE Entry 1pd2

Literature Report

IntroductionHematopoietic prostaglandin-D synthase (H-PGDS) is a homodimer in an asymmetric unit. Each monomer is complexed with one glutathione (GTT or GSH) molecule. H-PGDS is one of two types of prostaglandin-D synthase (PGDS) that catalyses the isomerisation of PGH2 to PGD2. PGD2 is a lipid mediator produced by a variety of cells of the immune system, including Th2 and mast cells, that accelerates allergic and inflammatory responses, regulates body temperature, inhibits platelet aggregation, promotes sleep and numerous other physiological functions. H-PGDS is also a member of the glutathione S-transferase (GST) gene family, a group of enzymes that catalyse the conjugation of GSH to an electrophilic substrate.
Mechansim Bound GSH is deprotonated by the formation of a hydrogen bond of gamma-S (of GSH) to O atom of Tyr8. Isomerization is initiated when PGH2 binds to the cleft in H-PGDS (formed by 3 active site pockets), the thiolic anion of the (bound) deprotonated GSH performs nucleophilic attack on the C-11 oxygen of PGH2. Successive base attack on C-11 hydrogen by a deprotonated GSH found free in solution (GS-) causes O-S bond cleavage, forming C-11 carbonyl in a concerted, sterically-restricted manner. Hydrogen transfer to C-9 hydroxyanion from GSH results in the completion of PGD2 formation and in the recycling of GSH. The presence of Mg2+ can increase the affinity of H-PGDS for GSH and cause a four-fold decrease of the Km.
Reaction

Catalytic Sites for 1pd2

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
Trp1104104macie:sideChainThe indole ring forms van der Waals interactions with hydrophobic PGH2 substrate for binding. Trp104 is important in the structural integrity of the catalytic site by creating the 'kinked' backbone responsible for the formation of the deep and wide pocket for the substrate.
Tyr188macie:sideChainEssential for GSH thiol activation for nucleophilic attack on PGH2 peroxide. H-bonding of (bound) GSH S atom to Tyr8 O atom considered to decrease pKa of thiol group resulting in deprotonated S- anion at neutral pH.
Arg11414macie:sideChainAssists GSH activation for nucleophilic attack by forming salt bridge with alpha-glutamyl carboxyanion of (bound) GSH, neutralising negative charge and maintaining active configuration of GSH. Also facilitates PGH2 binding by H-bonding to the omega chain at C-15 of PGH2.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
Trp2104104macie:sideChainThe indole ring forms van der Waals interactions with hydrophobic PGH2 substrate for binding. Trp104 is important in the structural integrity of the catalytic site by creating the 'kinked' backbone responsible for the formation of the deep and wide pocket for the substrate.
Tyr288macie:sideChainEssential for GSH thiol activation for nucleophilic attack on PGH2 peroxide. H-bonding of (bound) GSH S atom to Tyr8 O atom considered to decrease pKa of thiol group resulting in deprotonated S- anion at neutral pH.
Arg21414macie:sideChainAssists GSH activation for nucleophilic attack by forming salt bridge with alpha-glutamyl carboxyanion of (bound) GSH, neutralising negative charge and maintaining active configuration of GSH. Also facilitates PGH2 binding by H-bonding to the omega chain at C-15 of PGH2.

Literature References

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