Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase.
Lipocalin type prostaglandin D synthase (L-PGDS) is a multifunctional protein acting as a somnogen (PGD2)-producing enzyme, an extracellular transporter of various lipophilic ligands, and an amyloid-beta chaperone in human cerebrospinal fluid. In this study, we determined the crystal structures of two different conformers of mouse L-PGDS, one with an open cavity of the beta-barrel and the other with a closed cavity due to the movement of the flexible E-F loop. The upper compartment of the central large cavity contains the catalytically essential Cys65 residue and its network of hydrogen bonds with the polar residues Ser45, Thr67, and Ser81, whereas the lower compartment is composed of hydrophobic amino acid residues that are highly conserved among other lipocalins. SH titration analysis combined with site-directed mutagenesis revealed that the Cys65 residue is activated by its interaction with Ser45 and Thr67 and that the S45A/T67A/S81A mutant showed less than 10% of the L-PGDS activity. The conformational change between the open and closed states of the cavity indicates that the mobile calyx contributes to the multiligand binding ability of L-PGDS.
Kumasaka
Takashi
T
Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, Kouto, Sayo, Hyogo 679-5148, Japan.
Aritake
Kosuke
K
Department of Molecular and Behavioral Biology, Osaka Bioscience Institute, Furuedai, Suita, Osaka 565-0874, Japan.
Ago
Hideo
H
Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, Kouto, Sayo, Hyogo 679-5148, Japan.
Irikura
Daisuke
D
Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, Kouto, Sayo, Hyogo 679-5148, Japan; Department of Molecular and Behavioral Biology, Osaka Bioscience Institute, Furuedai, Suita, Osaka 565-0874, Japan.
Tsurumura
Toshiharu
T
Department of Molecular and Behavioral Biology, Osaka Bioscience Institute, Furuedai, Suita, Osaka 565-0874, Japan.
Yamamoto
Masaki
M
Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, Kouto, Sayo, Hyogo 679-5148, Japan.
Miyano
Masashi
M
Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, Kouto, Sayo, Hyogo 679-5148, Japan.
Urade
Yoshihiro
Y
Department of Molecular and Behavioral Biology, Osaka Bioscience Institute, Furuedai, Suita, Osaka 565-0874, Japan.
Hayaishi
Osamu
O
Department of Molecular and Behavioral Biology, Osaka Bioscience Institute, Furuedai, Suita, Osaka 565-0874, Japan.
D016229:Amyloid beta-Peptides / Q000378:metabolism; D000818:Animals; D002384:Catalysis; D018360:Crystallography, X-Ray / Q000379:methods; D003545:Cysteine / Q000737:chemistry; D004926:Escherichia coli / Q000378:metabolism; D019746:Intramolecular Oxidoreductases / Q000378:metabolism / Q000502:physiology*; D054834:Lipocalins / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology; D051379:Mice; D008958:Models, Molecular; D008968:Molecular Conformation; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D011487:Protein Conformation; D017433:Protein Structure, Secondary
D016229:Amyloid beta-Peptides; D054834:Lipocalins; D019746:Intramolecular Oxidoreductases; C022466:prostaglandin R2 D-isomerase; D003545:Cysteine