Crystal Structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity.
The enzyme acid sphingomyelinase-like phosphodiesterase 3B (SMPDL3B) was shown to act as a negative regulator of innate immune signaling, affecting cellular lipid composition and membrane fluidity. Furthermore, several reports identified this enzyme as an off target of the therapeutic antibody rituximab, with implications in kidney disorders. However, structural information for this protein is lacking. Here we present the high resolution crystal structure of murine SMPDL3B, which reveals a substrate binding site strikingly different from its paralogs. The active site is located in a narrow boot-shaped cavity. We identify a unique loop near the active site that appears to impose size constraints on incoming substrates. A structure in complex with phosphocholine indicates that the protein recognizes this head group via an aromatic box, a typical choline-binding motif. Although a potential substrate for SMPDL3B is sphingomyelin, we identify other possible substrates such as CDP-choline, ATP, and ADP. Functional experiments employing structure-guided mutagenesis in macrophages highlight amino acid residues potentially involved in recognition of endogenous substrates. Our study is an important step toward elucidating the specific function of this poorly characterized enzyme.
From the Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec H3G 0B1, Canada.
Alexei
A
Gorelik
the CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, 1090 Vienna, Austria, and.
Leonhard X
LX
Heinz
From the Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec H3G 0B1, Canada.
Katalin
K
Illes
the CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, 1090 Vienna, Austria, and.|the Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria.
Giulio
G
Superti-Furga
From the Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec H3G 0B1, Canada, bhushan.nagar@mcgill.ca.
Bhushan
B
Nagar
D000244:Adenosine Diphosphate / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000818:Animals; D002794:Choline / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018360:Crystallography, X-Ray; D054684:Cyclic Nucleotide Phosphodiesterases, Type 3 / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D051379:Mice; D000072417:Protein Domains; D017433:Protein Structure, Secondary; D061987:Sf9 Cells; D013109:Sphingomyelins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018411:Spodoptera; D013379:Substrate Specificity
D013109:Sphingomyelins; D000244:Adenosine Diphosphate; D000255:Adenosine Triphosphate; D054684:Cyclic Nucleotide Phosphodiesterases, Type 3; C000595964:sphingomyelinase-like phosphodiesterase 3b, mouse; D002794:Choline
SMPDL3B; cell surface enzyme; crystal structure; lipid metabolism; sphingomyelinase; substrate specificity
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