Title : Crystal structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity
Abstract :
The enzyme acid sphingomyelinase-like phosphodiesterase 3B ( SMPDL3B ) was shown to act as a negative regulator of innate immune signaling, affecting cellular lipid com position 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