Crystal Structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity

J Biol Chem. 2016 Nov 11;291(46):24054-24064. doi: 10.1074/jbc.M116.755801. Epub 2016 Sep 28.


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.

Keywords: SMPDL3B; cell surface enzyme; crystal structure; lipid metabolism; sphingomyelinase; substrate specificity.

MeSH terms

  • Adenosine Diphosphate / chemistry
  • Adenosine Diphosphate / genetics
  • Adenosine Diphosphate / metabolism
  • Adenosine Triphosphate / chemistry
  • Adenosine Triphosphate / genetics
  • Adenosine Triphosphate / metabolism
  • Animals
  • Choline / chemistry
  • Choline / genetics
  • Choline / metabolism
  • Crystallography, X-Ray
  • Cyclic Nucleotide Phosphodiesterases, Type 3 / chemistry*
  • Cyclic Nucleotide Phosphodiesterases, Type 3 / genetics
  • Cyclic Nucleotide Phosphodiesterases, Type 3 / metabolism
  • Mice
  • Protein Domains
  • Protein Structure, Secondary
  • Sf9 Cells
  • Sphingomyelins / chemistry
  • Sphingomyelins / genetics
  • Sphingomyelins / metabolism
  • Spodoptera
  • Substrate Specificity


  • Sphingomyelins
  • Adenosine Diphosphate
  • Adenosine Triphosphate
  • Cyclic Nucleotide Phosphodiesterases, Type 3
  • sphingomyelinase-like phosphodiesterase 3b, mouse
  • Choline

Associated data

  • PDB/5KAR
  • PDB/5KAS
  • PDB/5FC6
  • PDB/5HQN