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

Abstract

Edited by Norma AllewellThe 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 structureguided 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.

Phosphodiesterase SMPDL3B Gene Expression as Independent Outcome Prediction Marker in Localized Prostate Cancer

“…This, to date, little described protein is an enzymatic component of the lipid rafts of cell membranes and appears to be involved in a wide variety of molecular processes including the sphingomyelin metabolism [ 8 ]. Besides its relevance for membrane fluidity and lipid composition, SMPDL3B has been identified as a negative regulator of the innate immune signaling [ 14 ]. In addition, SMPDL3B overexpression reduces cell apoptosis and strengthens the actin skeleton.…”

“…Furthermore, amino acid residues close to the active center of SMPDL3B have been identified. These can recognize endogenous molecules that modulate macrophage function [ 14 ]. Studies could show that decreased SMPDL3B levels lead to membrane disorder and a TLR-moderated hyperinflammatory cell phenotype [ 14 ].…”

“…These can recognize endogenous molecules that modulate macrophage function [ 14 ]. Studies could show that decreased SMPDL3B levels lead to membrane disorder and a TLR-moderated hyperinflammatory cell phenotype [ 14 ]. One could speculate that high concentrations of SMPDL3B lead to a higher membrane stability and thus less disruption of cytoskeleton-lipid raft assemblies promoting carcinogenesis [ 18 ].…”

Macrophage-derived thrombospondin 1 promotes obesity-associated non-alcoholic fatty liver disease

“…J o u r n a l P r e -p r o o f SMPDL3B is a glycosylphosphatidylinositol (GPI)-anchored membrane associated protein with homology to acid sphingomyelinase (ASMase) and involves in the sphingomyelin catabolic process 43 . It has been reported that SMPDL3B plays a role in podocyte injury from diabetic nephropathy or focal segmental glomerulosclerosis 44,45 .…”

Role of Sphingolipid Signaling in Glomerular Diseases: Focus on DKD and FSGS

“…SMPDL3b is a glycosylphosphatidylinositol (GPI)anchored protein [ 86 , 87 ] with reported roles in inflammatory processes [ 88 ] and in kidney diseases [ 6 , 40 , 85 ]. Recently, the crystal structure of murine SMPDL3b was revealed and helped to identify possible substrates for SMPDL3b, which included CDP-choline, ATP and ADP [ 89 ]. Sphingomyelin could also be a potential substrate for SMPDL3b.…”