Structure of human nSMase2 reveals an interdomain allosteric activation mechanism for ceramide generation

Significance

Ceramide is a bioactive lipid involved in numerous cellular functions and disease states that are critically dependent on its site of generation. nSMase2 generates ceramide at the inner leaflet of the plasma membrane and is a therapeutic target for cancer and neurological disorders. Although much is known about the cellular functions of nSMase2, there is limited insight into the molecular mechanisms regulating its activity. Here we present the crystal structure of nSMase2 and identify the lipid-binding N-terminal domain as an allosteric activation domain. Key to activation is a catalytic motif termed the “DK switch,” whose conformation is allosterically gated. This study reveals one mechanism for nSMase2 regulation by lipids and will help guide structure-based development of nSMase2-targeted therapeutics.

Abstract

Neutral sphingomyelinase 2 (nSMase2, product of the SMPD3 gene) is a key enzyme for ceramide generation that is involved in regulating cellular stress responses and exosome-mediated intercellular communication. nSMase2 is activated by diverse stimuli, including the anionic phospholipid phosphatidylserine. Phosphatidylserine binds to an integral-membrane N-terminal domain (NTD); however, how the NTD activates the C-terminal catalytic domain is unclear. Here, we identify the complete catalytic domain of nSMase2, which was misannotated because of a large insertion. We find the soluble catalytic domain interacts directly with the membrane-associated NTD, which serves as both a membrane anchor and an allosteric activator. The juxtamembrane region, which links the NTD and the catalytic domain, is necessary and sufficient for activation. Furthermore, we provide a mechanistic basis for this phenomenon using the crystal structure of the human nSMase2 catalytic domain determined at 1.85-Å resolution. The structure reveals a DNase-I–type fold with a hydrophobic track leading to the active site that is blocked by an evolutionarily conserved motif which we term the “DK switch.” Structural analysis of nSMase2 and the extended N-SMase family shows that the DK switch can adopt different conformations to reposition a universally conserved Asp (D) residue involved in catalysis. Mutation of this Asp residue in nSMase2 disrupts catalysis, allosteric activation, stimulation by phosphatidylserine, and pharmacological inhibition by the lipid-competitive inhibitor GW4869. Taken together, these results demonstrate that the DK switch regulates ceramide generation by nSMase2 and is governed by an allosteric interdomain interaction at the membrane interface.