5UVG

Crystal structure of the human neutral sphingomyelinase 2 (nSMase2) catalytic domain with insertion deleted and calcium bound

Summary for 5UVG

• Entry DOI: 10.2210/pdb5uvg/pdb
• Descriptor: Sphingomyelin phosphodiesterase 3,Sphingomyelin phosphodiesterase 3, CALCIUM ION (3 entities in total)
• Functional Keywords: sphingomyelinase, hydrolase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 1
• Total formula weight: 41388.54

Authors

Airola, M.V.,Guja, K.E.,Garcia-Diaz, M.,Hannun, Y.A. (deposition date: 2017-02-20, release date: 2017-06-28, Last modification date: 2024-03-06)

Primary citation

Airola, M.V.,Shanbhogue, P.,Shamseddine, A.A.,Guja, K.E.,Senkal, C.E.,Maini, R.,Bartke, N.,Wu, B.X.,Obeid, L.M.,Garcia-Diaz, M.,Hannun, Y.A.
Structure of human nSMase2 reveals an interdomain allosteric activation mechanism for ceramide generation.
Proc. Natl. Acad. Sci. U.S.A., 114:E5549-E5558, 2017

PubMed Abstract: Neutral sphingomyelinase 2 (nSMase2, product of the 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.

PubMed: 28652336
DOI: 10.1073/pnas.1705134114

Experimental method

X-RAY DIFFRACTION (1.849 Å)