Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis

Xiong, Zi-Jian; Huang, Jingjing; Poda, Gennady; Pomès, Régis; Privé, Gilbert G.

doi:10.1016/j.jmb.2016.06.012

Cited by 53 publications

(89 citation statements)

References 54 publications

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“…ASMase (23,24) shows that in both cases, SM is positioned similarly and can insert into the active site with few clashes (Fig. 7A).…”

Section: Discussionmentioning

confidence: 95%

“…Briefly, a phosphate-containing substrate would bind in the active site mainly via strong electrostatic interactions between the zinc ions and the phosphate moiety. A zinc-activated nucleophilic water molecule would then attack the phosphate, resulting in departure of the leaving group, protonated by one of the neighboring histidines (21)(22)(23)(24). The nucleophilic water molecule coordinated midway between the two zinc ions is clearly visible in the high-resolution structure of SMPDL3B (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…On the other hand, its other homolog, SMPDL3A, is a nucleotide phosphodiesterase. The crystal structures of ASMase and SMPDL3A were recently reported (21)(22)(23)(24), but no structural information is as yet available for SMPDL3B.…”

Section: Sphingomyelins (Sm)mentioning

confidence: 99%

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

Gorelik

Heinz

Illés

et al. 2016

Journal of Biological Chemistry

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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.

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“…ASMase (23,24) shows that in both cases, SM is positioned similarly and can insert into the active site with few clashes (Fig. 7A).…”

Section: Discussionmentioning

confidence: 95%

Section: Resultsmentioning

confidence: 99%

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

Gorelik

Heinz

Illés

et al. 2016

Journal of Biological Chemistry

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“…Screening for this mutation among healthy individuals living in Santiago indicated that the carrier frequency for type B NPD within Chile was ~1/106, predicting a disease incidence of ~1/45,000. To facilitate further genotype-phenotype and mutational analysis, the crystal structure of recombinant ASM also has recently been reported [62,63]. …”

Section: Molecular Geneticsmentioning

confidence: 99%

Types A and B Niemann-Pick disease

Schuchman

Desnick

2017

Molecular Genetics and Metabolism

214

186

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The eponym Niemann-Pick disease (NPD) refers to a group of patients who present with varying degrees of lipid storage and foam cell infiltration in tissues, as well as overlapping clinical features including hepatosplenomegaly, pulmonary insufficiency and/or central nervous system (CNS) involvement. Due to the pioneering work of Roscoe Brady and co-workers, we now know that there are two distinct metabolic abnormalities that account for NPD. The first is due to the deficient activity of the enzyme acid sphingomyelinase (ASM; “types A & B” NPD), and the second is due to defective function in cholesterol transport (“type C” NPD). Herein only types A and B NPD will be discussed. Type A NPD patients exhibit hepatosplenomegaly in infancy and profound CNS involvement. They rarely survive beyond 2–3 years of age. Type B patients also have hepatosplenomegaly and pathologic alterations of their lungs, but there are usually no CNS signs. The age of onset and rate of disease progression varies greatly among type B patients, and they frequently live into adulthood. Intermediate patients also have been reported with mild to moderate neurological findings. All patients with types A and B NPD have mutations in the gene encoding ASM (SMPD1), and thus the disease is more accurately referred to as ASM deficiency (ASMD). Herein we will review the clinical, pathological, biochemical, and genetic findings in types A and B NPD, and emphasize the seminal contributions of Dr. Brady to this disease. We will also discuss the current status of therapy for this disorder.

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“…Rapid generation of ceramide in response to extracellular stimuli is mediated by the activation of sphingomyelinases (SMases), which hydrolyze sphingomyelin (SM), a major component of cell membranes, into ceramide and phosphocholine (3,4). Three families of SMases (acid, neutral, and alkaline) have been identified that are classified by their pH optima, subcellular localization, protein fold, and function (5)(6)(7)(8). Neutral sphingomyelinase 2 (nSMase2, product of the SMPD3 gene) is the major neutral sphingomyelinase (N-SMase) in mammalian cells for the stressinduced generation of ceramide (4).…”

mentioning

confidence: 99%

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

Airola

Shanbhogue

Shamseddine

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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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.sphingomyelinase | ceramide | enzyme | lipid | crystallography

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Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis

Cited by 53 publications

References 54 publications

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

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

Types A and B Niemann-Pick disease

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

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