A model of the acid sphingomyelinase phosphoesterase domain based on its remote structural homolog purple acid phosphatase

Abstract

Sequence profile and fold recognition methods identified mammalian purple acid phosphatase (PAP), a member of a dimetal-containing phosphoesterase (DMP) family, as a remote homolog of human acid sphingomyelinase (ASM). A model of the phosphoesterase domain of ASM was built based on its predicted secondary structure and the metal-coordinating residues of PAP. Due to the low sequence identity between ASM and PAP (∼15%), the highest degree of confidence in the model resides in the metal-binding motifs. The ASM model predicts residues Asp 206, Asp 278, Asn 318, His 425, and His 457 to be dimetal coordinating. A putative orientation for the phosphorylcholine head group of the ASM substrate, sphingomyelin (SM), was made based on the predicted catalysis of the phosphorus-oxygen bond in the active site of ASM and on a structural comparison of the PAP-phosphate complex to the C-reactive protein-phosphorylcholine complex. These complexes revealed similar spatial interactions between the metal-coordinating residues, the metals, and the phosphate groups, suggesting a putative orientation for the head group in ASM consistent with the mechanism considerations. A conserved sequence motif in ASM, NX 3 CX 3 N, was identified (Asn 381 to Asn 389) and is predicted to interact with the choline amine moiety in SM. The resulting ASM model suggests that the enzyme uses an S N 2-type catalytic mechanism to hydrolyze SM, similar to other DMPs. His 319 in ASM is predicted to protonate the ceramide-leaving group in the catalysis of SM. The putative functional roles of several ASM Niemann-Pick missense mutations, located in the predicted phosphoesterase domain, are discussed in context to the model. Keywords: acid sphingomyelinase; phosphoesterase; purple acid phosphatase; threading; structure predictions Human acid sphingomyelinase (ASM) is an enzyme that catalyzes the hydrolysis of sphingomyelin (SM) into ceramide and phosphorylcholine (Fig. 1). This zinc-dependent, membrane-associated glycoprotein has a pH optimum of ∼5.0, but has been shown to catalyze SM at both acidic and neutral pHs (Yamanaka and Suzuki 1982;Quintern et al. 1987;Schissel et al. 1998a). Two forms of ASM have been described, an intracellular form found in lysosomes and an extracellular secreted form (see Goni and Alonso Reprint requests to: Janet A. Meurer-Ogden, Department of Molecular Pharmacology, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, USA; e-mail: Janet_Meurer@Berlex.com; fax: (510) 262-7844.Abbreviations: ASM, acid sphingomyelinase; CRP, C-reactive protein; DMP, dimetal-containing phosphoesterase; HMM, hidden Markov model; LDL, low-density lipoproteins; MM1-MM5, predicted phosphatase metalcoordinating motifs 1 through 5; PAP, purple acid phosphatase; RMSD, root mean square deviation; SM, sphingomyelin; TRAP, tartrate-resistant acid phosphatase.Article and publication are at

Sphingomyelin Phosphodiesterase Acid-like 3A (SMPDL3A) Is a Novel Nucleotide Phosphodiesterase Regulated by Cholesterol in Human Macrophages

“…ClustalW2 multiple alignment of the amino acid sequences of SMPDL3A, SMPDL3B, and aSMase revealed the key residues of the GD/GNH phosphoesterase motif in SMPDL3A to be perfectly aligned with those of aSMase and SMPDL3B. All five key metal-binding residues predicted from a homology model of aSMase (20) were also found to be conserved and perfectly aligned within the sequences of SMPDL3A, SMPDL3B and aSMase (Fig. 3, indicated by boldface M).…”

“…3), which is predicted to be directly involved in the recognition of the phosphorylcholine headgroup of their sphingomyelin substrates (20). In human aSMase, the central cysteine (Cys-385) of the motif is also involved in a disulfide bridge with Cys-431 (21).…”

Epidemiological, clinical and biochemical characterization of the p.(Ala359Asp) SMPD1 variant causing Niemann–Pick disease type B

“…According to bioinformatic modeling of the ASM protein, alanine 359 forms part of, or is located near, the substrate-binding region of this hydrolase. 15,27 Indeed, this amino acid is highly conserved between diverse species such as human, mouse and worm. 27 In addition, the alanine to aspartic acid amino acid change, harbored by the p.(Ala359Asp) protein, is predicted to be damaging by several bioinformatics programs.…”

“…15,27 Indeed, this amino acid is highly conserved between diverse species such as human, mouse and worm. 27 In addition, the alanine to aspartic acid amino acid change, harbored by the p.(Ala359Asp) protein, is predicted to be damaging by several bioinformatics programs. This is consistent with the site-directed mutagenesis/expression evidence reported here, confirming that the p.(Ala359Asp) variant significantly reduces the ASM activity by 495% compared with the wild-type enzyme.…”

Potente und selektive Inhibition der sauren Sphingomyelinase durch Bisphosphonate

“…Darüber hinaus wurde der beste Inhibitor, 7 c, auf eine Inhibition der Ser/ThrPhosphathase 1 (PP1) getestet; PP1 gehört ebenso wie die Phosphoesterase-Domäne der aSMase zur Familie der Dimetall-Phosphoesterasen. [23] Dieses Enzym wurde durch 7 c bei Konzentrationen bis 2 mm ebenfalls nicht inhibiert (siehe die Hintergrundinformationen), und eine Selektivität gegenüber PP1 wurde somit ebenfalls gezeigt.…”