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