5KAS
Murine acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3B) with phosphocholine
Summary for 5KAS
| Entry DOI | 10.2210/pdb5kas/pdb |
| Related | 5KAR |
| Descriptor | Acid sphingomyelinase-like phosphodiesterase 3b, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (8 entities in total) |
| Functional Keywords | phosphoesterase, extracellular, membrane, phosphocholine, hydrolase |
| Biological source | Mus musculus (Mouse) |
| Total number of polymer chains | 1 |
| Total formula weight | 51193.46 |
| Authors | Gorelik, A.,Illes, K.,Heinz, L.X.,Superti-Furga, G.,Nagar, B. (deposition date: 2016-06-02, release date: 2016-10-05, Last modification date: 2024-11-06) |
| Primary citation | Gorelik, A.,Heinz, L.X.,Illes, K.,Superti-Furga, G.,Nagar, B. Crystal Structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity. J.Biol.Chem., 291:24054-24064, 2016 Cited by PubMed Abstract: The 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 structure-guided 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. PubMed: 27687724DOI: 10.1074/jbc.M116.755801 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.619 Å) |
Structure validation
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