5KAR

Murine acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3B)

5KAR の概要

• エントリーDOI: 10.2210/pdb5kar/pdb
• 関連するPDBエントリー: 5KAS
• 分子名称: 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)-[alpha-D-mannopyranose-(1-6)]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)
• 機能のキーワード: phosphoesterase, extracellular, membrane, hydrolase
• 由来する生物種: Mus musculus (Mouse)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 51067.32

構造登録者

Gorelik, A.,Illes, K.,Heinz, L.X.,Superti-Furga, G.,Nagar, B. (登録日: 2016-06-02, 公開日: 2016-10-05, 最終更新日: 2024-10-30)

主引用文献

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

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: 27687724
DOI: 10.1074/jbc.M116.755801

実験手法

X-RAY DIFFRACTION (1.142 Å)