Sphingomyelin phosphodiesterase

Sphingomyelinase phosphodiesterase or simply Sphingomyelinase (SMase) is a hydrolase enzyme that is involved in sphingolipid metabolism reactions. SMase is found in the lysosomes of both prokaryotic and eukaryotic cells and is responsible for breaking sphingomyelin (SM) down into phosphocholine and ceramide. Without SMase, SM builds up within the cell, eventually causing cell death and major organ failure; the disease associated with this disorder is Niemann-Pick disease^[1]. The crystal structure with required metal cations and mechanism of SMase are still being developed experimentally^[2].

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Overall Structure of SMase

There are six forms of SMase. The most studied of these is a neutral form of SMase that contains either Co²⁺ or Mg²⁺, divalent metal cations. The overall structure of these SMases is very similar to that of the DNase I family, with the exception of SMase’s hydrophobic β-hairpin region. SMase has two identical subunits; within each subunit are two β-sheets sandwiched in between α-helices^[2].

Active Site

The active site of SMase is the central cleft and is made up of Asn-16, Glu-53, Asp-195, Asn-197, and His-296, of which only Glu-53, Asp-195, and His-296 are known to be essential for activity. The relative catalytic activities of SMase when metal ions are bound to the active site have been studied for divalent metal ions Co²⁺, Mn²⁺, Mg²⁺, Ca²⁺, and Sr²⁺. Of these five metal ions, Co²⁺, Mn²⁺, and Mg²⁺ bound to the active site result in high catalytic activity of SMase. Ca²⁺ and Sr²⁺ bound to the active site exhibit much lower catalytic activity of SMase. When one Mg²⁺ ion or two Co²⁺ ions bind to the active site, double hexa-coordinated geometry results with two octahedral bi-pyramids for Co²⁺ and one octahedral bi-pyramid for Mg²⁺. When one Ca²⁺ ion binds to the active site, a hepta-coordinated geometry results. Therefore, the difference in catalytic activity for metal ions is predicted to be due to geometrical differences. Of Co²⁺ and Mg²⁺, SMase has better reactivity when two Co²⁺ ions are bound to SMase; when these Co²⁺ ions are bound, Glu-53 and His-296 each bind one divalent metal cation. These cations are surrounded by bridged water molecules and function as Lewis acids^[2].

Mechanism

The active site of SMase contains Glu and His residues that are each bound to one or two divalent metal cations, usually Co²⁺, Mg²⁺, or Ca²⁺ for optimum performance. These two cations assist in catalysis by recruiting SM to the active site of SMase. The divalent cation bound to the Glu residue interacts with the amido-oxygen and ester-oxygen between C1 and the phosphate group of SM; an Asn residue and the divalent metal cation bound to the His residue bind to the oxygen atoms of the phosphate group of SM. This stabilizes the phosphate group’s negative charge. The metal cation bound to the His residue and Asp and Asn side chains lower the pKa value of one of the bridged water molecules, thus activating a water molecule. This water molecule then acts as a nucleophile and attacks the phosphate group of SM, creating a pentavalent phosphorus atom whose negative charge is stabilized by the divalent metal cations. The phosphate then reforms its tetrahedral conformation and results in the products ceramide and phosphocholine^[2].

Genes

The six forms of SMase are encoded by the following genes:

• SMPD1 (SMPD1) - acid
• SMPD2 - neutral
• SMPD3 - neutral
• SMPD4 - neutral
• SMPDL3A - acid-like
• SMPDL3B - acid-like

References