Neutral sphingomyelinase Sphingomyelin phosphodiesterase

magnified view of smase active site co ions bound showing residues responsible divalent metal cation binding. pdb: 2dds​.

the solving of crystal structure of neutral sphingomyelinase listeria ivanovii , bacillus cereus has allowed fuller understanding of enzymatic site. active site of b. cereus smase comprises residues asn-16, glu-53, asp-195, asn-197, , his-296. of these, residues glu-53, asp-195, , his-296 known essential activity. relative catalytic activities of smase when metal ions bound active site have been studied divalent metal ions co, mn, mg, ca, , sr. of these 5 metal ions, co, mn, , mg bound active site result in high catalytic activity of smase. ca , sr bound active site exhibit lower catalytic activity of smase. when 1 mg ion or 2 co ions bind active site, double hexa-coordinated geometry results 2 octahedral bi-pyramids co , 1 octahedral bi-pyramid mg. when 1 ca ion binds active site, hepta-coordinated geometry results. therefore, difference in catalytic activity metal ions predicted due geometrical differences. of co , mg, smase has better reactivity when 2 co ions bound smase; when these co ions bound, glu-53 , his-296 each bind 1 divalent metal cation. these cations surrounded bridged water molecules , function lewis acids.

mechanism

the solving of crystal structure of neutral sphingomyelinase listeria ivanovii , bacillus cereus has shed light on catalytic mechanisms. active site of smase contains glu , residues each bound 1 or 2 divalent metal cations, co, mg, or ca optimum performance. these 2 cations assist in catalysis recruiting sm active site of smase. divalent cation bound glu residue interacts amido-oxygen , ester-oxygen between c1 , phosphate group of sm; asn residue , divalent metal cation bound residue bind oxygen atoms of phosphate group of sm. stabilizes phosphate group’s negative charge. metal cation bound residue , asp , asn side chains lower pka value of 1 of bridged water molecules, activating water molecule. water molecule acts nucleophile , attacks phosphate group of sm, creating pentavalent phosphorus atom negative charge stabilized divalent metal cations. phosphate reforms tetrahedral conformation , results in products ceramide , phosphocholine. however, not clear if mechanism of action of acidic sphingomyelinase same, owing lack of crystal structure.