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Structural basis for the high thermal stability and optimum pH of sphingomyelinase C from Streptomyces griseocarneus
Journal of Bioscience and Bioengineering ( IF 2.8 ) Pub Date : 2020-10-03 , DOI: 10.1016/j.jbiosc.2020.09.005
Ikuhide Fujisawa , Hiroaki Hamana , Yu Tomita , Yusaku Matsumoto , Kazutaka Murayama , Daisuke Sugimori

Sphingomyelinase C (SMC) hydrolyzes sphingomyelin to ceramide and phosphocholine. Prokaryotic SMCs share sequence homology with mammalian SMCs that have enzymatic pH optima at neutral pH. SMC from the nonpathogenic prokaryote Streptomyces griseocarneus shows notable enzymatic features such as higher optimum pH and thermostability than other prokaryotic SMCs. Determination of the three-dimensional structure of S. griseocarneus-SMC (Sg-SMC) and comparison with other SMC structures represents a promising strategy to elucidate the unique enzymatic features of Sg-SMC on a structural basis. Therefore, we determined the crystal structure of Sg-SMC at 2.0 Å resolution by X-ray crystallography. Comparison of the Sg-SMC structure with three other structurally known SMCs from Listeria ivanovii, Bacillus cereus, and Staphylococcus aureus indicated that Sg-SMC is more diverse in sequence and that structural differences in the main chain between these SMCs are primarily located on the molecular surface distant from the active site. Comparison of the surface area of the four SMCs revealed that Sg-SMC has the most compact structure, which may contribute to the enhanced thermostability of Sg-SMC. Regarding the hydrogen bond network in the active site of Sg-SMC, a basic amino acid, Arg278, is involved, whereas the corresponding residue in other SMCs (Ser or Asn) does not form hydrogen bonds with metal-coordinating water molecules. Hydrogen bond formation between Arg278 and a Mg2+ ion-coordinating water molecule may be responsible for the higher optimal pH of Sg-SMC compared to that of other SMCs.



中文翻译:

灰链霉菌鞘磷脂酶C的高热稳定性和最佳pH的结构基础

鞘磷脂酶C(SMC)将鞘磷脂水解为神经酰胺和磷酸胆碱。原核SMC与在中性pH下具有酶促pH最佳值的哺乳动物SMC具有序列同源性。非致病原核链霉菌的SMC显示出明显的酶促特性,例如比其他原核SMC更高的最佳pH和热稳定性。确定灰糖霉菌-SMC(Sg -SMC)的三维结构并与其他SMC结构进行比较代表了一种有前途的策略,可以在结构上阐明Sg - SMC的独特酶学特征。因此,我们通过X射线晶体学测定了Sg -SMC在2.0Å分辨率下的晶体结构。比较Sg -SMC结构与伊万氏李斯特菌蜡状芽孢杆菌金黄色葡萄球菌的其他三个结构上已知的SMCs表明,Sg -SMC的序列更加多样,这些SMCs之间的主链结构差异主要位于距离表面较远的分子表面上。活动站点。比较这四个SMC的表面积,发现Sg- SMC具有最致密的结构,这可能有助于提高Sg- SMC的热稳定性。关于Sg活性位点的氢键网络-SMC是一种碱性氨基酸Arg278,但其他SMC(Ser或Asn)中的相应残基不会与金属配位的水分子形成氢键。与其他SMC相比,Arg278和Mg 2+离子配位水分子之间的氢键形成可能是Sg -SMC最佳pH较高的原因。

更新日期:2020-10-03
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