A DISTANT EVOLUTIONARY RELATIONSHIP BETWEEN BACTERIAL SPHINGOMYELINASE AND MAMMALIAN DNASE-I

The three-dimensional structure of bacterial sphingomyelinase (SMase) was predicted using a protein fold recognition method; the search of a library of known structures showed that the SMase sequence is highly compatible with the mammalian DNase I structure, which suggested that SMase adopts a structure similar to that of DNase I. The amino acid se quence alignment based on the prediction revealed that, despite the la ck of overall sequence similarity (less than 10% identity), those resi dues of DNase I that are involved in the hydrolysis of the phosphodies ter bond, including two histidine residues (His 134 and His 252) of th e active center, are conserved in SMase. In addition, a conserved pent apeptide sequence motif was found, which includes two catalytically cr itical residues, Asp 251 and His 252. A sequence database search showe d that the motif is highly specific to mammalian DNase I and bacterial SMase. The functional roles of SMase residues identified by the seque nce comparison were consistent with the results from mutant studies. T wo Bacillus cereus SMase mutants (H134A and H252A) were constructed by site-directed mutagenesis. They completely abolished their catalytic activity. A model for the SMase-sphingomyelin complex structure was bu ilt to investigate how the SMase specifically recognizes its substrate . The model suggested that a set of residues conserved among bacterial SMases, including Trp 28 and Phe 55, might be important in the substr ate recognition. The predicted structural similarity and the conservat ion of the functionally important residues strongly suggest a distant evolutionary relationship between bacterial SMase and mammalian DNase I. These two phosphodiesterases must have acquired the specificity for different substrates in the course of evolution.