Metagenome analysis for the classification of enzymes related to hydrolysis of bacterial cell wall by sequential and enzymatic analysis

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The enzymes related to hydrolyze the bacterial peptidoglycan were explored from the genes sequenced by metagenome projects and were classified into the five groups defined by their catalytic sites in peptidoglycan. Among the five groups, the genes related to endopeptidase were most frequently found in the metagenomic data. We estimated that the three-dimensional structure and binding sites of about 2,500 proteins could be predicted. Furthermore, to predict the binding site precisely, the binding simulations between peptidoglycan were performed for lyzozyme and ALE-1, one of the endopeptidase. As results, twenty-four and thirteen amino acid residues were predicted to be interacted with the peptidoglycan in lysozyme and ALE-1, respectively. The protein functions and binding sites could be predicted by using the domain and structural information obtained from metagenomic data. In the future, we would construct the analysis system which could perform these analyses to design highly efficient enzymes.