Studies on the function and catalytic mechanism of O-methyltransferases SviOMT02, SviOMT03 and SviOMT06 from Streptomyces virginiae IBL14

•There are nine putative O-methyltransferase genes in Streptomyces virginiae IBL14 genome.•The expressed proteins of sviOMT03 and 06 are caffeic acid-O-methyltransferases.•The O-methylation of SviOMT03 and 06 probably runs in a SN2-like mechanism.•Certain conservative polar amino acids in O-methyltransferase are essential.

To identify the fuctions of the nine putative O-methyltransferase genes in Streptomyces virginiae IBL14, the evolutionary and functional relationship of these genes in its 8.0 Mb linear chromosome was set up via sequence comparison with those of other Streptomyces species. Further, the functions and catalytic mechanism of the three genes sviOMT02, sviOMT03 and sviOMT06 from this strain were studied through experimental and computational approaches. As a result, the nine putative O-methyltransferases belong to methyltransf_2 superfamily, amdomet-MTases superfamily, and leucine carboxyl methyltransferase superfamily, and are phylogenetically close to those of Streptomyces sp. C. The products of genes sviOMT03 and sviOMT06 could catalyze O-methylation of caffeic acid to form ferulic acid. Computational analysis indicated that the O-methylation mechanism of SviOMT03 and SviOMT06 proceeds from a direct transfer of the SAM-methyl group to caffeic acid with inversion of symmetry aided by a divalent metal ion in a SN2-like mechanism. Particularly, the conservative polar amino acid residues in SviOMT03 and SviOMT06, including Lys143 that reacts with caffeic acid, Ser74, Asp140 and Tyr149 that react with S-adenosyl methionine, and His142 (SviOMT03) or His171 (SviOMT06) that transfers the 3-hydroxyl proton of substrate caffeic acid, probably be essential in their O-methylation.