Genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles.
Abstract
Enzymes belonging to acyl:CoA synthetase (ACS) superfamily activate wide variety of substrates and play major role in increasing the structural and functional diversity of various secondary metabolites in microbes and plants. However, due to the large sequence divergence within the superfamily, it is difficult to predict their substrate preference by annotation transfer from the closest homolog. Therefore, a large number of ACS sequences present in public databases lack any functional annotation at the level of substrate specificity. Recently, several examples have been reported where the enzymes showing high sequence similarity to luciferases or coumarate:CoA ligases have been surprisingly found to activate fatty acyl substrates in experimental studies. In this work, we have investigated the relationship between the substrate specificity of ACS and their sequence/structural features, and developed a novel computational protocol for in silico assignment of substrate preference. We have used a knowledge-based approach which involves compilation of substrate specificity information for various experimentally characterized ACS and derivation of profile HMMs for each subfamily. These HMM profiles can accurately differentiate probab...Continue Reading
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