Clues to reaction specificity in PLP-dependent fold type I enzymes of monosaccharide biosynthesis

Novel functions can emerge in an enzyme family while conserving catalytic mechanism, motif or fold. PLP-dependent enzymes have evolved into seven fold types and catalyse diverse reactions using the same mechanism for the formation of external aldimine. Nucleotide sugar aminotransferases (NSATs) and dehydratases (NSDs) belong to fold type I and mediate the biosynthesis of several monosaccharides. NSATs use diverse substrates but are highly selective to the C3 or C4 carbon to which amine group is transferred. Factors responsible for reaction specificity in NSDs are known but remain unexplored in NSATs. Profile HMMs were able to identify NSATs but could not capture reaction specificity. A search for discriminating features led to the discovery of a sequence motif that is located near the pyranose binding site suggesting their role in imparting reaction specificity. Using a position weight matrix for this motif, we were able to assign reaction specificity to a large number of NSATs. Residues which upon mutation could convert NSD to NSAT have been reported in literature and we deduced that these are not conserved. This suggested the occurrence of non-generic family specific mutations underlying the evolution of dehydratases. Inferences from this analysis set way for future experiments that can shed light on mechanisms of functional diversification in enzymes of fold type I.