Structure-based phylogeny of class IIa tRNA synthetases in relation to an unusual biochemistry

The available three-dimensional information for class II aminoacyl-tRNA syn thetases has been used to generate sequence alignments that strictly adhere to the structural equivalencies between members of subclass IIa of these e nzymes. The resulting alignments were used to study their phylogenetic rela tionships. In particular, the entire set of available sequences of prolyl-t RNA synthetases was analyzed in this way. In contrast to recent reports, we conclude that the evolutionary pattern of prolyl-tRNA synthetases does not obviously conform to the canonical phylogenetic distribution. The pattern found for these enzymes may be related to their biochemical characteristics . Our results indicate a potential relationship between the evolutionary pa ttern of prolyl-tRNA synthetases and the emergence of two enzymatically dis tinct forms of these proteins.