title: Structure-based phylogeny of class IIa tRNA synthetases in relation to an unusual biochemistry.
abstract: The available three-dimensional information for class II aminoacyl-tRNA synthetases has been used to generate sequence alignments that strictly adhere to the structural equivalencies between members of subclass IIa of these enzymes. The resulting alignments were used to study their phylogenetic relationships. In particular, the entire set of available sequences of prolyl-tRNA 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 pattern of prolyl-tRNA synthetases and the emergence of two enzymatically distinct forms of these proteins.
authors.affiliation: Skaggs Institute for Chemical Biology, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. lluis@hermes.scripps.edu
authors.forename: L
authors.initials: L
authors.lastname: Ribas de Pouplana
authors.forename: J R
authors.initials: JR
authors.lastname: Brown
authors.forename: P
authors.initials: P
authors.lastname: Schimmel
mesh_terms: D000595:Amino Acid Sequence; D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry / Q000145:classification* / Q000235:genetics*; D000818:Animals; D001226:Aspartate-tRNA Ligase / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D017386:Sequence Homology, Amino Acid
chemical_list: D000604:Amino Acyl-tRNA Synthetases; D001226:Aspartate-tRNA Ligase; C100134:prolyl T RNA synthetase