title: Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases.
abstract: Glycyl tRNA synthetase (GlyRS) provides a unique case among class II aminoacyl tRNA synthetases, with two clearly widespread types of enzymes: a dimeric (α2) species present in some bacteria, archaea, and eukaryotes; and a heterotetrameric form (α2β2) present in most bacteria. Although the differences between both types of GlyRS at the anticodon binding domain level are evident, the extent and implications of the variations in the catalytic domain have not been described, and it is unclear whether the mechanism of amino acid recognition is also dissimilar. Here, we show that the α-subunit of the α2β2 GlyRS from the bacterium Aquifex aeolicus is able to perform the first step of the aminoacylation reaction, which involves the activation of the amino acid with ATP. The crystal structure of the α-subunit in the complex with an analog of glycyl adenylate at 2.8 Å resolution presents a conformational arrangement that properly positions the cognate amino acid. This work shows that glycine is recognized by a subset of different residues in the two types of GlyRS. A structural and sequence analysis of class II catalytic domains shows that bacterial GlyRS is closely related to alanyl tRNA synthetase, which led us to define a new subclassification of these ancient enzymes and to propose an evolutionary path of α2β2 GlyRS, convergent with α2 GlyRS and divergent from AlaRS, thus providing a possible explanation for the puzzling existence of two proteins sharing the same fold and function but not a common ancestor.
authors.affiliation: From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México.
authors.forename: Marco Igor
authors.initials: MI
authors.lastname: Valencia-Sánchez
authors.affiliation: From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México, the Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato 04510, México.
authors.forename: Annia
authors.initials: A
authors.lastname: Rodríguez-Hernández
authors.affiliation: the Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden.
authors.forename: Ruben
authors.initials: R
authors.lastname: Ferreira
authors.affiliation: From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México.
authors.forename: Hugo Aníbal
authors.initials: HA
authors.lastname: Santamaría-Suárez
authors.affiliation: From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México.
authors.forename: Marcelino
authors.initials: M
authors.lastname: Arciniega
authors.affiliation: the Laboratoire de Biologie Intégrative des Milieux Marins, CNRS UMR8227, 29680 Roscoff, France.
authors.forename: Anne-Catherine
authors.initials: AC
authors.lastname: Dock-Bregeon
authors.affiliation: the Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, CNRS UMR 7104, 1 Rue Laurent Fries, Illkirch, France, and.
authors.forename: Dino
authors.initials: D
authors.lastname: Moras
authors.affiliation: the Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, CNRS UMR 7104, 1 Rue Laurent Fries, Illkirch, France, and.
authors.forename: Brice
authors.initials: B
authors.lastname: Beinsteiner
authors.affiliation: the European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22603, Germany.
authors.forename: Haydyn
authors.identifier: 0000-0002-5664-744X
authors.initials: H
authors.lastname: Mertens
authors.affiliation: the European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22603, Germany.
authors.forename: Dmitri
authors.identifier: 0000-0003-0830-5696
authors.initials: D
authors.lastname: Svergun
authors.affiliation: the Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato 04510, México.
authors.forename: Luis G
authors.initials: LG
authors.lastname: Brieba
authors.affiliation: the Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden.
authors.forename: Morten
authors.initials: M
authors.lastname: Grøtli
authors.affiliation: From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México, torres@ifc.unam.mx.
authors.forename: Alfredo
authors.identifier: 0000-0002-0702-350X
authors.initials: A
authors.lastname: Torres-Larios
mesh_terms: D001419:Bacteria / Q000201:enzymology; D018360:Crystallography, X-Ray; D006032:Glycine-tRNA Ligase / Q000737:chemistry*; D008958:Models, Molecular; D010802:Phylogeny; D011487:Protein Conformation
chemical_list: D006032:Glycine-tRNA Ligase
keywords: aminoacyl tRNA synthetase; crystal structure; molecular evolution; structure-function; substrate specificity