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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. Furthermore, 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 newmore » 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.« less

Authors:
 [1];  [2];  [3];  [1];  [1];  [4];  [5];  [5]; ORCiD logo [6]; ORCiD logo [6];  [7];  [3]; ORCiD logo [1]
+ Show Author Affiliations
  1. Univ. Nacional Autonoma de Mexico, Mexico City (Mexico)
  2. Univ. Nacional Autonoma de Mexico, Mexico City (Mexico); Centro de Investigacion y Estudios Avanzados del Instituto Politecnico Nacional, Guanajuato (Mexico)
  3. Univ. of Gothenburg, Gothenburg (Sweden)
  4. Lab. de Biologie Integrative des Milieux Marins, Roscoff (France)
  5. Institute of Genetics and of Molecular and Cellular Biology, Illkirch (France)
  6. European Molecular Biology Lab., Hamburg (Germany)
  7. Centro de Investigacion y Estudios Avanzados del Instituto Politecnico Nacional, Guanajuato (Mexico)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1267479
Grant/Contract Number:  
AC02-06CH11357; 085P1000817
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 291; Journal Issue: 28; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; aminoacyl tRNA synthetase; crystal structure; molecular evolution; structure-function; substrate specificity

Citation Formats

Valencia-Sánchez, Marco Igor, Rodríguez-Hernández, Annia, Ferreira, Ruben, Santamaría-Suárez, Hugo Aníbal, Arciniega, Marcelino, Dock-Bregeon, Anne-Catherine, Moras, Dino, Beinsteiner, Brice, Mertens, Haydyn, Svergun, Dmitri, Brieba, Luis G., Grøtli, Morten, and Torres-Larios, Alfredo. Structural insights into the polyphyletic origins of glycyl tRNA synthetases. United States: N. p., 2016. Web. doi:10.1074/jbc.M116.730382.
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Valencia-Sánchez, Marco Igor, Rodríguez-Hernández, Annia, Ferreira, Ruben, Santamaría-Suárez, Hugo Aníbal, Arciniega, Marcelino, Dock-Bregeon, Anne-Catherine, Moras, Dino, Beinsteiner, Brice, Mertens, Haydyn, Svergun, Dmitri, Brieba, Luis G., Grøtli, Morten, & Torres-Larios, Alfredo. Structural insights into the polyphyletic origins of glycyl tRNA synthetases. United States. https://doi.org/10.1074/jbc.M116.730382
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Valencia-Sánchez, Marco Igor, Rodríguez-Hernández, Annia, Ferreira, Ruben, Santamaría-Suárez, Hugo Aníbal, Arciniega, Marcelino, Dock-Bregeon, Anne-Catherine, Moras, Dino, Beinsteiner, Brice, Mertens, Haydyn, Svergun, Dmitri, Brieba, Luis G., Grøtli, Morten, and Torres-Larios, Alfredo. Mon . "Structural insights into the polyphyletic origins of glycyl tRNA synthetases". United States. https://doi.org/10.1074/jbc.M116.730382. https://www.osti.gov/servlets/purl/1267479.
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@article{osti_1267479,
title = {Structural insights into the polyphyletic origins of glycyl tRNA synthetases},
author = {Valencia-Sánchez, Marco Igor and Rodríguez-Hernández, Annia and Ferreira, Ruben and Santamaría-Suárez, Hugo Aníbal and Arciniega, Marcelino and Dock-Bregeon, Anne-Catherine and Moras, Dino and Beinsteiner, Brice and Mertens, Haydyn and Svergun, Dmitri and Brieba, Luis G. and Grøtli, Morten and Torres-Larios, Alfredo},
abstractNote = {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. Furthermore, 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.},
doi = {10.1074/jbc.M116.730382},
journal = {Journal of Biological Chemistry},
number = 28,
volume = 291,
place = {United States},
year = {Mon May 23 00:00:00 EDT 2016},
month = {Mon May 23 00:00:00 EDT 2016}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1074/jbc.M116.730382
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Figures / Tables:

Figure 1 Figure 1: $α$-Subunit of the tetrameric $α$2$β$2 GlyRS from A. aeolicus ($α$-AaGlyRS) is able to activate the amino acid. A, schematic diagram of the first step of aminoacyation. B, control experiments. Comparison of full aminoacylation reaction versus amino acid activation. Lanes 1–10, aminoacylation reaction performed as described previously (57–59). Lanemore » 1, no enzyme added, and no P1 nuclease added. Lane 2, Anaeolinea thermophila, a protein that bears in the same sequence both subunits ($αβ$-GlyRS) added, and no P1 nuclease added. Lane 3, A. aeolicus ($α$+$β$-GlyRS) added, and no P1 nuclease added. Lane 4, no enzyme added, and P1 nuclease added. Lanes 5–7, 5, 10, and 15 min of aminoacylation reaction using$α$+$β$-GlyRS (with P1 nuclease added). Lanes 8–10, 5, 10, and 15 min of aminoacylation reaction using $αβ$-GlyRS (with P1 nuclease added). Lanes 11–22, glycine activation reaction. Lane 11, zero time point using $α$-AaGlyRS. Lanes 12–16, 10, 20, 30, 40, and 50 min of the glycine activation reaction using$α$-AaGlyRS. Lane 17, zero time point using $αβ$-GlyRS. Lanes 18–22, 10, 20, 30, 40,and 50 min of the glycine activation reaction using the $αβ$-GlyRS. C, amino acid activation. $α$-AaGglyRS at 40 $μ$M, in the presence of decreasing glycine concentrations, 0.5mM ATP, 50mM Tris, pH 8.0, 50mM KCl, 10mM MgCl2. Time points were taken every 10 min for 60 min for each concentration, and the formation ofAMPwas monitored for each point. D, initial velocities (kinetics of AMP formation from the experiment in C). Steady state time courses using different glycine concentrations. E, Michaelis-Menten plot. Initial velocities were plotted against substrate concentration; error bars indicate the standard deviation for each point.« less
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