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J Mol Biol. 2018 May 25;430(11):1590-1606. doi: 10.1016/j.jmb.2018.04.011. Epub 2018 Apr 17.

Structure of Escherichia coli Arginyl-tRNA Synthetase in Complex with tRNAArg: Pivotal Role of the D-loop.

Author information

1
Laboratory of Molecular Endocrinology, CHU Research Center and Laval University, Québec, Canada.
2
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
3
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Shanghai Institutes of Biochemistry and Cell Biology, SIBS, Shanghai, China. Electronic address: rzhang@ibp.ac.cn.
4
Shanghai Institutes of Biochemistry and Cell Biology, SIBS, Shanghai, China. Electronic address: edwang@sibcb.ac.cn.
5
Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, Strasbourg Cedex, France.
6
Laboratory of Molecular Endocrinology, CHU Research Center and Laval University, Québec, Canada; Shanghai Institutes of Biochemistry and Cell Biology, SIBS, Shanghai, China. Electronic address: sxlin@crchul.ulaval.ca.

Abstract

Aminoacyl-tRNA synthetases are essential components in protein biosynthesis. Arginyl-tRNA synthetase (ArgRS) belongs to the small group of aminoacyl-tRNA synthetases requiring cognate tRNA for amino acid activation. The crystal structure of Escherichia coli (Eco) ArgRS has been solved in complex with tRNAArg at 3.0-Å resolution. With this first bacterial tRNA complex, we are attempting to bridge the gap existing in structure-function understanding in prokaryotic tRNAArg recognition. The structure shows a tight binding of tRNA on the synthetase through the identity determinant A20 from the D-loop, a tRNA recognition snapshot never elucidated structurally. This interaction of A20 involves 5 amino acids from the synthetase. Additional contacts via U20a and U16 from the D-loop reinforce the interaction. The importance of D-loop recognition in EcoArgRS functioning is supported by a mutagenesis analysis of critical amino acids that anchor tRNAArg on the synthetase; in particular, mutations at amino acids interacting with A20 affect binding affinity to the tRNA and specificity of arginylation. Altogether the structural and functional data indicate that the unprecedented ArgRS crystal structure represents a snapshot during functioning and suggest that the recognition of the D-loop by ArgRS is an important trigger that anchors tRNAArg on the synthetase. In this process, A20 plays a major role, together with prominent conformational changes in several ArgRS domains that may eventually lead to the mature ArgRS:tRNA complex and the arginine activation. Functional implications that could be idiosyncratic to the arginine identity of bacterial ArgRSs are discussed.

KEYWORDS:

arginine identity; conformational adaptation; tRNA arginylation

PMID:
29678554
DOI:
10.1016/j.jmb.2018.04.011

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