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

Stephen, Preyesh; Ye, Sheng; Zhou, Ming; Song, Jian; Zhang, Rongguang; Wang, En‐Duo; Giegé, Richard; Lin, Szu-Yuan

doi:10.1016/j.jmb.2018.04.011

Cited by 14 publications

(18 citation statements)

References 61 publications

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“…C73 for His, G20 for Phe and A20 for Arg identities (Galili et al, 2016); interestingly, these positions were found as positive aminoacylation determinants in Aeropyrum pernix tRNA His and tRNA Phe and in bacterial tRNA Arg (Table 1). In agreement, the crystal structure of E. coli ArgRS in complex with tRNA Arg shows contacts of A20 with 6 amino acids of ArgRS, notably Asn84 which replacement by Ser leads to an important loss of catalytic efficiency (Stephen et al, 2018). Finally, a computational approach unveiled identity clusters in tRNA isoacceptors that contain positions experimentally validated as tRNA aminoacylation determinants.…”

Section: Computational Predictions Versus Experimental Findingsmentioning

confidence: 56%

“…These form a specific three-dimensional arrangement that can be recognised by aaRSs. In this pocket, residue A20 of E. coli tRNA Arg specifies Arg identity in a major fashion in anchoring tRNA Arg on ArgRS, as demonstrated by crystallography (Stephen et al, 2018). Note that the degenerated N20 position (U/C) in the yeast tRNA Arg isoacceptors intervenes in the identity of the isoacceptor with ICG anticodon (McShane et al, 2016).…”

Section: Other Recognition Sitesmentioning

confidence: 88%

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Transfer RNA Recognition and Aminoacylation by Synthetases

Giegé

Eriani

2021

Encyclopedia of Life Sciences

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Fidelity of transfer ribonucleic acid (tRNA) charging by amino acids ensures correct translation of the genetic code into proteins. Charging is catalysed by a set of enzymes known as aminoacyl-tRNA synthetases. Owing to the degeneracy of the genetic code, some of the different tRNAs have the same amino acid attached to them. Specificity of charging obeys universal rules and is ensured by positive elements, the identity determinants unique to each tRNA and responsible for its recognition by the cognate synthetase, and negative elements, the antideterminants that prevent false recognitions. To fulfil the aminoacylation specificity and prevent noncognate aminoacyl-tRNA delivery to the ribosome, some synthetases also mediate proofreading reactions that increase fidelity of the tRNA charging. In such reactions, misactivated amino acids or mischarged tRNAs are checked in specific sites and noncognate products are hydrolysed. However, mischarging is beneficial under certain stress circumstances or when catalysed by nondiscriminatory synthetases, and represents a driving force in evolution. Key Concepts:•Translational expression of the genetic code refers to aminoacyl-tRNA-and ribosomedependent decoding of genes into proteins, a process highly dependent on fidelity of tRNA aminoacylation by synthetases.•The rules that account for the aminoacylation identity of tRNAs are referred to as the second genetic code.•The RNA operational code is encoded in the acceptor stem of tRNA and is crucial for recognition by aminoacyl-tRNA synthetases and specific aminoacylation.•Allostery in tRNA-synthetase systems concerns long-range transfer of chemical information (up to 75 Å) to the synthetase catalytic site (through the body of tRNA and/or synthetase) triggered by contacts of tRNA identity determinants with the synthetase.•Engineering the identity of tRNA-synthetase systems allows reprogramming the genetic code.

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Section: Computational Predictions Versus Experimental Findingsmentioning

confidence: 56%

Section: Other Recognition Sitesmentioning

confidence: 88%

Transfer RNA Recognition and Aminoacylation by Synthetases

Giegé

Eriani

2021

Encyclopedia of Life Sciences

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“…On the other hand, the features discovered in the structure of the E coli tRNA Arg :ArgRS complex were unprecedented. Indeed, in contrast with the yeast complex, the anticodon loop of tRNA Arg does not interact with E coli ArgRS, so that stability of the complex relies solely on a tight binding of the tRNA on ArgRS via its identity determinant A20 from the D‐loop . As to MetRSs, the enzyme from T thermophilus was shown to share all the attributes found in other MetRSs .…”

Section: Refined Fundamentalsmentioning

confidence: 99%

“…As to class I aaRSs, several crystal structures identified new features in eukaryal and prokaryal ArgRSs. Thus, comparing the yeast ternary complex tRNA Arg :ArgRS:L‐Arg with the binary complex tRNA Arg :ArgRS revealed how arginine controls the positioning of the tRNA on the aaRS .…”

Section: Refined Fundamentalsmentioning

confidence: 99%

History of tRNA research in strasbourg

Florentz

Giegé

2019

IUBMB Life

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The tRNA molecules, in addition to translating the genetic code into protein and defining the second genetic code via their aminoacylation by aminoacyl‐tRNA synthetases, act in many other cellular functions and dysfunctions. This article, illustrated by personal souvenirs, covers the history of ~60 years tRNA research in Strasbourg. Typical examples point up how the work in Strasbourg was a two‐way street, influenced by and at the same time influencing investigators outside of France. All along, research in Strasbourg has nurtured the structural and functional diversity of tRNA. It produced massive sequence and crystallographic data on tRNA and its partners, thereby leading to a deeper physicochemical understanding of tRNA architecture, dynamics, and identity. Moreover, it emphasized the role of nucleoside modifications and in the last two decades, highlighted tRNA idiosyncrasies in plants and organelles, together with cellular and health‐focused aspects. The tRNA field benefited from a rich local academic heritage and a strong support by both university and CNRS. Its broad interlinks to the worldwide community of tRNA researchers opens to an exciting future. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1066–1087, 2019

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“…In the hamster cytoplasmic system (Guigou and Mirande 2005) and in plants (Aldinger et al 2012) additionally position A20 in the D-loop emerged as an essential determinant. A20 is also a major site of recognition in bacteria (Tamura et al 1992;McClain 1993;Shimada et al 2001a) and its tight binding to the enzyme has been confirmed by crystallography (Stephen et al 2018) but has been ruled out as such in yeast, both by transcript studies (Liu et al 1999) and by the viability of mutants in vivo (Geslain et al 2003b).…”

Section: Introductionmentioning

confidence: 99%

The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms

Igloi

2021

J Mol Evol

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During the endosymbiotic evolution of mitochondria, the genes for aminoacyl-tRNA synthetases were transferred to the ancestral nucleus. A further reduction of mitochondrial function resulted in mitochondrion-related organisms (MRO) with a loss of the organelle genome. The fate of the now redundant ancestral mitochondrial aminoacyl-tRNA synthetase genes is uncertain. The derived protein sequence for arginyl-tRNA synthetase from thirty mitosomal organisms have been classified as originating from the ancestral nuclear or mitochondrial gene and compared to the identity element at position 20 of the cognate tRNA that distinguishes the two enzyme forms. The evolutionary choice between loss and retention of the ancestral mitochondrial gene for arginyl-tRNA synthetase reflects the coevolution of arginyl-tRNA synthetase and tRNA identity elements.

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

Cited by 14 publications

References 61 publications

Transfer RNA Recognition and Aminoacylation by Synthetases

Transfer RNA Recognition and Aminoacylation by Synthetases

History of tRNA research in strasbourg

The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms

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