Parameters for the molecular recognition of transfer RNAs

Schimmel, Paul

doi:10.1021/bi00433a001

Cited by 124 publications

(67 citation statements)

References 78 publications

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“…The same intensifications of phosphate cleavage as in the wild-type tRNAASP transcript are also observed, which suggests that similar conformational changes are occurring in the tRNAPhe transcript with aspartic acid identity elements as in wild-type tRNAASP. These experiments graphically illustrate that the interactions between tRNA and cognate synthetase required for correct aminoacylation are directed by a small number of nucleotides (7,8).…”

Section: Discussionmentioning

confidence: 95%

“…Despite a large number of functional studies on interaction of mutant or noncognate tRNAs with synthetases (6)(7)(8), little is known about the structural basis of these interactions. In this paper, we compare the interaction of wild-type and mutant tRNAASP transcripts with AspRS by using footpninting experiments based on cleavage of phosphorothioate-containing transcripts by 12; this technique has recently been applied to the interaction of Escherichia coli tRNASer and SerRS (9).…”

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confidence: 99%

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Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase.

Rudinger

Puglisi

Pütz

et al. 1992

Proc. Natl. Acad. Sci. U.S.A.

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The interaction of wild-type and mutant yeast tRNAfsP transcripts with yeast aspartyl-tRNA synthetase (AspRS; EC 6.1.1.12) has been probed by using iodine cleavage of phosphorothioate-substituted transcripts. Accurate aminoacylation of tRNAs requires specific interaction between tRNA and its cognate aminoacyl-tRNA synthetase (aaRS). The complex of yeast tRNAASP with aspartyltRNA synthetase (AspRS; EC 6.1.1.12) has been studied by footprinting with a number of probes in solution (1, 2), and a high-resolution x-ray structure (3) is presently being refined. As a result, regions of contact between protein and tRNA were defined; the tRNA interacts with AspRS along the variable-loop side of the L-shaped tertiary structure, including the anticodon loop and stem, the base of the D-stem, and the 3' extremity of the acceptor stem. Nucleotides functionally important for specific aspartylation (Fig. 1) were recently identified by kinetic analysis of in vitro transcripts (5); they correspond to nucleotides G34, U35, and C36 in the anticodon, G73 at the acceptor end, and-base pair G10U25 at the base of the D-stem. Mutation of these nucleotides resulted in a dramatic loss of aspartylation activity and suggested that the wild-type identity nucleotides are in direct contact with the protein in the enzyme-substrate complex and that these stabilizing interactions are disrupted upon mutation. Unfortunately, the present state of refinement of the crystal structure is not sufficient to identify the exact contacts between tRNA and protein.

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Section: Discussionmentioning

confidence: 95%

mentioning

confidence: 99%

Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase.

Rudinger

Puglisi

Pütz

et al. 1992

Proc. Natl. Acad. Sci. U.S.A.

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“…Aminoacyl-tRNA synthetases (AARSs) 1 catalyze the attachment of amino acids to their cognate tRNAs to establish the genetic code. To obtain the high degree of accuracy that is observed in translation, these enzymes must exhibit strict substrate specificity for their cognate amino acids and tRNAs.…”

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confidence: 99%

“…To obtain the high degree of accuracy that is observed in translation, these enzymes must exhibit strict substrate specificity for their cognate amino acids and tRNAs. Recognition of tRNA by AARSs is facilitated by both positive and negative identity elements contained within the RNA structure that ensure binding to the proper enzyme (1)(2)(3). To select the correct amino acid AARSs must discriminate between all standard and nonstandard amino acids that are available in the cell, many of which are structurally similar.…”

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Genetic Code Ambiguity

Nangle

Lagard

Döring³

et al. 2002

Journal of Biological Chemistry

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The rules of the genetic code are established in reactions that aminoacylate tRNAs with specific amino acids. Ambiguity in the code is prevented by editing activities whereby incorrect aminoacylations are cleared by specialized hydrolytic reactions of aminoacyl tRNA synthetases. Whereas editing reactions have long been known, their significance for cell viability is still poorly understood. Here we investigated in vitro and in vivo four different mutations in the center for editing that diminish the proofreading activity of valyl-tRNA synthetase (ValRS). The four mutant enzymes were shown to differ quantitatively in the severity of the defect in their ability to clear mischarged tRNA in vitro. Strikingly, in the presence of excess concentrations of ␣-aminobutyrate, one of the amino acids that is misactivated by ValRS, growth of bacterial strains bearing these mutant alleles is arrested. The concentration of misactivated amino acid required for growth arrest correlates inversely in a rank order with the degree of the editing defect seen in vitro. Thus, cell viability depends directly on the suppression of genetic code ambiguity by these specific editing reactions and is finely tuned to any perturbation of these reactions.Aminoacyl-tRNA synthetases (AARSs) 1 catalyze the attachment of amino acids to their cognate tRNAs to establish the genetic code. To obtain the high degree of accuracy that is observed in translation, these enzymes must exhibit strict substrate specificity for their cognate amino acids and tRNAs. Recognition of tRNA by AARSs is facilitated by both positive and negative identity elements contained within the RNA structure that ensure binding to the proper enzyme (1-3). To select the correct amino acid AARSs must discriminate between all standard and nonstandard amino acids that are available in the cell, many of which are structurally similar. (Special amino acids such as formylmethionine (4) and selenocysteine (5) are formed after the amino acid recognition step and are created by special postaminoacylation reactions.) Discrimination is primarily achieved by preferential binding of cognate amino acids to the correct active site and by exclusion of larger substrates (6, 7). For several synthetases, including valyl-tRNA synthetase (ValRS) and isoleucyl-tRNA synthetase (IleRS), the affinity difference between the cognate amino acid and sterically similar amino acids is not sufficient to prevent errors in protein synthesis on the order of 0.5-1% (8 -10), far greater than observed in vivo (ϳ0.0001%) (11). To avoid errors, the enzymes evolved proofreading mechanisms that are tRNAdependent (12-15). The combination of substrate selection and tRNA-dependent editing provides the low error rate observed in protein synthesis.ValRS catalyzes specific aminoacylation of tRNA Val in a reaction initiated by the binding of valine at the active site where it is condensed with ATP to form valyl adenylate (Val-AMP). The activated amino acid is subsequently transferred to the 3Ј-end of tRNAVal to generate Val-tRNA V...

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Parameters for the molecular recognition of transfer RNAs

Cited by 124 publications

References 78 publications

Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase.

Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase.

Genetic Code Ambiguity

Alanine Transfer RNA Synthetase: Structure–Function Relationships and Molecular Recognition of Transfer RNA

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