Escherichia coli Seryl-tRNA Synthetase Recognizes tRNASer by Its Characteristics Tertiary Structure

Asahara, Haruichi; Himeno, Hyouta; Tamura, Koji; Nameki, Nobukazu; Hasegawa, Tsunemi; Shimizu, Mikio

doi:10.1006/jmbi.1994.1186

Cited by 74 publications

(109 citation statements)

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“…As many SerRSs serylate tRNA Sec species, whose variable arm lengths often exceed those of tRNAs Ser (42), enlarged variable arms of tRNAs Ser are not unexpected as reasonably good substrates. Similarly, changes of length and identity of the nucleotides in the variable arm loop had negligible effect on serylation (mutants 16 -18), in accordance with the published results (27) and absence of the sequence conservation. In contrast, the only base pair in the variable arm shared between the isoacceptors (Ce17:Ge27) seems to be important either structurally or specifically, as its mutation shows a moderate but notable effect on the serylation efficiency of both enzymes (mutant 19).…”

Section: Barkeri Possesses Two Functional Serrs Enzymes-bothsupporting

confidence: 90%

“…These results imply that conservation of the G10:C25 base pair among M. barkeri and a significant number of other archaeal tRNAs Ser is not coincidental. The anticodon was expectedly shown not to contribute to serine identity (mutant 15), in accordance with the published results of other serine systems (27). However, mutation of G30:C40 in the anticodon stem resulted in a significant loss of serylation activity (mutants 13 and 14) for both enzymes with notable K m effect.…”

Section: Barkeri Possesses Two Functional Serrs Enzymes-bothsupporting

confidence: 86%

“…This position has been identified as an identity determinant for human phenylalanyl-tRNA synthetase (40 tRNA Ser Recognition in M. barkeri 48782 tors, it makes the largest contribution to serine identity, as confirmed by different experimental approaches (9,17,41). Despite direct contacts that have been observed between T. thermophilus SerRS and the variable arm stem (7), sequence alterations of the variable arm only insignificantly affected the serylation efficiency (27). It was therefore concluded that the variable arm of tRNA Ser is not recognized sequence specifically, but its length was shown to be most critical for efficient serylation.…”

Section: Barkeri Possesses Two Functional Serrs Enzymes-bothmentioning

confidence: 89%

“…Contrary to the identity requirements of the majority of aminoacyl-tRNA synthetases, Escherichia coli seryl-tRNA synthetase (SerRS) was found to recognize neither the anticodon nor the discriminator base of tRNA Ser (27). Instead, the length of the variable arm and the characteristic tRNA Ser tertiary structure were shown to be crucial for serylation.…”

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confidence: 91%

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Differential Modes of Transfer RNASer Recognition in Methanosarcina barkeri

Korenčić

Polycarpo

Weygand-Đurašević

et al. 2004

Journal of Biological Chemistry

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Two dissimilar seryl-transfer RNA (tRNA) synthetases (SerRSs) exist in Methanosarcina barkeri, one of bacterial type and the other resembling SerRSs present only in some methanogenic archaea. To investigate the requirements of these enzymes for tRNA Ser recognition, serylation of variant transcripts of M. barkeri tRNA Ser was kinetically analyzed in vitro with pure enzyme preparations. Characteristically for the serine system, the length of the variable arm was shown to be crucial for both enzymes, as was the identity of the discriminator base (G73). Moreover, a novel determinant for the specific tRNA Ser recognition was identified as the anticodon stem base pair G30:C40; its contribution to the efficiency of serylation was remarkable for both SerRSs. However, despite these similarities, the two SerRSs do not possess a uniform mode of tRNA Ser recognition, and additional determinants are necessary for serylation specificity by the methanogenic enzyme. In particular, the methanogenic SerRS relies on G1:C72 identity and on the number of unpaired nucleotides at the base of the variable stem for tRNA Ser recognition, unlike its bacterial type counterpart. We propose that such a distinction between the two enzymes in tRNA Ser identity determinants reflects their evolutionary pathways, hence attesting to their diversity.To maintain translational accuracy, aminoacyl-transfer RNA (tRNA) 1 synthetases are highly selective toward their amino acid and tRNA substrates. In the process of tRNA recognition, the cognate and non-cognate substrates are discriminated according to characteristic nucleotides in certain positions of the tRNA, specific for the tRNA/synthetase system.

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Section: Barkeri Possesses Two Functional Serrs Enzymes-bothsupporting

confidence: 90%

Section: Barkeri Possesses Two Functional Serrs Enzymes-bothsupporting

confidence: 86%

Section: Barkeri Possesses Two Functional Serrs Enzymes-bothmentioning

confidence: 89%

mentioning

confidence: 91%

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Differential Modes of Transfer RNASer Recognition in Methanosarcina barkeri

Korenčić

Polycarpo

Weygand-Đurašević

et al. 2004

Journal of Biological Chemistry

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“…In addition to positive recognition by cognate aminoacyl-tRNA synthetase, negative elements prevent a tRNA from being recognized by a non-cognate synthetase [8,9]. Recently, systematic studies of recognition sets in several organisms have enabled comparisons of the tRNA recognition between prokaryotes and eukaryotes, which have indicated not only similarities, but also differences [10][11][12][13][14][15][16][17][18]. Recognition by threonyl-tRNA synthetase (ThrRS) has been extensively studied in Escherichia coli and Saccharomyces cerevisiae [19,20].…”

Section: Introductionmentioning

confidence: 99%

Identity elements of Thermus thermophilus tRNA^Thr

1996

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In this study, we identified nucleotides that specify aminoacylation of tRNA TM by Thermus thermophilus threonyltRNA synthetase (ThrRS) using in vitro transcripts. Mutation studies showed that the first base pair in the acceptor stem as well as the second and third positions of the anticodon are major identity elements of T. thermophilus tRNA TM, which are essentially the same as those of Escherichia coli tRNA TM. The discriminator base, U73, also contributed to the specific aminoacylation, but not the second base pair in the acceptor stem. These findings are in contrast to E. coli tRNA TM, where the second base pair is required for threonylation, with the discriminator base, A73, playing no roles. In addition, among several mutations at the third base pair in the acceptor stem, only the G3-U70 mutant was a poor substrate for ThrRS, suggesting that the G3-UTo wobble pair, which is the identity determinant of tRNA Aj", acts as a negative element for ThrRS. Similar results were obtained in E. coli and yeast. Thus, this manner of rejection of tRNA Ala is also likely to have been retained in the threonine system throughout evolution.

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Transfer RNA recognition by aminoacyl-tRNA synthetases

Beuning¹,

Musier‐Forsyth²

1999

Biopolymers

155

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The aminoacyl‐tRNA synthetases are an ancient group of enzymes that catalyze the covalent attachment of an amino acid to its cognate transfer RNA. The question of specificity, that is, how each synthetase selects the correct individual or isoacceptor set of tRNAs for each amino acid, has been referred to as the second genetic code. A wealth of structural, biochemical, and genetic data on this subject has accumulated over the past 40 years. Although there are now crystal structures of sixteen of the twenty synthetases from various species, there are only a few high resolution structures of synthetases complexed with cognate tRNAs. Here we review briefly the structural information available for synthetases, and focus on the structural features of tRNA that may be used for recognition. Finally, we explore in detail the insights into specific recognition gained from classical and atomic group mutagenesis experiments performed with tRNAs, tRNA fragments, and small RNAs mimicking portions of tRNAs. © 2000 John Wiley & Sons, Inc. Biopoly 52: 1–28, 1999

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Escherichia coli Seryl-tRNA Synthetase Recognizes tRNASer by Its Characteristics Tertiary Structure

Cited by 74 publications

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Differential Modes of Transfer RNASer Recognition in Methanosarcina barkeri

Differential Modes of Transfer RNASer Recognition in Methanosarcina barkeri

Identity elements of Thermus thermophilus tRNA^Thr

Transfer RNA recognition by aminoacyl-tRNA synthetases

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Escherichia coli Seryl-tRNA Synthetase Recognizes tRNASer by Its Characteristics Tertiary Structure

Cited by 74 publications

References 0 publications

Differential Modes of Transfer RNASer Recognition in Methanosarcina barkeri

Differential Modes of Transfer RNASer Recognition in Methanosarcina barkeri

Identity elements of Thermus thermophilus tRNAThr

Transfer RNA recognition by aminoacyl-tRNA synthetases

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Identity elements of Thermus thermophilus tRNA^Thr