The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site.

Cusack, Stephen; Yaremchuk, A.; Tukalo, M. A.

doi:10.1002/j.1460-2075.1996.tb00644.x

Cited by 164 publications

(188 citation statements)

References 36 publications

(124 reference statements)

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“…This clearly suggests that induced fit may be a major mechanism for enhancement of discrimination between cognate and noncognate tRNAs provided the conformational change gives rise to an active site with greater complimentarity to the transition state. Such a mechanism has been suggested before for other aminoacyl-tRNA synthetases (Cusack et al, 1996). We thus conclude that the binding interactions of the cognate and the noncognate tRNAs are similar.…”

Section: Discussionsupporting

confidence: 84%

A cognate tRNA specific conformational change in glutaminyl‐tRNA synthetase and its implication for specificity

Mandal¹,

Bhattacharyya²,

Bhattacharyya³

et al. 1998

Protein Science

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Conformational changes that occur upon substrate binding are known to play crucial roles in the recognition and specific aminoacylation of cognate tRNA by glutaminyl-tRNA synthetase. In a previous study we had shown that glutaminyltRNA synthetase labeled selectively in a nonessential sulfhydryl residue by an environment sensitive probe, acrylodan, monitors many of the conformational changes that occur upon substrate binding. In this article we have shown that the conformational change that occurs upon tRNAG'" binding to glnRS/ATP complex is absent in a noncognate tRNA tRNAG1"-glnRS/ATP complex. CD spectroscopy indicates that this cognate tRNAG1"-induced conformational change may involve only a small change in secondary structure. The Van? Hoff plot of cognate and noncognate tRNA binding in the presence of ATP is similar, suggesting similar modes of interaction. It was concluded that the cognate tRNA induces a local conformational change in the synthetase that may be one of the critical elements that causes enhanced aminoacylation of the cognate tRNA over the noncognate ones.Keywords: conformational change; discrimination; fluorescence; synthetase: tRNA Translation of nucleotide sequences in mRNAs to amino acid sequences in proteins is characterized by high degree of accuracy. This level of accuracy is primarily determined at the level of aminoacylation of tRNAs by aminoacyl-tRNA synthetases (Schimme1 & Soll, 1979;Schimmel, 1987;Carter, 1993). The correct aminoacylation of all the tRNAs involves positive recognition of the cognate tRNAs (McClain, 1993) and negative discrimination of the noncognate tRNAs (Schmitt et al., 1993). Recognition of cognate tRNAs has been studied intensively, and structural elements that are responsible for recognition have now been mapped for many systems (Normanly & Abelson, 1989;Mechulam et al., 1995). Very little is known, however, about the factors that are responsible for negative discrimination.Even in the case of recognition of cognate tRNAs where the identity elements have been mapped, it is not clear exactly how this elements influence enzymatic properties and translates recognition into catalytic competence. Due to pioneering work by Soll and co-workers, glutaminyl-tRNA synthetase has emerged as one Reprint requests to: Siddhartha Roy, Department of Biophysics, Bose Institute, P 1/12. C.I.T. Scheme VI1 M, Calcutta 700054, India; e-mail: siddarth@boseinst.ernet.in.Abbreviations: GlnRS, glutaminyl-tRNA synthetase; acrylodan, 6-acryloyl-2-dimethyl aminonaphthalene; CD, circular dichroism: tempol, (4-hydroxy-2,2,6,6-tetramethylpiperidine-I -0xyl): GluRS, glutamyl-tRNA synthetase.of the best systems to study the recognition and the consequent catalytic activation process. Jahn et al. (1991) and Ibba et al. (1996) have shown that the correct recognition of anti-codon bases increases kc,, of the enzyme glutaminyl-tRNA synthetase of Escherichia coli significantly. Because the anti-codon binding pocket is approximately 35 A away from the active site, a protein conformational ...

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Section: Discussionsupporting

confidence: 84%

A cognate tRNA specific conformational change in glutaminyl‐tRNA synthetase and its implication for specificity

Mandal¹,

Bhattacharyya²,

Bhattacharyya³

et al. 1998

Protein Science

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“…However, sequence alignments may suggest participation of methanogenic M. barkeri SerRS Glu-338 in discriminator base recognition. As to the bacterial enzyme, its motif 2 loop shows a great degree of similarity with the loop of T. thermophilus SerRS; therefore, it may be proposed that Glu-230 of the M. barkeri SerRS is involved in G73 recognition analogous to Glu-260 in the T. thermophilus structure (47). Unfortunately, the available data are insufficient to comment on anticodon stem recognition.…”

Section: Trnamentioning

confidence: 99%

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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“…2). 18,19 P. horikoshii SerRS also has additional basic residues in the region proximal to the extra arm: Arg41, Arg49, Arg51, Lys396 and Arg398. Our mutational analyses revealed that these residues indeed contribute to the tRNA recognition by P. horikoshii SerRS (Table 3).…”

Section: Discussionmentioning

confidence: 99%

“…15 Consistent with the biochemical studies, the crystal structure of the Thermus thermophilus SerRS and tRNA Ser complex clearly revealed that SerRS interacts with the first six base-pairs in the extra stem, and the first six base-pairs in the acceptor stem, but does not interact with the anticodon arm. 18,19 The crystal structure also revealed the enzyme interaction with G73 and C74.…”

Section: Introductionmentioning

confidence: 92%

Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeonPyrococcus horikoshii

Itoh¹,

Sekine²,

Kuroishi³

et al. 2008

RNA Biology

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Seryl-tRNA synthetase (SerRS) catalyzes the ligation of serine to the 3'-end of serine tRNA (tRNA Ser ), which is typical of the type-2 tRNAs characterized by a long extra arm. The SerRSs are divided into two types, the archaeal/eukaryal and bacterial types. In this study, we solved the crystal structures of the SerRS from the archaeon Pyrococcus horikoshii bound with 5'-O-[N-(L-seryl)-sulfamoyl]-adenosine at 2.6 Å and with ATP at 2.8 Å, as well as in the apo form at 3.0 Å. P. horikoshii SerRS recognizes the seryl and adenylate moieties in a manner similar to those of the bacterial and mitochondrial SerRSs from Thermus thermophilus and Bos taurus, respectively, but different from that of the unusual SerRS from the methanogenic archaeon Methanosarcina barkeri. P. horikoshii SerRS efficiently aminoacylated not only P. horikoshii tRNA Ser but also bacterial tRNA Ser s from T. thermophilus and Escherichia coli. Models of P. horikoshii SerRS bound with the T. thermophilus and P. horikoshii tRNA Ser s suggested that the helical domain of P. horikoshii SerRS is involved in the extra arm binding. This region of P. horikoshii SerRS has additional basic residues as compared with T. thermophilus SerRS, and a Trp residue specific to the archaeal/eukaryal SerRSs. Mutational analyses revealed that the basic and Trp residues are important for tRNA aminoacylation. P. horikoshii SerRS has the archaea-specific insertion, which collaborates with the core domain to form a basic channel leading to the active site. Two sulfate ions are bound to the channel, suggesting that the tRNA 3' region might bind to the channel.

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The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site.

Cited by 164 publications

References 36 publications

A cognate tRNA specific conformational change in glutaminyl‐tRNA synthetase and its implication for specificity

A cognate tRNA specific conformational change in glutaminyl‐tRNA synthetase and its implication for specificity

Differential Modes of Transfer RNASer Recognition in Methanosarcina barkeri

Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeonPyrococcus horikoshii

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