Dual-mode recognition of noncanonical tRNAsSer by seryl-tRNA synthetase in mammalian mitochondria

Chimnaronk, Sarin; Jeppesen, Mads Gravers; Suzuki, Tsutomu; Nyborg, Jens; Watanabe, Kimitsuna

doi:10.1038/sj.emboj.7600811

Cited by 93 publications

(117 citation statements)

References 46 publications

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“…On the other hand, although the coiled-coiled N-terminal domain exists in the metazoan mitochondrial SerRS, it does not bind the tRNA extra arm, because its cognate tRNA structures markedly deviate from the canonical cloverleaf secondary structure with highly truncated and/or intrinsically missing arms (40). Consequently, biochemical (41) and recent structural studies (19) have revealed a truly distinctive mode of tRNA binding by mammalian mitochondrial SerRS. The SerRSs from methanogenic archaea also differ markedly from their bacterial-type counterparts, most notably through the absence of the N-terminal coiled-coil (21).…”

Section: Idiosyncratic N-terminal Domains Of Serrs Enzymes Provide Trnamentioning

confidence: 99%

“…18), with exception of the mammalian mitochondrial enzyme (19 or domains of life) and bacterial tRNA Tyr species (20). In bacterial-type SerRS, the N-terminal domain forms an antiparallel ␣-helical coiled-coil structure (3,16), whereas in the methanogenic-type counterpart it is significantly larger and composed of a six-stranded antiparallel ␤-sheet capped by a bundle of three helices (H1, H2, and H4) with up-down topology and an additional short helix (H3) that runs almost perpendicular to helix H4 (21) (see Fig.…”

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confidence: 99%

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Identification of Amino Acids in the N-terminal Domain of Atypical Methanogenic-type Seryl-tRNA Synthetase Critical for tRNA Recognition

Jarić

Bilokapić

Lesjak

et al. 2009

Journal of Biological Chemistry

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The aminoacyl-tRNA synthetases (aaRSs) 2 catalyze the activation of cognate amino acids and their transfer to the 3Ј-end of corresponding tRNA molecules. The aaRSs are a highly conserved family of enzymes comprised of two distinct structural groups referred to as classes I and II (1-3), with a notable exception of LysRS representatives, which belong to both classes (4). Although the catalytic mechanisms of various aaRSs are broadly similar (5), each enzyme has developed a high specificity in recognizing its cognate amino acid and tRNA, which is pivotal for accurate translation of the genetic code (1). The discrimination of the amino acids is based on recognizing the differences in the size and charge of the molecules (6). The specificity of tRNA selection depends on a set of identity determinants that are mostly located at two distal extremities: the anticodon loop and the amino acid accepting stem. In a few instances, identity elements are also found in the D-arm, T-arm, and variable loop. They can either act as positive determinants that enhance aminoacylation or negative ones that prevent aminoacylation. The recognition of tRNAs by synthetases can also be affected by the modification of particular nucleotides (7,8). AaRSs show divergent strategies for tRNA recognition. Most notably, class I and class II aaRSs (including pyrrolysyl-tRNA synthetase, see Ref. 9) approach tRNAs from the minor and major groove sides of the acceptor stem, respectively (10). Although the majority of determinants are in direct contact with cognate synthetases (8), the aminoacylation fidelity is controlled by kinetic differences more than by binding affinities (11).Seryl-tRNA synthetases (SerRSs), which catalyze the aminoacylation of several tRNA Ser isoacceptors and tRNA Sec with serine, can be divided into two structurally different groups: bacterial-type SerRSs function in a variety of archaeal, bacterial, and eukaryotic organisms, whereas the methanogenic-type was found only in methanogenic archaea (12, 13). Furthermore, based on sequence comparison (14, 15) and x-ray analyses, two subgroups of bacterial-type SerRSs were identified: one consists of the enzymes from bacterial sources, best represented by those from Thermus thermophilus (16) and Escherichia coli (3), and an archaeal/eukaryal-type, structurally related to SerRS from archaeon Pyrococcus horikoshii (17).All SerRSs are functional homodimers with a C-terminal active site domain typical for class II aaRSs and an N-terminal domain that is responsible for binding of the long

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Section: Idiosyncratic N-terminal Domains Of Serrs Enzymes Provide Trnamentioning

confidence: 99%

mentioning

confidence: 99%

Identification of Amino Acids in the N-terminal Domain of Atypical Methanogenic-type Seryl-tRNA Synthetase Critical for tRNA Recognition

Jarić

Bilokapić

Lesjak

et al. 2009

Journal of Biological Chemistry

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“…The manner of the Ser-SA interaction by P. horikoshii SerRS is the same as that by T. thermophilus SerRS and Bos taurus mitochondrial SerRS, 27,37 except for the involvement of Ser411 with Ser-SA in the former (Figs. 1C and 2).…”

Section: Introductionmentioning

confidence: 71%

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 transfer of activated amino acids to different thiols was confirmed by TLC analysis of the reaction mixtures containing 14 C-amino acids (Figure 2). Examination of TLC plates revealed that radiolabeled amino acids were converted into the new products in the presence of the enzymes and various thiols.…”

Section: Thiol Aminoacylation By Aa:cp Ligasesmentioning

confidence: 91%

“…10,11 All seryl-tRNA synthetases (SerRSs) are functional homodimers with a C-terminal active site domain typical for class II aaRSs and an Nterminal domain that is responsible for tRNA binding. [12][13][14][15] We have recently shown that methanogenictype SerRSs display several idiosyncratic structural features and exhibit a different mode of substrate recognition in comparison with bacterial-type SerRSs. [15][16][17] Full-length or truncated SerRS-like proteins, homologous to both types of housekeeping SerRSs have been identified.…”

Section: Introductionmentioning

confidence: 99%

Substrate Recognition by Novel Family of Amino Acid:[Carrier Protein] Ligases

Močibob¹,

Ivić²,

Subasic³

et al. 2011

Croat. Chem. Acta

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Abstract. Amino acid:[carrier protein] ligases (aa:CP ligases) are newly discovered homologs of aminoacyl-tRNA synthetases (aaRS) which aminoacylate carrier proteins instead of tRNA. Activated amino acids are attached to prosthetic group of carrier proteins by thioester bond. Weak thioacylation activity was observed for many conventional aaRS. Therefore, different thiols were investigated as substrate analogs for aa:CP ligases. Here we show that coenzyme A, dithiothreitol and cysteine are efficiently aminoacylated by aa:CP ligases. The crystal structure of aa:CP ligase from Bradyrhizobium japonicum in complex with coenzyme A was solved, and revealed that CoA, besides acting as the substrate analog of the carrier protein, also competes with ATP for binding to the active site. aa:CP ligases do not aminoacylate tRNA, although they remarkably resemble catalytic core of atypical seryl-tRNA synthetases (aSerRS) from methanogenic archaea. Since aa:CP ligases lack tRNA-binding domain, fusion proteins of aa:CP ligases and aSerRS tRNA-binding domain were prepared in attempt to restore tRNA aminoacylation activity. Although fusion proteins were able to bind tRNA through appended domain, tRNA could not substitute carrier proteins in aminoacylation reaction. (doi: 10.5562/cca1818)

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Dual-mode recognition of noncanonical tRNAsSer by seryl-tRNA synthetase in mammalian mitochondria

Cited by 93 publications

References 46 publications

Identification of Amino Acids in the N-terminal Domain of Atypical Methanogenic-type Seryl-tRNA Synthetase Critical for tRNA Recognition

Identification of Amino Acids in the N-terminal Domain of Atypical Methanogenic-type Seryl-tRNA Synthetase Critical for tRNA Recognition

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

Substrate Recognition by Novel Family of Amino Acid:[Carrier Protein] Ligases

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