Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon<i>Pyrococcus horikoshii</i>

Itoh, Yuzuru; Sekine, S.; Kuroishi, Chizu; Terada, Takaho; Shirouzu, Mikako; Kuramitsu, Seiki; Yokoyama, Shigeyuki

doi:10.4161/rna.5.3.6876

Cited by 28 publications

(33 citation statements)

References 51 publications

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“…This elongated variable arm is well conserved throughout the evolutionary process from prokaryotes to eukaryotes (with the only exception being metazoan mitochondria). Accordingly, SerRS enzymes have acquired a unique N-terminal domain, mostly structured as a coiled-coil (3,16,17), for recognizing the variable arm. The N-terminal coiledcoil of P. horikoshii SerRS (17) comprises additional basic residues as compared with bacterial SerRSs (3, 16) and a Trp residue (Trp 40 ) found in other archaeal/eukaryal serine-specific synthetases (17).…”

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

confidence: 99%

“…Accordingly, SerRS enzymes have acquired a unique N-terminal domain, mostly structured as a coiled-coil (3,16,17), for recognizing the variable arm. The N-terminal coiledcoil of P. horikoshii SerRS (17) comprises additional basic residues as compared with bacterial SerRSs (3, 16) and a Trp residue (Trp 40 ) found in other archaeal/eukaryal serine-specific synthetases (17). An insertion of 20 amino acids into the N-terminal sequences of metazoans and trypanosomatid SerRS sequences, at the center of the predicted coiled-coil motif, suggests that this region may extend beyond the length seen in the structures solved so far (39).…”

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

confidence: 99%

“…Despite pronounced structural differences between the tRNA-binding domains in two SerRS types, in each case the N-terminal domain of one subunit interacts with the extra arm of tRNA Ser , to position the 3Ј-end of tRNA into the C-terminal active site of another subunit (23)(24)(25). The recent crystal structure of the first archaeal/eukaryal SerRS from the archaeon P. horikoshii, and the structure-based model of the enzyme bound with the T. thermophilus and P. horikoshii tRNAs Ser , suggested that the helical N-terminal domain of P. horikoshii SerRS is also involved in the binding of the extra arm of tRNA (17).…”

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confidence: 99%

“…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).…”

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confidence: 99%

“…However, the tRNA specificity of the archaeal/eukaryal SerRS from P. horikoshii seems to depend mainly on the extra arm, but not on the acceptor stem. Indeed, this enzyme exhibits quite relaxed specificity for tRNA Ser recognition (17). Archaeon Methanosarcina barkeri, which possesses two dissimilar SerRSs, one of a bacterial-and the other of methanogenic-type, provides an excellent system for studying the evolution of tRNA Ser determinants.…”

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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%

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

confidence: 99%

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confidence: 99%

mentioning

confidence: 99%

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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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Evolutionarily conserved cysteines in plant cytosolic seryl‐tRNA synthetase are important for its resistance to oxidation

Evic,

Soic,

Mocibob

et al. 2023

FEBS Letters

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We have previously identified a unique disulfide bond in the crystal structure of Arabidopsis cytosolic seryl‐tRNA synthetase involving cysteines evolutionarily conserved in all green plants. Here, we discovered that both cysteines are important for protein stability, but with opposite effects, and that their microenvironment may promote disulfide bond formation in oxidizing conditions. The crystal structure of the C244S mutant exhibited higher rigidity and an extensive network of noncovalent interactions correlating with its higher thermal stability. The activity of the wild‐type showed resistance to oxidation with H2O2, while the activities of cysteine‐to‐serine mutants were impaired, indicating that the disulfide link may enable the protein to function under oxidative stress conditions which can be beneficial for an efficient plant stress response.

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Emergence and Evolution

Bullwinkle

Ibba

2013

Topics in Current Chemistry

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The aminoacyl-tRNA synthetases (aaRSs) are essential components of the protein synthesis machinery responsible for defining the genetic code by pairing the correct amino acids to their cognate tRNAs. The aaRSs are an ancient enzyme family believed to have origins that may predate the last common ancestor and as such they provide insights into the evolution and development of the extant genetic code. Although the aaRSs have long been viewed as a highly conserved group of enzymes, findings within the last couple of decades have started to demonstrate how diverse and versatile these enzymes really are. Beyond their central role in translation, aaRSs and their numerous homologs have evolved a wide array of alternative functions both inside and outside translation. Current understanding of the emergence of the aaRSs, and their subsequent evolution into a functionally diverse enzyme family, are discussed in this chapter.

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

Cited by 28 publications

References 51 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

Evolutionarily conserved cysteines in plant cytosolic seryl‐tRNA synthetase are important for its resistance to oxidation

Emergence and Evolution

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