A new crystal form of the complex between seryl‐tRNA synthetase and tRNA<sup>Ser</sup> from <i>Thermus thermophilus</i> that diffracts to 2.8 Å resolution

Yaremchuk, A.; Tukalo, M. A.; Krikliviy, I. A.; Mal'chenko, N. N.; Biou, Valérie; Berthet-Colominas, C.; Cusack, Stephen

doi:10.1016/0014-5793(92)81319-h

Cited by 17 publications

(9 citation statements)

References 14 publications

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“…Form four crystals of the Tthermophilus SerRS-tRNASer (GGA) complex were grown as described (Yaremchuk et al, 1992) but in the presence of 300 jM (5'-O-[N-(L-seryl)-sulfamoyl]adenosine} a synthetic analogue of seryl-adenylate (Belrhali et al, 1994). These crystals contain a single tRNA molecule bound to the SerRS dimer in the crystal asymmetric unit.…”

Section: Methodsmentioning

confidence: 99%

“…Here we present an improved structure in which the interactions of the acceptor stem with the synthetase are now visible, even though bases 74-76 at the extreme 3' end of the tRNA remain poorly ordered. Data has been remeasured on the same crystal form as that previously described (Yaremchuk et al, 1992;Biou et al, 1994) which contains a single tRNA bound to the SerRS dimer. However, there are two significant differences: firstly, the complex was cocrystallized in the presence of the sulfamoyl analogue of the natural intermediate seryl-adenylate (Ser-AMS, Belrhali et al 1994) and secondly, data collection was performed on frozen crystals at low temperature.…”

Section: Introductionmentioning

confidence: 99%

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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.

1996

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The low temperature crystal structure of the ternary complex of Thermus thermophilus seryl‐tRNA synthetase with tRNA(Ser) (GGA) and a non‐hydrolysable seryl‐adenylate analogue has been refined at 2.7 angstrom resolution. The analogue is found in both active sites of the synthetase dimer but there is only one tRNA bound across the two subunits. The motif 2 loop of the active site into which the single tRNA enters interacts within the major groove of the acceptor stem. In particular, a novel ring‐ring interaction between Phe262 on the extremity of this loop and the edges of bases U68 and C69 explains the conservation of pyrimidine bases at these positions in serine isoaccepting tRNAs. This active site takes on a significantly different ordered conformation from that observed in the other subunit, which lacks tRNA. Upon tRNA binding, a number of active site residues previously found interacting with the ATP or adenylate now switch to participate in tRNA recognition. These results shed further light on the structural dynamics of the overall aminoacylation reaction in class II synthetases by revealing a mechanism which may promote an ordered passage through the activation and transfer steps.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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.

1996

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“…Arginine 94 is located in the loop between helix H2 and ␤-strand A4 and according to the docking model positioned to interact with the T-loop of the tRNA Ser . The crystal structure of the SerRS⅐tRNA Ser complex from T. thermophilus (23,26,46) revealed that the tRNA-binding coiled-coil of bacterial SerRS is buried between the TC arm and the long extra arm of tRNA Ser . Likewise, biochemical studies on the mammalian mitochondrial system pointed to the importance of the T-loop, which is the main identity element for two unusual tRNA Ser isoacceptors.…”

Section: Identification Of Amino Acids In the N-terminal Domain Of MMmentioning

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 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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“…When the saturation-binding data from Figure 3a was fit to the Hill equation (Figure 3b) the Hill coefficients in the absence and the presence of the MtArgRS were calculated (Table 3). The observed cooperativity for binding of tRNA Ser to SerRS (Figure 3a) is also reflected in the Hill coefficient, which for MtSerRS:tRNA Ser (Table 3) 11,30 and biochemical studies on heterodimers. 12,32 SerRS from the yeast Saccharomyces cerevisiae has also been found to bind one or two tRNA Ser cooperatively 24 .…”

Section: Alteration Of K D Value In Mtserrs:trna Ser Association Uponmentioning

confidence: 86%

Arginyl-tRNA Synthetase Facilitates Complex Formation Between Seryl-tRNA Synthetase and its Cognate Transfer RNA

Godinić-Mikulčić¹,

Jarić²,

Weygand-Đurašević³

2012

Croat. Chem. Acta

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Abstract. Several studies have revealed the involvement of multi aminoacyl-tRNA synthetase complexes (MSC) in archaeal and eukaryotic translation. Here we analyzed interactions of atypical Methanothermobacter thermautotrophicus seryl-tRNA synthetase (MtSerRS), transfer RNA (tRNA Ser ) and arginyl-tRNA synthetase (ArgRS). Surface plasmon resonance (SPR) was used to determine dissociation constants for the MtSerRS:tRNA Ser complex and the results were consistent with cooperative binding of tRNA Ser . This finding was supported by the ability of MtSerRS to bind two tRNAs in gel mobility shift assay. Notably, the MtSerRS:tRNA Ser complex formation was stimulated by MtArgRS, previously determined interacting partner of MtSerRS. MtArgRS decreases K d for MtSerRS:tRNA Ser two-fold, but does not affect cooperative properties or stoichiometry of the complex. Further investigation of complex formation between MtSerRS and tRNA Ser showed that this molecular interaction is salt-dependent. The most pronounced improvements in binding were determined at high ionic strength, using Tris as a buffering agent, while the addition of Mg 2+ ions led to the same SPR response. (doi: 10.5562/cca2146)

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A new crystal form of the complex between seryl‐tRNA synthetase and tRNA^Ser from Thermus thermophilus that diffracts to 2.8 Å resolution

Abstract: A new crystal form of the complex between seryl-tRNA synthetase and tRNASer from Thermus thermophilus that diffracts to 2.8 A resolution

Cited by 17 publications

References 14 publications

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.

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.

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

Arginyl-tRNA Synthetase Facilitates Complex Formation Between Seryl-tRNA Synthetase and its Cognate Transfer RNA

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A new crystal form of the complex between seryl‐tRNA synthetase and tRNASer from Thermus thermophilus that diffracts to 2.8 Å resolution

Abstract: A new crystal form of the complex between seryl-tRNA synthetase and tRNASer from Thermus thermophilus that diffracts to 2.8 A resolution

Cited by 17 publications

References 14 publications

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.

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.

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

Arginyl-tRNA Synthetase Facilitates Complex Formation Between Seryl-tRNA Synthetase and its Cognate Transfer RNA

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A new crystal form of the complex between seryl‐tRNA synthetase and tRNA^Ser from Thermus thermophilus that diffracts to 2.8 Å resolution