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356 a.a.
Key reference
DOI no: 10.1093/emboj/cdg148 EMBO J 22:1632-1643 (2003) PubMed id: 12660169
Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain. C.Charron, H.Roy, M.Blaise, R.Giegé, D.Kern. ABSTRACT
In most organisms, tRNA aminoacylation is ensured by 20 aminoacyl-tRNA synthetases (aaRSs). In eubacteria, however, synthetases can be duplicated as in Thermus thermophilus, which contains two distinct AspRSs. While AspRS-1 is specific, AspRS-2 is non-discriminating and aspartylates tRNA(Asp) and tRNA(Asn). The structure at 2.3 A resolution of AspRS-2, the first of a non-discriminating synthetase, was solved. It differs from that of AspRS-1 but has resemblance to that of discriminating and archaeal AspRS from Pyrococcus kodakaraensis. The protein presents non-conventional features in its OB-fold anticodon-binding domain, namely the absence of a helix inserted between two beta-strands of this fold and a peculiar L1 loop differing from the large loops known to interact with tRNA(Asp) identity determinant C36 in conventional AspRSs. In AspRS-2, this loop is small and structurally homologous to that in AsnRSs, including conservation of a proline. In discriminating Pyrococcus AspRS, the L1 loop, although small, lacks this proline and is not superimposable with that of AspRS-2 or AsnRS. Its particular status is demonstrated by a loop-exchange experiment that renders the Pyrococcus AspRS non-discriminating.
Selected figure(s)
Figure 1.
Figure 1 Stereoviews of the MAD electron density map (contoured at 1.0) of part of the catalytic site (A) and anticodon-binding (B) domains of T.thermophilus AspRS-2. In (A), the
-strands A2, A3, A4, A5, and A6 are labelled as in the P.kodakaraensis AspRS structure (Schmitt et al., 1998). In (B), displaying an amino acid stretch (residues 65 -75) comprising loop L1, notice the functionally important Pro72 and the lack of density for the side chain of Lys70 (see text).
Figure 2.
Figure 2 Structure of T.thermophilus AspRS-2. (A) Ribbon representation of the dimeric synthetase. Subunit A is drawn in yellow (N-terminal domain) and in orange (catalytic domain), and subunit B is in blue (N-terminal domain) and purple (catalytic domain). The N- and C-terminal ends of each subunit are labelled. (B) Electrostatic potential mapped on the molecular surface of dimeric AspRS-2, as computed with Swiss-Pdb Viewer (Guex and Peitsch, 1997). Blue, white and red regions correspond to positive, neutral and negative electrostatic potentials, respectively. The putative location of a backbone model of tRNA^Asp, as in the complex with T.thermophilus AspRS-1 (Briand et al., 2000), covering 'blue' regions of positive potential, is indicated. The orientation of the synthetase is as in (A).The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 1632-1643) copyright 2003. Figures were selected by an automated process.
Literature references that cite this PDB file's key reference
PubMed id Reference 17620724 K.Suzuki, Y.Sato, Y.Maeda, S.Shimizu, M.T.Hossain, S.Ubukata, T.Sekiguchi, and A.Takénaka (2007).
Crystallization and preliminary X-ray crystallographic study of a putative aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7.Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 608-612.
17533454 T.Cathopoulis, P.Chuawong, and T.L.Hendrickson (2007).
Novel tRNA aminoacylation mechanisms.Mol Biosyst, 3, 408-418.
17881821 Y.Sato, Y.Maeda, S.Shimizu, M.T.Hossain, S.Ubukata, K.Suzuki, T.Sekiguchi, and A.Takénaka (2007).
Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodons.Acta Crystallogr D Biol Crystallogr, 63, 1042-1047.
PDB code: 1wyd
16352843 D.Bernard, P.M.Akochy, D.Beaulieu, J.Lapointe, and P.H.Roy (2006).
Two residues in the anticodon recognition domain of the aspartyl-tRNA synthetase from Pseudomonas aeruginosa are individually implicated in the recognition of tRNAAsn.J Bacteriol, 188, 269-274.
16059752 H.L.Wu, S.Bagby, and J.M.van den Elsen (2005).
Evolution of the genetic triplet code via two types of doublet codons.J Mol Evol, 61, 54-64.
15706032 J.Rinehart, B.Krett, M.A.Rubio, J.D.Alfonzo, and D.Söll (2005).
Saccharomyces cerevisiae imports the cytosolic pathway for Gln-tRNA synthesis into the mitochondrion.Genes Dev, 19, 583-592.
15781458 L.Feng, J.Yuan, H.Toogood, D.Tumbula-Hansen, and D.Söll (2005).
Aspartyl-tRNA synthetase requires a conserved proline in the anticodon-binding loop for tRNA(Asn) recognition in vivo.J Biol Chem, 280, 20638-20641.
12766171 A.Brevet, J.Chen, S.Commans, C.Lazennec, S.Blanquet, and P.Plateau (2003).
Anticodon recognition in evolution: switching tRNA specificity of an aminoacyl-tRNA synthetase by site-directed peptide transplantation.J Biol Chem, 278, 30927-30935.
14665676 P.O'Donoghue, and Z.Luthey-Schulten (2003).
On the evolution of structure in aminoacyl-tRNA synthetases.Microbiol Mol Biol Rev, 67, 550-573. The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.
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