E. coli tRNA coding for glutamine TTG anti-codon
E. coli tRNA1(Gln) (TTG anticodon) is one of two isoacceptor tRNAs responsible for delivering glutamine to the ribosome, decoding both CAA and CAG glutamine codons during translation. The wobble position U34 of this tRNA carries the hypermodified nucleoside 5-carboxyaminomethyl-2-thiouridine (cmnm⁵s²U) in its native form; mass spectrometric analysis of affinity-purified native tRNA1(Gln) confirmed this as the complete modification. The 2-thio moiety alone improves binding affinity to glutaminyl-tRNA synthetase (GlnRS) by 10-fold over an unmodified transcript, with the cmnm⁵ modification contributing a further 4-fold improvement. While the listed tRNA does not possess these modifications, it serves as a useful control tRNA for structure-function studies. GlnRS is a Class I aminoacyl-tRNA synthetase that recognizes tRNA(Gln) through contacts spanning the entire inside of the L-shaped molecule, from the anticodon to the acceptor stem. The primary identity elements are all three anticodon bases and key acceptor stem positions, including the discriminator base G73 and the G1·U72 pair; contacts with the 2-amino groups of G2 and G3 via the minor groove further contribute to discrimination. Upon binding GlnRS, the anticodon loop undergoes a major conformational rearrangement in which the anticodon stem is extended by two non-Watson-Crick base pairs, leaving the three anticodon bases fully unpaired and splayed into three separate complementary pockets on the enzyme surface, a binding mode that provides the structural basis for synthetase discrimination among tRNA species. Across species, U34 has been identified as the dominant single identity element governing recognition by related glutamyl-tRNA synthetases.
Applications:
1) RNAcentral ID: URS000059276A_511145
2) Rould, M.A., Perona, J.J. & Steitz, T.A. (1991). Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature 352(6332):213–218
3) Rogers, K.C. & Söll, D. (1993). Discrimination among tRNAs intermediate in glutamate and glutamine acceptor identity. Biochemistry 32(51):14210–14219
4) Rogers, M.J., Weygand-Durasević, I., Schwob, E., Sherman, J.M., Rogers, K.C., Adachi, T., Inokuchi, H. & Söll, D. (1993). Selectivity and specificity in the recognition of tRNA by E. coli glutaminyl-tRNA synthetase. Biochimie 75(12):1083–1090
5) Kim, S.I. & Söll, D. (1998). Major identity element of glutamine tRNAs from Bacillus subtilis and Escherichia coli in the reaction with B. subtilis glutamyl-tRNA synthetase. Mol. Cells 8(4):459–465
6) Rodriguez-Hernandez, A., Spears, J.L., Gaston, K.W., Limbach, P.A., Gamper, H., Hou, Y.-M., Kaiser, R., Agris, P.F. & Perona, J.J. (2013). Structural and mechanistic basis for enhanced translational efficiency by 2-thiouridine at the tRNA anticodon wobble position. J. Mol. Biol. 425(20):3888–3906 RCSB PDB: 4JYZ
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