Search tips
Search criteria 


Logo of narLink to Publisher's site
Nucleic Acids Res. 1997 June 1; 25(11): 2083–2090.
PMCID: PMC146727

Structure of the acceptor stem of Escherichia coli tRNA Ala: role of the G3.U70 base pair in synthetase recognition.


The fidelity of translation of the genetic code depends on accurate tRNA aminoacylation by cognate aminoacyl-tRNA synthetases. Thus, each tRNA has specificity not only for codon recognition, but also for amino acid identity; this aminoacylation specificity is referred to as tRNA identity. The primary determinant of the acceptor identity of Escherichia coli tRNAAlais a wobble G3.U70 pair within the acceptor stem. Despite extensive biochemical and genetic data, the mechanism by which the G3.U70 pair marks the acceptor end of tRNAAla for aminoacylation with alanine has not been clarified at the molecular level. The solution structure of a microhelix derived from the tRNAAla acceptor end has been determined at high precision using a very extensive set of experimental constraints (approximately 32 per nt) obtained by heteronuclear multidimensional NMR methods. The tRNAAla acceptor end is overall similar to A-form RNA, but important differences are observed. The G3.U70 wobble pair distorts the conformation of the phosphodiester backbone and presents the functional groups of U70 in an unusual spatial location. The discriminator base A73 has extensive stacking overlap with G1 within the G1.C72 base pair at the end of the double helical stem and the -CCA end is significantly less ordered than the rest of the molecule.

Full Text

The Full Text of this article is available as a PDF (238K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Ibba M, Hong KW, Sherman JM, Sever S, Söll D. Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme. Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):6953–6958. [PubMed]
  • Saks ME, Sampson JR. Variant minihelix RNAs reveal sequence-specific recognition of the helical tRNA(Ser) acceptor stem by E.coli seryl-tRNA synthetase. EMBO J. 1996 Jun 3;15(11):2843–2849. [PubMed]
  • McClain WH. Transfer RNA identity. FASEB J. 1993 Jan;7(1):72–78. [PubMed]
  • Rould MA, Perona JJ, Söll D, Steitz TA. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution. Science. 1989 Dec 1;246(4934):1135–1142. [PubMed]
  • Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science. 1991 Jun 21;252(5013):1682–1689. [PubMed]
  • Biou V, Yaremchuk A, Tukalo M, Cusack S. The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science. 1994 Mar 11;263(5152):1404–1410. [PubMed]
  • Goldgur Y, Mosyak L, Reshetnikova L, Ankilova V, Lavrik O, Khodyreva S, Safro M. The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe. Structure. 1997 Jan 15;5(1):59–68. [PubMed]
  • Cusack S, Yaremchuk A, Tukalo M. The crystal structures of T. thermophilus lysyl-tRNA synthetase complexed with E. coli tRNA(Lys) and a T. thermophilus tRNA(Lys) transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue. EMBO J. 1996 Nov 15;15(22):6321–6334. [PubMed]
  • Cusack S, Yaremchuk A, Tukalo M. 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. EMBO J. 1996 Jun 3;15(11):2834–2842. [PubMed]
  • Rould MA, Perona JJ, Steitz TA. Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature. 1991 Jul 18;352(6332):213–218. [PubMed]
  • Cavarelli J, Rees B, Ruff M, Thierry JC, Moras D. Yeast tRNA(Asp) recognition by its cognate class II aminoacyl-tRNA synthetase. Nature. 1993 Mar 11;362(6416):181–184. [PubMed]
  • Hou YM, Schimmel P. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature. 1988 May 12;333(6169):140–145. [PubMed]
  • McClain WH, Foss K. Changing the identity of a tRNA by introducing a G-U wobble pair near the 3' acceptor end. Science. 1988 May 6;240(4853):793–796. [PubMed]
  • Gale AJ, Shi JP, Schimmel P. Evidence that specificity of microhelix charging by a class I tRNA synthetase occurs in the transition state of catalysis. Biochemistry. 1996 Jan 16;35(2):608–615. [PubMed]
  • Imura N, Weiss GB, Chambers RW. Reconstitution of alanine acceptor activity from fragments of yeast tRNA-Ala II. Nature. 1969 Jun 21;222(5199):1147–1148. [PubMed]
  • Francklyn C, Schimmel P. Aminoacylation of RNA minihelices with alanine. Nature. 1989 Feb 2;337(6206):478–481. [PubMed]
  • Francklyn C, Shi JP, Schimmel P. Overlapping nucleotide determinants for specific aminoacylation of RNA microhelices. Science. 1992 Feb 28;255(5048):1121–1125. [PubMed]
  • Doudna JA, Cormack BP, Szostak JW. RNA structure, not sequence, determines the 5' splice-site specificity of a group I intron. Proc Natl Acad Sci U S A. 1989 Oct;86(19):7402–7406. [PubMed]
  • Abramovitz DL, Friedman RA, Pyle AM. Catalytic role of 2'-hydroxyl groups within a group II intron active site. Science. 1996 Mar 8;271(5254):1410–1413. [PubMed]
  • Perrotta AT, Been MD. Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage. Nucleic Acids Res. 1996 Apr 1;24(7):1314–1321. [PMC free article] [PubMed]
  • Musier-Forsyth K, Usman N, Scaringe S, Doudna J, Green R, Schimmel P. Specificity for aminoacylation of an RNA helix: an unpaired, exocyclic amino group in the minor groove. Science. 1991 Aug 16;253(5021):784–786. [PubMed]
  • Schimmel P, Musier-Forsyth K. 'Distorted' RNA helix recognition. Nature. 1996 Dec 5;384(6608):422–422. [PubMed]
  • McClain WH, Chen YM, Foss K, Schneider J. Association of transfer RNA acceptor identity with a helical irregularity. Science. 1988 Dec 23;242(4886):1681–1684. [PubMed]
  • Gabriel K, Schneider J, McClain WH. Functional evidence for indirect recognition of G.U in tRNA(Ala) by alanyl-tRNA synthetase. Science. 1996 Jan 12;271(5246):195–197. [PubMed]
  • Limmer S, Reif B, Ott G, Arnold L, Sprinzl M. NMR evidence for helix geometry modifications by a G-U wobble base pair in the acceptor arm of E. coli tRNA(Ala). FEBS Lett. 1996 Apr 29;385(1-2):15–20. [PubMed]
  • Limmer S, Hofmann HP, Ott G, Sprinzl M. The 3'-terminal end (NCCA) of tRNA determines the structure and stability of the aminoacyl acceptor stem. Proc Natl Acad Sci U S A. 1993 Jul 1;90(13):6199–6202. [PubMed]
  • Batey RT, Battiste JL, Williamson JR. Preparation of isotopically enriched RNAs for heteronuclear NMR. Methods Enzymol. 1995;261:300–322. [PubMed]
  • Allain FH, Varani G. Divalent metal ion binding to a conserved wobble pair defining the upstream site of cleavage of group I self-splicing introns. Nucleic Acids Res. 1995 Feb 11;23(3):341–350. [PMC free article] [PubMed]
  • Allain FH, Varani G. Structure of the P1 helix from group I self-splicing introns. J Mol Biol. 1995 Jul 14;250(3):333–353. [PubMed]
  • Aboul-ela F, Karn J, Varani G. The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein. J Mol Biol. 1995 Oct 20;253(2):313–332. [PubMed]
  • Varani G, Aboul-ela F, Allain F, Gubser CC. Novel three-dimensional 1H-13C-31P triple resonance experiments for sequential backbone correlations in nucleic acids. J Biomol NMR. 1995 Apr;5(3):315–320. [PubMed]
  • Avis JM, Allain FH, Howe PW, Varani G, Nagai K, Neuhaus D. Solution structure of the N-terminal RNP domain of U1A protein: the role of C-terminal residues in structure stability and RNA binding. J Mol Biol. 1996 Mar 29;257(2):398–411. [PubMed]
  • Diamond R. Coordinate-based cluster analysis. Acta Crystallogr D Biol Crystallogr. 1995 Mar 1;51(Pt 2):127–135. [PubMed]
  • Babcock MS, Pednault EP, Olson WK. Nucleic acid structure analysis: a users guide to a collection of new analysis programs. J Biomol Struct Dyn. 1993 Dec;11(3):597–628. [PubMed]
  • Allain FH, Varani G. How accurately and precisely can RNA structure be determined by NMR? J Mol Biol. 1997 Mar 28;267(2):338–351. [PubMed]
  • Wang YX, Huang S, Draper DE. Structure of a U.U pair within a conserved ribosomal RNA hairpin. Nucleic Acids Res. 1996 Jul 15;24(14):2666–2672. [PMC free article] [PubMed]
  • Lietzke SE, Barnes CL, Berglund JA, Kundrot CE. The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of stable RNA structures and the diversity of recognition sites. Structure. 1996 Aug 15;4(8):917–930. [PubMed]
  • Wu M, Turner DH. Solution structure of (rGCGGACGC)2 by two-dimensional NMR and the iterative relaxation matrix approach. Biochemistry. 1996 Jul 30;35(30):9677–9689. [PubMed]
  • Ladner JE, Jack A, Robertus JD, Brown RS, Rhodes D, Clark BF, Klug A. Structure of yeast phenylalanine transfer RNA at 2.5 A resolution. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4414–4418. [PubMed]
  • Puglisi EV, Puglisi JD, Williamson JR, RajBhandary UL. NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11467–11471. [PubMed]
  • Musier-Forsyth K, Schimmel P. Functional contacts of a transfer RNA synthetase with 2'-hydroxyl groups in the RNA minor groove. Nature. 1992 Jun 11;357(6378):513–515. [PubMed]
  • Ott G, Arnold L, Limmer S. Proton NMR studies of manganese ion binding to tRNA-derived acceptor arm duplexes. Nucleic Acids Res. 1993 Dec 25;21(25):5859–5864. [PMC free article] [PubMed]
  • Cate JH, Doudna JA. Metal-binding sites in the major groove of a large ribozyme domain. Structure. 1996 Oct 15;4(10):1221–1229. [PubMed]
  • Park SJ, Hou YM, Schimmel P. A single base pair affects binding and catalytic parameters in the molecular recognition of a transfer RNA. Biochemistry. 1989 Mar 21;28(6):2740–2746. [PubMed]
  • Lee CP, Mandal N, Dyson MR, RajBhandary UL. The discriminator base influences tRNA structure at the end of the acceptor stem and possibly its interaction with proteins. Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):7149–7152. [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press