Structure of yeast phenylalanine tRNA at 3 Å resolution

Robertus, Jon D.; Ladner, Jane E.; Finch, J. T.; Rhodes, Daniela; Brown, Raymond S.; Clark, Brian F. C.; Klug, A.

doi:10.1038/250546a0

Cited by 1,008 publications

(572 citation statements)

References 21 publications

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“…We characterized the conformation of two RNA oligonucleotides which correspond to the acceptor stem of mutants of tRNAfmet and which differ only in the discriminator base. An A at the discriminator position yields a structure in which the 3'-ACCA sequence continues the A-form stacking of the acceptor stem, as seen in the x-ray structure of yeast tRNAPhe (18,19). A U at the discriminator position disrupts the continuous stacking of the 3' end.…”

Section: Discussionmentioning

confidence: 99%

NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end.

Puglisi

Williamson

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

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An important step in initiation of protein synthesis in Escherichia col is the specific formylation of the initiator methionyl-tRNA (Met-tRNA) by Met-tRNA transformylase. The deterinants for formylation are clustered mostly in the acceptor stem of the initiator tRNA. Here we use NMR spectroscopy to characterize the conformation of two RNA microhelces, which correspond to the acceptor stem of mutants of E. coUi initator tRNA and which differ only at the position corresponding to the "discriminator base" in tRNAs.One of the mutant tRNAs is an extremely poor substrate for Met-tRNA trausformylase, whereas the other one is a much better substrate. We show that one microhelix forms a struchire in which its 3'-ACCA sequence extends the tacklng of the acceptor stem. The other microhelix forms a structure in which its 3'-UCCA sequence folds back such that the 3'-terminal A22 is in dose proximity to GI. These results highiight the importance of the discriminator base in determining tRNA conformation at the 3' end. They also suggest a correlation between tRNA structure at the 3' end and its recognition by Met-tRNA trandormylase.Protein synthesis in Escherichia coli is initiated with formylmethionyl-tRNA (tMet-tRNA). A crucial step in this process is the specific formylation of methionine attached to tRNAfmet by Met-tRNA transformylase (EC 2.1.2.9) (1, 2). We showed previously that the major determinants for formylation are clustered in the acceptor stem of tRNA (3). One of these determinants is a mismatch (as found in tRNAfmet) or a weak base pair at the end of the acceptor stem. tRNAs carrying the wild-type ClxA72 or virtually any other mismatch are good substrates, whereas those carrying stable base pairs such as ClG72 or GlFC72 are extremely poor substrates (4-6). These results suggest a requirement for nucleotides 1 and 72 to be unpaired during formylation.The strong negative effect of ClG72 or G1C72 base pairs on formylation can be compensated for by an additional mutation of A73, the discriminator base, which precedes the CCA sequence common to all tRNAs, to a pyrimidine such as U73 (4). For example, in contrast to the ClG72 mutant, which is a very poor substrate (V 1/K aPP down by a factor of495 compared to wild-type tRNA), the ClG72/U73 mutant is almost as good a substrate as wild-type tRNA (V./KIPP down only by a factor of 3.7). Similarly, compared to the G1*C72 mutant, the G1'C72/U73 mutant is a better substrate for Met-tRNA transformylase (V./KIPP down by a factor of 60, while the factor is 1035 for the G1-C72 mutant). On the basis of these results, we proposed that the discriminator base influences the stability of the terminal base pair in the acceptor stem and/or structure of tRNA at the 3' end (4, 6).In this paper, we use NMR spectroscopy (7) to study the effect of the discriminator base (8) on tRNA conformation at the 3' end. Two RNA oligonucleotides that correspond to variants of the acceptor stem of initiator tRNAfmet were designed for NMR study (Fig. 1A). These oligonucleotides contain the seven ...

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Section: Discussionmentioning

confidence: 99%

NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end.

Puglisi

Williamson

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

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“…The A9 is novel to initiator tRNAs, but is present in non-initiator tRNA Met sequences. The presence of A9 may be partially responsible for the thermal lability of the algal tRNA, since this position is directly involved in at least two tertiary interactions [ 17,18].…”

Section: Discussionmentioning

confidence: 99%

The preliminary sequence of tRNA^Met_F from Anacystis nidulans compared with other initiator tRNAs

Ecarot-Charrier

Cedergren

1976

FEBS Letters

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“…In view of the fact that the TYM virus valyl-RNA can donate its valyl moiety for protein synthesis [8], it is worth noting that the TYM virus RNA 3Lterminal fragment contains the sequence C-A-C, an anticodon to the valine codon G-U-G, in an appropriate location. A detailed comparison of this or other possible structures, with those of tRNAs, including correlation of the basepaired stems and of the individual loops with the corresponding structures in tRNAs and possible tertiary folding [49,50] will, however, have to await further studies including the establishment of a totally unambiguous sequence for this RNA.…”

Section: Discussionmentioning

confidence: 99%

Studies on the Sequence of the 3′‐Terminal Region of Turnip‐Yellow‐Mosaic‐Virus RNA

Silberklang

Prochiantz

Haenni

et al. 1977

European Journal of Biochemistry

193

107

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A fragment representing the 3′‐terminal ‘tRNA‐like’ region of turnip yellow mosaic (TYM) virus RNA has been purified following incubation of intact TYM virus RNA with Escherichia coli‘RNase P’. This fragment, which is 112 ± 3‐nucleotides long has been completely digested with T1 RNase and pancreatic RNase and all the oligonucleotides present in such digests have been sequenced using 32P‐end labelling techniques in vitro. The TYM virus RNA fragment is free of modified nucleosides and does not contain a G‐U‐U‐C‐R sequence. Using nuclease P1 from Penicillium citrinum, the sequence of 26 nucleotides from the 5′ end and 16 nucleotides from the 3′ end of this fragment has been deduced. The nucleotide sequence at the 5′ end of the TYM virus RNA fragment indicates that this fragment includes the end of the TYM virus coat protein gene.

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Structure of yeast phenylalanine tRNA at 3 Å resolution

Cited by 1,008 publications

References 21 publications

NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end.

NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end.

The preliminary sequence of tRNA^Met_F from Anacystis nidulans compared with other initiator tRNAs

Studies on the Sequence of the 3′‐Terminal Region of Turnip‐Yellow‐Mosaic‐Virus RNA

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Structure of yeast phenylalanine tRNA at 3 Å resolution

Cited by 1,008 publications

References 21 publications

NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end.

NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end.

The preliminary sequence of tRNAMetF from Anacystis nidulans compared with other initiator tRNAs

Studies on the Sequence of the 3′‐Terminal Region of Turnip‐Yellow‐Mosaic‐Virus RNA

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The preliminary sequence of tRNA^Met_F from Anacystis nidulans compared with other initiator tRNAs