Mechanism of codon—anticodon interaction in ribosomes

Kirillov, S.V.; Katunin, Vladimir I.; Semenkov, Yu.P.

doi:10.1016/0014-5793(81)80986-6

Cited by 12 publications

(3 citation statements)

References 23 publications

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“…1). All three functional forms of tRNA (aminoacyl‐tRNA, peptidyl‐tRNA and deacylated tRNA) have a higher affinity for this site (10–50‐fold, depending on the magnesium concentration) than for the A/P′‐site [55, 60–65]. The relative binding affinities are: deacylated tRNA>Phe‐tRNA>AcPhe‐tRNA [55, 64] which also correlates with the observation that the 3′‐pentanucleotide fragment CACCA‐Phe binds at least as strongly as its acetylated form [37].…”

Section: Trna Binding Sitessupporting

confidence: 55%

Movement of the 3′‐end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics

et al. 1997

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Determining how antibiotics inhibit ribosomal activity requires a detailed understanding of the interactions and relative movement of tRNA, mRNA and the ribosome. Recent models for the formation of hybrid tRNA binding sites during the elongation cycle have provided a basis for re-evaluating earlier experimental data and, especially, those relevant to substrate movements through the peptidyl transferase centre. With the exception of deacylated tRNA, which binds at the E-site, ribosomal interactions of the 3'-ends of the tRNA substrates generate only a small part of the total free energy of tRNA-ribosome binding. Nevertheless, these relatively weak interactions determine the unidirectional movement of tRNAs through the ribosome and, moreover, they appear to be particularly susceptible to perturbation by antibiotics. Here we summarise current ideas relating particularly to the movement of the 3'-ends of tRNA through the ribosome and consider possible inhibitory mechanisms of the peptidyl transferase antibiotics.

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Section: Trna Binding Sitessupporting

confidence: 55%

Movement of the 3′‐end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics

et al. 1997

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“…The same authors showed with phage RNA that in addition to m e t -t R N A two aminoacyl tRNAs can be bound to the ribosome [5]. Kirillov et al postulated two binding sites on the 30-S ribosomal subunit and two sites on the 70-S ribosome, albeit with different affinities [6,7]. Lake derived from immune electron microscopy data the existence of the so-called recognition site (R site) as an entry site for aminoacyl tRNA [8].…”

mentioning

confidence: 99%

Binding of tRNA to Escherichia coli Ribosomes as Measured by Velocity Sedimentation

Schmitt¹,

Möller²,

Riesner³

et al. 1981

European Journal of Biochemistry

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We followed the binding of initiator and elongator tRNA to 70-S ribosomes and its subunits by velocity sedimentation in the analytical ultracentrifuge. This technique shows the advantage over the previously used methods (adsorption of the complexes to nitrocellulose filters or fluorescence titrations) in that no kinetic effects obscure the equilibrium data and that none of the components has to be chemically modified. The concentrations of the macromolecular compounds are kept constant and the binding equilibria are shifted by varying the Mg2+ concentration in a range which is accessible to experimental analysis.Free 30-S ribosomes bind no tRNA, whereas one tRNA molecule is bound to 50-S ribosomal subunits. In thc presence of the cognate codon one tRNA can be associated with the small subunit. Free, programmcd, or misprogrammed 70-S ribosomes bind exactly two elongator tRNAs. Only the initiator t RNA does discriminate significantly between the two ribosomal sites when bound to a ribosome . A-U-G complex.The current picture of the mechanism of protein synthesis is still consistent with the original proposal by Watson [l]. The 70-S ribosome contains two tRNA binding sites, the socalled aminoacyl-tRNA binding site (A site) and the peptidyltRNA binding site (P site). Both centers are capable of interacting with two types of tRNA each, the A site with the ternary complex aminoacyl-tRNA . EF-Tu . GTP and the peptidyl-tRNA; the P site with peptidyl-tRNA and the deacylated tRNA. In both instances the first type of tRNA represents the substrate, the latter the product for the respective binding sites. The experimental distinction between the two sites relies on the fact that the peptidyl group of the tRNA when bound to the P site is transferable to puromycin but not when bound to the A site.However, additional tRNA binding sites with functional roles in protein synthesis have been suggested [2,3]. Matthaei and his colleagues postulated from Phe-tRNA binding to poly(U)-programmed ribosomes three functionally defined sites on a 70-S ribosome [4]. The same authors showed with phage RNA that in addition to m e t -t R N A two aminoacyl tRNAs can be bound to the ribosome [5]. Kirillov et al. postulated two binding sites on the 30-S ribosomal subunit and two sites on the 70-S ribosome, albeit with different affinities [6,7]. Lake derived from immune electron microscopy data the existence of the so-called recognition site (R site) as an entry site for aminoacyl tRNA [8]. This site shares the anticodon region with the A site, but the remaining parts of the tRNA are bound to the exterior of the 30-S subunit. Recently Rheinberger and Nierhaus presented evidence for a third site as well which they defined as an exit site for the deacylated tRNA. The existence of the E site was concluded from the binding of two tRNAPh" molecules to a ribosome . poly(U) . AcPhe-tRNA complex 191.Ahbrcviations. A site, aminoacyl-tRNA binding site of the ribosome; P sitc, peptidyl-tRNA binding site; t R N A y and tRNAM,", the methionine tRNAs which can a...

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“…However, contrary to the binding of tRNA at the A-site, P-site binding of aminoacyland acylaminoacyl-tRNA proceeds in the absence of a template as well as in its presence as revealed from 'puromycin reactivity [ 1,3]. The same is known for deacylated tRNA as has been demonstrated from competition tests with aminoacyl-tRNA [ 11.…”

Section: Introductionmentioning

confidence: 99%

The effect of poly(U) on the arrangement of tRNA^Phe in donor tRNA‐binding site of Escherichia coli ribosomes

Vladimirov¹,

Graifer²,

Карпова³

1982

FEBS Letters

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Mechanism of codon—anticodon interaction in ribosomes

Cited by 12 publications

References 23 publications

Movement of the 3′‐end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics

Movement of the 3′‐end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics

Binding of tRNA to Escherichia coli Ribosomes as Measured by Velocity Sedimentation

The effect of poly(U) on the arrangement of tRNA^Phe in donor tRNA‐binding site of Escherichia coli ribosomes

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Mechanism of codon—anticodon interaction in ribosomes

Cited by 12 publications

References 23 publications

Movement of the 3′‐end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics

Movement of the 3′‐end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics

Binding of tRNA to Escherichia coli Ribosomes as Measured by Velocity Sedimentation

The effect of poly(U) on the arrangement of tRNAPhe in donor tRNA‐binding site of Escherichia coli ribosomes

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The effect of poly(U) on the arrangement of tRNA^Phe in donor tRNA‐binding site of Escherichia coli ribosomes