Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit

Hansen, J. Lundsgaard; Moore, Peter B.; Steitz, Thomas A.

doi:10.1016/s0022-2836(03)00668-5

Cited by 371 publications

(419 citation statements)

References 77 publications

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“…The type of inhibition and the tightness of complex C*I prompt us to suppose that the binding site of blasticidin S in C*I complex coincides with that of blasticidin I ( Fig. 2A), identified by crystallographic studies (10). On the basis of the above observations we assume that blasticidin S (blasticidin I in Fig.…”

Section: Discussionmentioning

confidence: 68%

“…The first molecule interferes with the binding of puromycin to the A-site (competitive kinetics) transiently. In fact, interactions of blasticidin S with the A-site were not identified in the one published crystallographic study (10), probably because the competitive phase is transient. Soon after this initial competitive interaction, the antibiotic is slowly accommodated in its final position (C*I complex), so that puromycin is accepted and peptide bonds are still formed but with a lower catalytic rate constant (partial-noncompetitive kinetics).…”

Section: Discussionmentioning

confidence: 93%

“…In the current report, we extend this study by examining the effect of polyamines on the binding of two other antibiotics, blasticidin S and spiramycin, which bind the large ribosomal subunit at the P-site and at the entrance to the exit tunnel, respectively. At the same time, we seize the chance to revisit the mechanism of action of these two antibiotics on peptide-bond formation, in light of the high resolution crystal structures for their binding sites on the ribosome (10,12).…”

Section: Discussionmentioning

confidence: 99%

“…Evidence supporting the latter hypothesis is provided by chemical probing with DMS indicating that spermine crosslinking increases the reactivity of the adjacent A2247 nucleoside. With respect to A2439, various experimental approaches, including footprinting (7), mutational (38), and x-ray crystallographic analyses (10), have demonstrated that this bulged nucleoside as well as the adjacent U2438 are implicated in the binding of aminoacylaminonucleoside antibiotics. Both nucleosides are very susceptible to metal ion-catalyzed hydrolysis (39) and probably constitute a general cation binding site.…”

Section: Discussionmentioning

confidence: 99%

“…In fact, the reactivity of A2439 is also affected by P-site-bound Phe-tRNA, and A2439 is susceptible to crosslinking by P-site-bound Phe-tRNA. The situation is further complicated by the finding of a recent crystallographic study in Haloarcula marismortui, revealing that blasticidin S binds at two, nonoverlapping sites, with different affinities (10). In the primary binding site (see Fig.…”

mentioning

confidence: 99%

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Polyamines Affect Diversely the Antibiotic Potency

Πετρόπουλος

Xaplanteri

Dinos

et al. 2004

Journal of Biological Chemistry

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The effects of spermine on peptidyltransferase inhibition by an aminohexosylcytosine nucleoside, blasticidin S, and by a macrolide, spiramycin, were investigated in a model system derived from Escherichia coli, in which a peptide bond is formed between puromycin and AcPhe-tRNA bound at the P-site of poly(U)-programmed ribosomes. Kinetics revealed that blasticidin S, after a transient phase of interference with the A-site, is slowly accommodated near to the P-site so that peptide bond is still formed but with a lower catalytic rate constant. At high concentrations of blasticidin S (>10 ؋ K i ), a second drug molecule binds to a weaker binding site on ribosomes, and this may account for the onset of a subsequent mixed-noncompetitive inhibition phase. Spermine enhances the blasticidin S inhibitory effect by facilitating the drug accommodation to both sites. On the other hand, spiramycin (A) was found competing with puromycin for the A-site of AcPhe-tRNA⅐poly(U)⅐70 S ribosomal complex (C) via a two-step mechanism, according to which the fast formation of the encounter complex CA is followed by a slow isomerization to a tighter complex, termed C*A. In contrast to that observed with blasticidin S, spermine reduced spiramycin potency by decreasing the formation and stability of complex C*A. Polyamine effects on drug binding were more pronounced when a mixture of spermine and spermidine was used, instead of spermine alone. Our kinetic results correlate well with cross-linking and crystallographic data and suggest that polyamines bound at the vicinity of the antibiotic binding pockets modulate diversely the interaction of these drugs with ribosomes.Blasticidin S and spiramycin are representatives of two distinct antibiotic families, the aminohexosylcytosine nucleosides and the 16-membered lactone ring macrolides, respectively, both of which have been proposed to inhibit protein synthesis by binding to the large ribosomal subunit. Blasticidin S consists of a cytosine bonded to a pyranose ring, to which an amino acid-like substituent is attached (see Fig. 1). Therefore, it is not surprising that blasticidin S and puromycin have been considered as iso-structural, both with one another and with the 3Ј-end of aminoacyl-tRNA (1, 2). Consistently, blasticidin S has been found to inhibit the binding of CACCA (Phe) to the A-site of ribosomes (3) and to compete with designated A-site inhibitors (4). In addition, the inhibition of peptidyl-or AcPhe 1 -puromycin synthesis by this antibiotic shows a competitive phase in concert with noncompetitive or mixed-noncompetitive phases (5, 6), a fact supporting the notion that blasticidin S influences, at least transiently, the affinity of the A-site. Further support derives from chemical probing studies in Escherichia coli ribosomes (7), suggesting that blasticidin S protects A2439, one of the three nucleosides in domain V of 23 S rRNA, which show altered chemical reactivity on removal of the aminoacyl group from A-site-bound tRNAs (8). Moreover, A2439 is one of the preferable cross-linking...

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Section: Discussionmentioning

confidence: 68%

Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Polyamines Affect Diversely the Antibiotic Potency

Πετρόπουλος

Xaplanteri

Dinos

et al. 2004

Journal of Biological Chemistry

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Therapeutic Agents Acting on RNA Targets

Rife

2010

Burger's Medicinal Chemistry and Drug Discovery

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There are many therapeutics that target RNA, such as streptomycin, gentamicin, and tetracycline; some of them have been in existence for many years. All of them bind to ribosomal RNA and alter normal ribosome function. The modern strategies of drug discovery and design pertain nearly exclusively to protein targets. However, the field of drug discovery for RNA targets is maturing rapidly, largely due to the exciting ribosome/drug complexes that have recently been solved. Potential RNA drug targets abound for bacterial, viral, and cellular systems. Nevertheless, questions remain as to whether or not compounds can be found that simultaneously satisfy RNA binding and pharmacological properties, such as absorption and membrane permeation. The range of interactions observed, from Coulombic to hydrophobic, and the predicted “drug‐like” qualities of several ribosome binding antibiotics, suggest that the discovery of drugs that target RNA can be a general phenomenon.

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Tetracycline, Aminoglycoside, Macrolide, and Miscellaneous Antibiotics

Mitscher

2010

Burger's Medicinal Chemistry and Drug Discovery

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Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit

Cited by 371 publications

References 77 publications

Polyamines Affect Diversely the Antibiotic Potency

Polyamines Affect Diversely the Antibiotic Potency

Therapeutic Agents Acting on RNA Targets

Tetracycline, Aminoglycoside, Macrolide, and Miscellaneous Antibiotics

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