Chloramphenicol, erythromycin, carbomycin and vernamycin B protect overlapping sites in the peptidyl transferase region of 23S ribosomal RNA

Erythromycin, Roxithromycin, and Clarithromycin: Use of Slow-Binding Kinetics to Compare Their in Vitro Interaction with a Bacterial Ribosomal Complex Active in Peptide Bond Formation

“…This conclusion cannot be easily drawn from the footprinting results. All three antibiotics, in agreement with previous observations (Moazed and Noller, 1987;Hansen et al, 1999;Douthwaite et al, 2000;Poulsen et al, 2000), exhibit identical footprinting patterns in the central loop of 23S rRNA V domain (Fig. 6).…”

Erythromycin, Roxithromycin, and Clarithromycin: Use of Slow-Binding Kinetics to Compare Their in Vitro Interaction with a Bacterial Ribosomal Complex Active in Peptide Bond Formation

“…This conclusion cannot be easily drawn from the footprinting results. All three antibiotics, in agreement with previous observations (Moazed and Noller, 1987;Hansen et al, 1999;Douthwaite et al, 2000;Poulsen et al, 2000), exhibit identical footprinting patterns in the central loop of 23S rRNA V domain (Fig. 6).…”

The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center

“…This observation raises the intriguing possibility that peptidyl-D-aa-tRNA-mediated translation arrest at the PTC is coupled to stabilization of particular conformations of the ETE. Such a possibility is consistent with the observation that at least one antibiotic that binds at the PTC and inhibits peptidyl transfer (i.e., chloramphenicol) also perturbs the conformations of distally located nucleotides at the ETE (28,29) and that resistance to such antibiotics can be conferred by mutations at the ETE (30,31). Indeed, at least one previously reported interpretation of these results is that the PTC and ETE are conformationally coupled such that direct stabilization of a particular PTC conformation via antibiotic binding also stabilizes a particular ETE conformation (i.e., binding of the antibiotic to the PTC stabilizes a single PTC-ETE conformer) (29).…”

Insights into the Chloramphenicol Inhibition Effect on Peptidyl Transferase Activity, Using Two New Analogs of the Drug

“…Meanwhile, the protection at G2505 and U2506 softens, a new footprint at A2059 is raised, and the reactivity of A2058 is enhanced. The footprinting pattern of complex C I resembles better than the CI pattern to that published by others [17,18] and generally correlates well with recent crystallographic data [13,14]. This may be due to the fact that both footprinting and crystallographic analyses have been performed by incubating ribosomes with CAM for prolonged time.…”

“…However, both nucleotides C2452 and A2503 are implicated in CAM binding, as deduced by crystallography [12][13][14] and mutagenesis [31] studies. The footprinting pattern of complex CI differs from those previously reported [17,18], given that drug-induced effects at A2058, A2059 and A2062 are absent. Nevertheless, this footprinting pattern suggests that CAM binds adjacently to the crevice of A-site on the 50S ribosomal subunit.…”

Erythromycin, Roxithromycin, and Clarithromycin: Use of Slow-Binding Kinetics to Compare Their in Vitro Interaction with a Bacterial Ribosomal Complex Active in Peptide Bond Formation

“…This conclusion cannot be easily drawn from the footprinting results. All three antibiotics, in agreement with previous observations (Moazed and Noller, 1987;Hansen et al, 1999;Douthwaite et al, 2000;Poulsen et al, 2000), exhibit identical footprinting patterns in the central loop of 23S rRNA V domain (Fig. 6).…”

The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center

“…This observation raises the intriguing possibility that peptidyl-D-aa-tRNA-mediated translation arrest at the PTC is coupled to stabilization of particular conformations of the ETE. Such a possibility is consistent with the observation that at least one antibiotic that binds at the PTC and inhibits peptidyl transfer (i.e., chloramphenicol) also perturbs the conformations of distally located nucleotides at the ETE (28,29) and that resistance to such antibiotics can be conferred by mutations at the ETE (30,31). Indeed, at least one previously reported interpretation of these results is that the PTC and ETE are conformationally coupled such that direct stabilization of a particular PTC conformation via antibiotic binding also stabilizes a particular ETE conformation (i.e., binding of the antibiotic to the PTC stabilizes a single PTC-ETE conformer) (29).…”

Insights into the Chloramphenicol Inhibition Effect on Peptidyl Transferase Activity, Using Two New Analogs of the Drug

“…Meanwhile, the protection at G2505 and U2506 softens, a new footprint at A2059 is raised, and the reactivity of A2058 is enhanced. The footprinting pattern of complex C I resembles better than the CI pattern to that published by others [17,18] and generally correlates well with recent crystallographic data [13,14]. This may be due to the fact that both footprinting and crystallographic analyses have been performed by incubating ribosomes with CAM for prolonged time.…”

“…However, both nucleotides C2452 and A2503 are implicated in CAM binding, as deduced by crystallography [12][13][14] and mutagenesis [31] studies. The footprinting pattern of complex CI differs from those previously reported [17,18], given that drug-induced effects at A2058, A2059 and A2062 are absent. Nevertheless, this footprinting pattern suggests that CAM binds adjacently to the crevice of A-site on the 50S ribosomal subunit.…”

Erythromycin, Roxithromycin, and Clarithromycin: Use of Slow-Binding Kinetics to Compare Their in Vitro Interaction with a Bacterial Ribosomal Complex Active in Peptide Bond Formation

“…This conclusion cannot be easily drawn from the footprinting results. All three antibiotics, in agreement with previous observations (Moazed and Noller, 1987;Hansen et al, 1999;Douthwaite et al, 2000;Poulsen et al, 2000), exhibit identical footprinting patterns in the central loop of 23S rRNA V domain (Fig. 6).…”

The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center

“…This observation raises the intriguing possibility that peptidyl-D-aa-tRNA-mediated translation arrest at the PTC is coupled to stabilization of particular conformations of the ETE. Such a possibility is consistent with the observation that at least one antibiotic that binds at the PTC and inhibits peptidyl transfer (i.e., chloramphenicol) also perturbs the conformations of distally located nucleotides at the ETE (28,29) and that resistance to such antibiotics can be conferred by mutations at the ETE (30,31). Indeed, at least one previously reported interpretation of these results is that the PTC and ETE are conformationally coupled such that direct stabilization of a particular PTC conformation via antibiotic binding also stabilizes a particular ETE conformation (i.e., binding of the antibiotic to the PTC stabilizes a single PTC-ETE conformer) (29).…”

Insights into the Chloramphenicol Inhibition Effect on Peptidyl Transferase Activity, Using Two New Analogs of the Drug

“…Meanwhile, the protection at G2505 and U2506 softens, a new footprint at A2059 is raised, and the reactivity of A2058 is enhanced. The footprinting pattern of complex C I resembles better than the CI pattern to that published by others [17,18] and generally correlates well with recent crystallographic data [13,14]. This may be due to the fact that both footprinting and crystallographic analyses have been performed by incubating ribosomes with CAM for prolonged time.…”

“…However, both nucleotides C2452 and A2503 are implicated in CAM binding, as deduced by crystallography [12][13][14] and mutagenesis [31] studies. The footprinting pattern of complex CI differs from those previously reported [17,18], given that drug-induced effects at A2058, A2059 and A2062 are absent. Nevertheless, this footprinting pattern suggests that CAM binds adjacently to the crevice of A-site on the 50S ribosomal subunit.…”