1JZX

Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria

Summary for 1JZX

• Entry DOI: 10.2210/pdb1jzx/pdb
• Related: 1JZY 1JZZ 1K00 1K01
• Descriptor: 23S rRNA, Ribosomal Protein L4, Ribosomal Protein L22, ... (6 entities in total)
• Functional Keywords: ribosome, 50s, 23s, 5s, antibiotics, clindamycin, peptidyl transferase center
• Biological source: Deinococcus radiodurans; More
• Total number of polymer chains: 4
• Total formula weight: 978187.63

Authors

Schluenzen, F.,Zarivach, R.,Harms, J.,Bashan, A.,Tocilj, A.,Albrecht, R.,Yonath, A.,Franceschi, F. (deposition date: 2001-09-17, release date: 2001-10-26, Last modification date: 2024-02-07)

Primary citation

Schlunzen, F.,Zarivach, R.,Harms, J.,Bashan, A.,Tocilj, A.,Albrecht, R.,Yonath, A.,Franceschi, F.
Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria.
Nature, 413:814-821, 2001

PubMed Abstract: Ribosomes, the site of protein synthesis, are a major target for natural and synthetic antibiotics. Detailed knowledge of antibiotic binding sites is central to understanding the mechanisms of drug action. Conversely, drugs are excellent tools for studying the ribosome function. To elucidate the structural basis of ribosome-antibiotic interactions, we determined the high-resolution X-ray structures of the 50S ribosomal subunit of the eubacterium Deinococcus radiodurans, complexed with the clinically relevant antibiotics chloramphenicol, clindamycin and the three macrolides erythromycin, clarithromycin and roxithromycin. We found that antibiotic binding sites are composed exclusively of segments of 23S ribosomal RNA at the peptidyl transferase cavity and do not involve any interaction of the drugs with ribosomal proteins. Here we report the details of antibiotic interactions with the components of their binding sites. Our results also show the importance of putative Mg+2 ions for the binding of some drugs. This structural analysis should facilitate rational drug design.

PubMed: 11677599
DOI: 10.1038/35101544

Experimental method

X-RAY DIFFRACTION (3.1 Å)