title: Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.
abstract: Two structurally unique ribosomal antibiotics belonging to the orthosomycin family, avilamycin and evernimicin, possess activity against Enterococci, Staphylococci, and Streptococci, and other Gram-positive bacteria. Here, we describe the high-resolution crystal structures of the eubacterial large ribosomal subunit in complex with them. Their extended binding sites span the A-tRNA entrance corridor, thus inhibiting protein biosynthesis by blocking the binding site of the A-tRNA elbow, a mechanism not shared with other known antibiotics. Along with using the ribosomal components that bind and discriminate the A-tRNA-namely, ribosomal RNA (rRNA) helices H89, H91, and ribosomal proteins (rProtein) uL16-these structures revealed novel interactions with domain 2 of the CTC protein, a feature typical to various Gram-positive bacteria. Furthermore, analysis of these structures explained how single nucleotide mutations and methylations in helices H89 and H91 confer resistance to orthosomycins and revealed the sequence variations in 23S rRNA nucleotides alongside the difference in the lengths of the eukaryotic and prokaryotic α1 helix of protein uL16 that play a key role in the selectivity of those drugs. The accurate interpretation of the crystal structures that could be performed beyond that recently reported in cryo-EM models provide structural insights that may be useful for the design of novel pathogen-specific antibiotics, and for improving the potency of orthosomycins. Because both drugs are extensively metabolized in vivo, their environmental toxicity is very low, thus placing them at the frontline of drugs with reduced ecological hazards.
authors: Department of Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel.
authors: Miri
authors: M
authors: Krupkin
authors: Department of Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel.
authors: Itai
authors: I
authors: Wekselman
authors: Department of Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel.
authors: Donna
authors: D
authors: Matzov
authors: Department of Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel.
authors: Zohar
authors: Z
authors: Eyal
authors: Department of Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel.
authors: Yael
authors: Y
authors: Diskin Posner
authors: Department of Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel.
authors: Haim
authors: H
authors: Rozenberg
authors: Department of Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel.
authors: Ella
authors: E
authors: Zimmerman
authors: Department of Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel.
authors: Anat
authors: A
authors: Bashan
authors: Department of Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel ada.yonath@weizmann.ac.il.
authors: Ada
authors: A
authors: Yonath
mesh_terms: D000617:Aminoglycosides / Q000737:chemistry / Q000494:pharmacology*; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000187:drug effects*; D001665:Binding Sites / Q000187:drug effects*; D018360:Crystallography, X-Ray; D024881:Drug Resistance, Bacterial / Q000187:drug effects / Q000235:genetics; D006094:Gram-Positive Bacteria / Q000187:drug effects; D008826:Microbial Sensitivity Tests; D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D009844:Oligosaccharides / Q000737:chemistry / Q000494:pharmacology*; D014176:Protein Biosynthesis / Q000187:drug effects; D012335:RNA, Ribosomal; D012338:RNA, Ribosomal, 23S / Q000187:drug effects / Q000235:genetics; D012343:RNA, Transfer / Q000187:drug effects* / Q000378:metabolism; D012269:Ribosomal Proteins / Q000187:drug effects* / Q000378:metabolism; D012270:Ribosomes / Q000187:drug effects / Q000378:metabolism; D016415:Sequence Alignment; D013045:Species Specificity
chemical_list: D000617:Aminoglycosides; D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D009844:Oligosaccharides; D012335:RNA, Ribosomal; D012338:RNA, Ribosomal, 23S; D012269:Ribosomal Proteins; C001202:evernimicin; C006653:avilamycin; D012343:RNA, Transfer
keywords: Gram-positive; degradable antibiotics; resistance; ribosomes; species-specific antibiotics