Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding

Krupkin, Miri; Wekselman, Itai; Matzov, Donna; Eyal, Zohar; Posner, Yael Diskin; Rozenberg, Haim; Zimmerman, Ella; Bashan, Anat; Yonath, Ada

doi:10.1073/pnas.1614297113

Title: Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding

Journal Article · Wed Oct 19 00:00:00 EDT 2016 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1614297113· OSTI ID:1332583

Krupkin, Miri ^[1]; Wekselman, Itai ^[1]; Matzov, Donna ^[1]; Eyal, Zohar ^[1]; Posner, Yael Diskin ^[1]; Rozenberg, Haim ^[1]; Zimmerman, Ella ^[1]; Bashan, Anat ^[1]; Yonath, Ada ^[1]

Weizmann Inst., Rehovot (Israel)

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. Here, 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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Inst. of Health; European Research Council (ERC)

Grant/Contract Number:: GM34360; 322581

OSTI ID:: 1332583

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, Issue 44; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 15 works

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59 BASIC BIOLOGICAL SCIENCES
degradable antibiotics
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resistance
species-specific antibiotics
Gram-positive

Title: Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding

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