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TitleMechanistic insights into 50 precursor recognition and targeting by erythromycin resistance methyltransferase.
Journal, issue, pagesSci Adv, Vol. 11, Issue 48, Page eaea1545, Year 2025
Publish dateNov 28, 2025
AuthorsSombuddha Sengupta / Rajat Mukherjee / Michael Pilsl / Siddharam Bagale / Arijit Das Adhikary / Aditi N Borkar / Pushpangadan Indira Pradeepkumar / Christoph Engel / Arindam Chowdhury / Prem S Kaushal / Ruchi Anand /
PubMed AbstractErythromycin resistance methyltransferases (Erms) confer resistance to macrolide, lincosamide, and streptogramin B antibiotics by methylating an internal base (A2058, numbering) in an elusive ...Erythromycin resistance methyltransferases (Erms) confer resistance to macrolide, lincosamide, and streptogramin B antibiotics by methylating an internal base (A2058, numbering) in an elusive precursor ribosomal state. Here, we capture the 50 ribosomal precursor-Erm complex by cryo-EM and show that a transient pocket formed in the early steps of ribosome biogenesis, situated 35 angstrom from the methylation site, serves as an anchor for the auxiliary C-terminal domain of Erm, thereby playing a crucial role in achieving specificity in this short-lived substrate with evolving structural features. Cryo-EM reveals that the catalytic Rossman fold of Erm undergoes a swaying motion to facilitate substrate scouting. Corroboratory smFRET studies show that for effective catalysis, Erm transitions between multiple conformations, an effective strategy adopted to orient the dynamic helix where methylation occurs. Unraveling this unique mechanism of targeting adopted by Erm paves the way for selective design of allosteric inhibitors directed toward reversing MLS resistance.
External linksSci Adv / PubMed:41296849 / PubMed Central
MethodsEM (single particle)
Resolution4.0 - 4.7 Å
Structure data

61605

9jmk

EMDB-61605, PDB-9jmk:
50S Ribosomal Subunit precursor state III
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-61613: 50S subunit precursor state I
Method: EM (single particle) / Resolution: 4.5 Å

61625

9jns

EMDB-61625, PDB-9jns:
50S precursor - Erm complex (C-II)
Method: EM (single particle) / Resolution: 4.7 Å

61781

9jsr

EMDB-61781, PDB-9jsr:
50S precursor - Erm complex (C-I)
Method: EM (single particle) / Resolution: 4.0 Å

Chemicals

ChemComp-AN6:
5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine

Source
  • escherichia coli k-12 (bacteria)
  • bacillus subtilis (bacteria)
KeywordsRIBOSOME / 50S subunit / Precursor / Ribosome assembly intermediate / 50S precursor / Erm / methyltransferase / antibiotic resistance / ribosome-protein complex

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