Download MendeleyStructural Analysis of 23S rRNA Methylating Enzyme Cfr Reveals RNA-Binding Determinants for Methylation Regiospecificity and Antibiotic Resistance.
Fruci, M., Rodriguez Hernandez, A., Skarina, T., Verellen, L.A., Tsai, K., Virta, J.M., Fujimori, D.G., Savchenko, A., Stogios, P.J.(2026) ACS Infect Dis 12: 653-664
- PubMed: 41615325 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1021/acsinfecdis.5c00828
- Primary Citation Related Structures:
9P0P - PubMed Abstract:
The 23S rRNA methylating enzyme Cfr, found in pathogens including Staphylococcus aureus , Clostridium difficile , Escherichia coli , and Klebsiella pneumoniae , confers resistance to phenicols, lincosamides, oxazolidinones (including linezolid), pleuromutilins, and streptogramins A (the PhLOPS A phenotype). Cfr catalyzes methylation of the C8 position of the A2503 base in 23S rRNA, the recognition site of the above antibiotic classes. Along with the RlmN housekeeping enzyme, Cfr can also promote methylation of the C2 position of the same base. The molecular and structural basis of Cfr's dual substrate specificity is not known, which hinders our ability to design Cfr-targeting inhibitors necessary to curb PhLOPS A resistance. Here, we present the first crystal structure of Cfr and a detailed analysis of its possible interactions with rRNA. Using structure-guided mutagenesis, mass spectrometry analysis of in cellulo 23S rRNA methylated species, and in cellulo resistance studies, we identify the key amino acids essential for Cfr methylation and multidrug resistance activity. In particular, we found that Cfr's Q329 residue is important for C8-specific methylation. These data provide a framework for further studies of the biochemistry, structure, and inhibition of this important resistance determinant.
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3, Canada.
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