Abstract
Pathogens often receive antibiotic resistance genes through horizontal gene transfer from bacteria that produce natural antibiotics. ErmE is a methyltransferase (MTase) from Saccharopolyspora erythraea that dimethylates A2058 in 23S rRNA using S-adenosyl methionine (SAM) as methyl donor, protecting the ribosomes from macrolide binding. To gain insights into the mechanism of macrolide resistance, the crystal structure of ErmE was determined to 1.75 Å resolution. ErmE consists of an N-terminal Rossmann-like α/ß catalytic domain and a C-terminal helical domain. Comparison with ErmC’ that despite only 24% sequence identity has the same function, reveals highly similar catalytic domains. Accordingly, superposition with the catalytic domain of ErmC’ in complex with SAM suggests that the cofactor binding site is conserved. The two structures mainly differ in the C-terminal domain, which in ErmE contains a longer loop harboring an additional 310 helix that interacts with the catalytic domain to stabilize the tertiary structure. Notably, ErmE also differs from ErmC’ by having long disordered extensions at its N- and C-termini. A C-terminal disordered region rich in arginine and glycine is also a present in two other MTases, PikR1 and PikR2, which share about 30% sequence identity with ErmE and methylate the same nucleotide in 23S rRNA.
Highlights
The ribosome is the large macromolecular machine responsible for the sequential template-dependent polymerization of amino acids into a polypeptide chain[1], and an important drug target for antibiotics[2,3]
In light of the danger of horizontal transfer of macrolide and ketolide resistance genes, there is an urgent need for better understanding of the respective resistance mechanisms, including information on the structural and functional properties of ribosome-modifying enzymes
Smaller, band was present after IMAC purification of the N-terminally His8-tagged PikR1, we hypothesized that it was the result of a C-terminal proteolytic degradation
Summary
The ribosome is the large macromolecular machine responsible for the sequential template-dependent polymerization of amino acids into a polypeptide chain[1], and an important drug target for antibiotics[2,3]. We present the crystal structure of rRNA MTase ErmE, and analyze the similarities and differences to PikR1, PikR2, ErmC’ and other similar MTases. For PikR2 and ErmE, C-terminal regions of 64 and 93 residues were predicted to be disordered (Fig. 2).
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