| Summary: | Erm38 is a methyltransferase from Mycolicibacterium smegmatis that methylates the A2058 position in 23S rRNA using S-adenosyl methionine (SAM) as methyl donor. It confers resistance to macrolides, lincosamides and streptogramins in Gram-positive bacteria and mycobacteria. In this project, we obtained apo crystals of Erm38 and revealed its structure information. Erm38 has a N-terminal Rossmann-like α/β catalytic domain and a C-terminal helical domain. Superposition and sequence alignment revealed a highly conserved SAM-binding pocket to ErmE and ErmC in the family. We also determined the binding between Erm38 and its natural RNA substrate, with a Kd of 164nM(±36nM). We then performed fragment-based screening using Thermal Shift Assay on a library of 1000 fragments. 74 hits were identified, out of which 33 were selected and soaked into apo Erm38 crystals. One fragment, Fragment 26, was validated by X-ray Crystallography and its crystal structure determined to 2.3A resolution. We revealed that fragment 26 binds within the SAM-binding pocket, its tail forming hydrogen bonds with residues E72 and V73, while its head interacting with L105 and other surrounding residues. A potential competitive SAM inhibitor, Fragment 26 serves as an important anchor for further optimization to increase its selectivity and binding affinity.
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