Crystal Structure of ErmC‘, an rRNA Methyltransferase Which Mediates Antibiotic Resistance in Bacteria

Abstract

The prevalent mechanism of bacterial resistance to erythromycin and other antibiotics of the macrolide-lincosamide-streptogramin B group (MLS) is methylation of the 23S rRNA component of the 50S subunit in bacterial ribosomes. This sequence-specific methylation is catalyzed by the Erm group of methyltransferases (MTases). They are found in several strains of pathogenic bacteria, and ErmC is the most studied member of this class. The crystal structure of ErmC' (a naturally occurring variant of ErmC) from Bacillus subtilis has been determined at 3.0 A resolution by multiple anomalous diffraction phasing methods. The structure consists of a conserved alpha/beta amino-terminal domain which binds the cofactor S-adenosyl-l-methionine (SAM), followed by a smaller, alpha-helical RNA-recognition domain. The beta-sheet structure of the SAM-binding domain is well-conserved between the DNA, RNA, and small-molecule MTases. However, the C-terminal nucleic acid binding domain differs from the DNA-binding domains of other MTases and is unlike any previously reported RNA-recognition fold. A large, positively charged, concave surface is found at the interface of the N- and C-terminal domains and is proposed to form part of the protein-RNA interaction surface. ErmC' exhibits the conserved structural motifs previously found in the SAM-binding domain of other methyltransferases. A model of SAM bound to ErmC' is presented which is consistent with the motif conservation among MTases.

Methyltransferase Erm(37) Slips on rRNA to Confer Atypical Resistance in Mycobacterium tuberculosis

“…NMR studies on Erm(B) (formerly ErmAM) (28) and crystals of Erm(C)Ј (29,30) show identical structural folds organized into distinct N-and C-terminal domains. The larger N-terminal domain contains the catalytic site adjacent to the binding site for the S-adenosylmethionine cofactor (30).…”

Identification of the Binding Site for the Extrahelical Target Base in N 6-Adenine DNA Methyltransferases by Photo-cross-linking with Duplex Oligodeoxyribonucleotides Containing 5-Iodouracil at the Target Position

“…Tyr-122 in M.CviBIII and Tyr-108 in M.TaqI belong to the conserved motif IV ((N/D/S)(P/I)P(Y/F/W)) found in all N 6 -adenine and N 4 -cytosine DNA Mtases as well as in N 6 -adenine RNA Mtases (N-DNA/RNA Mtases) (39). In addition, the structures of several other N-DNA/RNA Mtases in the absence of DNA or RNA were determined and it was found that their cofactor binding domain structures are very similar (10,40,41). Thus, the spatial relationship between the target base and the aromatic amino acid residue within motif IV is expected to be similar for all N-DNA/RNA Mtases.…”

Crystal structure of RlmA I : Implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site

“…These structural differences provide a basis for these enzymes' specificities to their respective substrates, different parts of bacterial rRNA. Among the above discussed three rRNA MTase structures, the reported structures of ErmCЈ (33) and AviRa (35) have no well defined RNAbinding cleft͞pocket and the RNA-binding cleft that has been described for dimeric RlmB (32) is very different from that of RlmA I (Fig. 4).…”

“…3). The relative positions and orientations of the bound SAM molecules in RlmA I differ significantly from those of the ErmCЈ structure (33). In addition, the putative rRNA-recognizing domains (e.g., the Zn-binding domain of RlmA I ) of the two enzymes have different tertiary fold and are positioned differently with respect to superimposed MTase domains (Fig.…”