title: Characterization of the Staphylococcus aureus rRNA methyltransferase encoded by orfX, the gene containing the staphylococcal chromosome Cassette mec (SCCmec) insertion site.
abstract: The gene orfX is conserved among all staphylococci, and its complete sequence is maintained upon insertion of the staphylococcal chromosome cassette mec (SCCmec) genomic island, containing the gene encoding resistance to β-lactam antibiotics (mecA), into its C terminus. The function of OrfX has not been determined. We show that OrfX was constitutively produced during growth, that orfX could be inactivated without altering bacterial growth, and that insertion of SCCmec did not alter gene expression. We solved the crystal structure of OrfX at 1.7 Å and found that it belongs to the S-adenosyl-L-methionine (AdoMet)-dependent α/β-knot superfamily of SPOUT methyltransferases (MTases), with a high structural homology to YbeA, the gene product of the Escherichia coli 70 S ribosomal MTase RlmH. MTase activity was confirmed by demonstrating the OrfX-dependent methylation of the Staphylococcus aureus 70 S ribosome. When OrfX was crystallized in the presence of its AdoMet substrate, we found that each monomer of the homodimeric structure bound AdoMet in its active site. Solution studies using isothermal titration calorimetry confirmed that each monomer bound AdoMet but with different binding affinities (K(d) = 52 ± 0.4 and 606 ± 2 μm). In addition, the structure shows that the AdoMet-binding pocket, formed by a deep trefoil knot, contains a bound phosphate molecule, which is the likely nucleotide methylation site. This study represents the first characterization of a staphylococcal ribosomal MTase and provides the first crystal structure of a member of the α/β-knot superfamily of SPOUT MTases in the RlmH or COG1576 family with bound AdoMet.
authors.affiliation: Division of Infectious Diseases, Department of Medicine, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298 USA.
authors.forename: Sam
authors.initials: S
authors.lastname: Boundy
authors.forename: Martin K
authors.initials: MK
authors.lastname: Safo
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.forename: Faik N
authors.initials: FN
authors.lastname: Musayev
authors.forename: Heather C
authors.initials: HC
authors.lastname: O'Farrell
authors.forename: Jason P
authors.initials: JP
authors.lastname: Rife
authors.forename: Gordon L
authors.initials: GL
authors.lastname: Archer
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray / Q000379:methods; D004926:Escherichia coli / Q000378:metabolism; D007700:Kinetics; D008780:Methyltransferases / Q000737:chemistry* / Q000235:genetics; D008957:Models, Genetic; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012335:RNA, Ribosomal / Q000378:metabolism*; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism; D013211:Staphylococcus aureus / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D012335:RNA, Ribosomal; D008780:Methyltransferases