- 2’-O-methyl RNA methyltransferase:
The 2’-O-methylation of ribosomal RNA is one of the most common ways bacteria can obtain antibiotic resistance. The structure of the 2’-O-methyl RNA methyltransferase from B. pseudomallei (BupsA.00072.a) contains a 31 (trefoil) protein knot. According to the protein knot server (http://knots.mit.edu/), which confirmed that this structure has a knot, there are only 40 similar structures in the PDB, including several SpoU-like RNA methyltransferases. The fold of these RNA methyltransferases is quite different from the classical methyltransferase fold, although related to the other SpoU-like RNA methyltransferases. The ribbon diagram in the figure shows it to be a dimer and the thread of the knot can be seen as the orange-red section passing through the yellow-green section in the bottom dimer. Most SpoU-like RNA methyltransferases also contain an RNA binding domain (RBD), but this RNA methyltransferase does not contain this domain, suggesting it may bind an accessory protein, or perhaps target a different substrate than other enzymes of this family. For more information, please see the Protein Data Bank entry 3e5y.