Catalyzes the isomerization of L-lysine to (2R,3R)-3-methylornithine via a radical-based mechanism, a step in the biosynthesis pathway of pyrrolysine. L-lysine = (3R)-3-methyl-D-ornithine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 S-adenosyl-L-methionine per subunit. Amino-acid biosynthesis; L-pyrrolysine biosynthesis. Belongs to the radical SAM superfamily. PylB family.