Is required for the biosynthesis of pyrrolysine (By similarity). Catalyzes the ATP-dependent ligation between (3R)-3-methyl-D-ornithine and L-lysine, leading to (3R)-3-methyl-D-ornithyl-N6-L-lysine (Probable). (3R)-3-methyl-D-ornithine + ATP + L-lysine = (3R)-3-methyl-D-ornithyl-N(6)-L-lysine + ADP + H(+) + phosphate Binds 2 magnesium ions per subunit. Amino-acid biosynthesis; L-pyrrolysine biosynthesis. Contains two adenine nucleotides bound at the active site. One ATP molecule is involved in catalysis, the second adenine nucleotide functions as a selective anchor for the C- and N-terminus of the Lys substrate and is responsible for protein stability. Belongs to the PylC family.