PylD enzyme acts as
PylD finalizes pyrrolysine formation acting as NAD-dependent dehydrogenase or oxidase converting N6-(3-methylornithyl)-lysine intermediate into pyrrolysine via oxidation at epsilon position generating amino aldehyde that spontaneously cyclizes forming imine bond of pyrroline ring. Enzyme releases ammonia and water producing L-pyrrolysine with defined stereochemistry at C2 and C4 recognized by PylRS active site hydrophobic pocket. PylD possesses Rossmann-fold nucleotide-binding domain coordinating NAD cofactor similar to ornithine cyclodeaminases. Oxidation-driven ring closure logic elegantly converts linear pseudopeptide into heterocyclic amino acid, completing pathway from simple lysine precursors and providing selective advantage for methylamine-dependent methanogenesis under anaerobic conditions encountered environmentally.
Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 3: PylD Oxidase and Cyclization to Pyrrolysine