Post-translational modifications of amino acids can be used to generate novel cofactors capable of chemistries inaccessible to conventional amino acid side chains. The biosynthesis of these sites often requires one or more enzyme or protein accessory factors, the functions of which are quite diverse and often difficult to isolate in cases where multiple enzymes are involved. Herein is described the current knowledge of the biosynthesis of urease and nitrile hydratase metal centers, pyrroloquinoline quinone, hypusine, and tryptophan tryptophylquinone cofactors along with the most recent work elucidating the functions of individual accessory factors in these systems. These examples showcase the breadth and diversity of this continually expanding field.