This paper characterizes the amide ligases in peptidyl nucleoside antifungal biosynthesis and demonstrates that the cryptic phosphorylation retains until the last step of these pathways. Cryptic phosphorylation is a mechanism recently identified in these pathways and emerging in other nucleoside and aminoglycoside pathways. The results provide further insights into the crytpic phosphorylation in natural product biosynthesis in general.