Involved in the maturation of [NiFe] hydrogenases. Along with HypF, it catalyzes the synthesis of the CN ligands of the active site iron of [NiFe]-hydrogenases. HypE catalyzes the ATP-dependent dehydration of the carboxamido group attached to its C-terminal cysteine to a cyano group. ATP + C-terminal S-carboxamide-L-cysteinyl-[HypE protein] = ADP + C-terminal S-cyanate-L-cysteinyl-[HypE protein] + H(+) + phosphate Protein modification; [NiFe] hydrogenase maturation. Modified by HypF, which adds a carboxamido group to the thiolate of the C-terminal cysteine, yielding a protein-S-carboxamide. The carboxamido group is then dehydrated by HypE itself to yield a protein-thiocyanate. Insertion mutant lacks any hydrogenase activity in symbiosis with peas, but is still able to synthesize the polypeptide for the hydrogenase large subunit. Belongs to the HypE family.