Catalyzes the cross-linking of a glutamate residue and a tyrosine residue in the PqqA protein as part of the biosynthesis of pyrroloquinoline quinone (PQQ). [PQQ precursor protein] + S-adenosyl-L-methionine = 5'-deoxyadenosine + E-Y cross-linked-[PQQ precursor protein] + H(+) + L-methionine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. Interacts with PqqD. The interaction is necessary for activity of PqqE. Belongs to the radical SAM superfamily. PqqE family. An expected iron ligand Cys residue was not found at position 29 in this sequence.