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.