The crystal structure of a quinohemoprotein amine dehydrogenase from Pseudomonas putida has been determined at 1.9-Å resolution. The enzyme comprises three non-identical subunits: a four-domain ␣-subunit that harbors a di-heme cytochrome c, a seven-bladed -propeller -subunit that provides part of the active site, and a small ␥-subunit that contains a novel crosslinked, proteinous quinone cofactor, cysteine tryptophylquinone. More surprisingly, the catalytic ␥-subunit contains three additional chemical cross-links that encage the cysteine tryptophylquinone cofactor, involving a cysteine side chain bridged to either an Asp or Glu residue all in a hitherto unknown thioether bonding with a methylene carbon atom of acidic amino acid side chains. Thus, the structure of the 79-residue ␥-subunit is quite unusual, containing four internal cross-links in such a short polypeptide chain that would otherwise be difficult to fold into a globular structure.Recently, a number of modified amino acids have been identified in proteins that are generated by post-translational oxidation or non-oxidation processes (1, 2). Such a controlled modification of a specific amino acid residue forming part of the active site provides catalytic power to the protein. In the case of a certain class of amine-oxidizing enzymes, depending on the enzyme concerned, oxidation of a specific tyrosine or tryptophan residue leads to the generation of a redox-active quinone cofactor: 2,4,5-trihydroxyphenylalanine quinone (topaquinone) (3), lysine tyrosylquinone (4), or tryptophan tryptophylquinone (TTQ) 1 (5). Together with several enzymes containing the first identified, non-proteinous quinone cofactor, pyrroloquinoline quinone (PQQ), the enzymes containing those cofactors constitute a quinoprotein family of enzymes (6).Quinohemoprotein amine dehydrogenases (QH-AmDH) from Gram-negative bacteria represent a new type in the quinoprotein class of amine-oxidizing enzymes because they contain not only a quinone but also one or two hemes as a redox active group (7, 8) providing an opportunity for intramolecular electron transfer. Intermolecular electron transfer from QHAmDH has been demonstrated with the natural electron acceptors azurin for the enzyme from Pseudomonas putida (7) and cytochrome c-550 for the enzyme from Paracoccus denitrificans (9). The structure of the presumed quinone cofactor in QH-AmDH remain to be settled, although biochemical and spectroscopic analyses have suggested the presence of a quinone group similar to, but not identical, with TTQ (7, 8).To identify the quinone cofactor and its position in the protein, we (10) have recently determined the primary structure of the quinone-containing small subunit of QH-AmDH from P. putida using a combination of automated Edman degradation and mass spectrometry, and we have also cloned the genes coding for the three subunits of the heterotrimeric enzyme. Although we initially encountered difficulties in the interpretation of the chemical and mass data, the progress in elucidating the crystal struct...