The active site structure of quinohemoprotein amine dehydrogenase inhibited by p-nitrophenylhydrazine

Quinohemoprotein amine dehydrogenase (QH-AmDH) catalyzes the oxidative deamination of aliphatic and aromatic amines. The enzyme from Pseudomonas putida has an alpha beta gamma heterotrimeric structure with two heme c groups in the largest alpha subunit, and a novel quinone cofactor [cysteine tryptophylquinone (CTQ)] and hitherto unknown internal cross-bridges in the smallest gamma subunit. The crystal structure of the enzyme in the complex with the inhibitor [p-nitrophenylhydrazine (pNPH)] has been determined at a 2.0 A resolution.(1) The hydrazone of the cofactor with the inhibitor was nicely modeled into the omit electron density map, identifying the C6 carbonyl group as the reactive site of the cofactor. The Asp33 gamma is unambiguously determined as the catalytic base to abstract the alpha-proton from a substrate, because N beta atom of the inhibitor corresponding to the C alpha atom of the substrate amine is neighbored to Asp33 gamma. The bound inhibitor is completely enclosed in the active site pocket formed by the residues from the beta- and gamma-subunits. The cofactor-inhibitor adduct may be predominantly in the hydrazone with the azo form as a minor component. The binding of the inhibitor causes minor but important conformational changes in the residues surrounding the active site. The inhibitor may have access to the active site pocket through the water-filled crevice between the beta- and gamma-subunits.