'Built-in' type cofactors are defined as the cofactors that are integrated within the enzyme polypeptides as a part of amino acid side-chains. Distinct from the orthodox cofactors that are synthesized from various vitamins and bound to the enzyme proteins after the biosynthesis, built-in cofactors are encoded as normal amino acid codons in the genes and thus should be produced by post- or co-translational modifications of their mother proteins. Over the recent decade, a number of unique built-in cofactors have been discovered in various enzyme proteins, such as topa quinone (TPQ) of copper amine oxidase and tryptophan tryptophylquinone (TTQ) of bacterial amine dehydrogenase. Using the inactive precursor form of a recombinant copper amine oxidase from Arthrobacter globiformis, we first demonstrated that TPQ is generated through self-processing of the enzyme protein with the participation of the bound copper ion. Subsequent X-ray crystallographic studies of the Cu/TPQ-less inactive enzyme (apoenzyme) as well as the Cu/TPQ-containing active form (holoenzyme) revealed the structural difference only in the active site. More recently, we have analyzed the process of TPQ biogenesis by time-resolved X-ray crystallography and determined the structures of freeze-trapped intermediates. Furthermore, we have identified a novel quinone cofactor, cysteine tryptophylquinone (CTQ) in quinohemoprotein amine dehydrogenases from Paracoccus denitrificans and Pseudomonas putida. CTQ is the forth quinone cofactor derived from amino acids, following TPQ, TTQ, and lysine tyrosylquinone (LTQ) found in lysyl oxidase.

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