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1. In some cases, the cofactor completes the active site of the enzyme or modifies it in such a manner that substrate binding can ensue. 2. The cofactor acts as a donor of electrons or atoms to the substrate and following the reaction is returned to its former state.
In a number of enzymes, the moiety that acts as a cofactor is formed by post-translational modification of a part of the protein sequence. Examples include tryptophan tryptophylquinone (TTQ), derived from two tryptophan side chains, and 4-methylidene-imidazole-5-one (MIO), derived from an Ala-Ser-Gly motif.