||The presence of an iterative type I polyketide synthase (PKS) is a central feature of the biosynthetic gene cluster of all enediyne natural products. This PKS is generally believed to be responsible for the first step in the enediyne core biosynthesis. However, the exact role of the synthase is still controversial. Here, we report the finding of a new product for the iterative PKS SgcE involved in biosynthesis of the nine-membered enediyne antitumor antibiotics C-1027. This product was formed under oxidative conditions with an optical absorption maximum at 420 nm. Its UV-Vis spectrum and its elution profile in reverse-phase HPLC are very different from that of the reported products of enediyne PKSs. In comparison to a reported polyene natural product, we propose that this new product may be a dehydrogenated product of a previously reported nonaketide precursor of the C-1027 enediyne core. In addition, we characterized a pyridoxal phosphate (PLP)-dependent enzyme CalE6 and a possible oxidoreductase CalS6 in the biosynthetic gene cluster of calicheamicin γI. Apo-CalE6 was obtained by removal of the cofactor and the holo-enzyme was then reconstituted to determine the ratio of PLP cofactor to peptide to be 1:1. Nonetheless, the real function of CalE6 is still unclear in the enediyne biosynthesis. Meanwhile, based on steady state kinetic studies, CalS6 was characterized to be a NADPH-dependent flavin reductase. This latter enzyme utilizes NADPH 10 times better than NADH in the presence of FMN, and reduces FAD almost as efficiently as FMN in the presence of NADPH. These findings deepen our understanding of the enediyne biosynthetic proteins and will help us to move forward in our effort to decode the chemical logics underlying the biogenesis of the complex enediyne natural products.