The DNA cleavage experiments show that C-1027 chromophore is selectively incorporated into C-1027 apoprotein and is strongly protected by the apoprotein from loss of its DNA cleaving activity. Fluorescence and circular dichroism spectra reveal (1) important participation of tertiary structure of C-1027 apoprotein for the chromophore binding, (2) specific 1:1 binding of C-1027 chromophore to the apoprotein, and (3) significant interaction of the benzoxazine group in the chromophore-apoprotein complex. On the other hand, C-1027 apoprotein does not contribute to sequence-specificity DNA cleavage by C-1027 antibiotics.