Figure 2.

Influence of ssDNA directionality on substrate turnover. (A) The 5′ → 3′ sequence TTCA but not the corresponding 3′ → 5′ TTCA (equivalent to 5′-ACTT-3′) oligonucleotide is deaminated by A3B CTD. (B) Binding of 3′ → 5′ deoxycytidine monophosphate (dCMP, orange), but not 5′ → 3′ dCMP (green) results in severe clashes with the A3B protein (blue cartoon/spheres and gray surface). Therefore, only the 5′ → 3′ dCMP is compatible with binding; the crystal structure conformation of the base is fixed in a productive binding mode; PDB entry 5TD5 was used.¹³ (C) Due to the chirality of the deoxyribose sugar, the 3′ and 5′ ends adopt different vectors in 5′ → 3′ and 3′ → 5′ dCMP; the cytosine base is depicted in the same orientation, which is required for productive deamination (Figure 2B).