Figure 4. Model of SgrAI DNA-bound dimer (DBD) activation and enzymatic function.

(AC) SgrAI DBDs contain, at a minimum, two conformational states, which account for an inactive, or minimally active, (red) and an active (green) enzymatic state. The two exist in equilibrium, the extent of which is dependent upon whether (A) primary-site (blue) or (B-C) secondary-site (yellow) DNA is bound. DNA-recognition sites are displayed underneath, with the varying nucleotide in red. In the active, dimeric form, both primary- and secondary-site DNA can undergo cleavage at a slow rate that is determined by the frequency of occupation of the active state. (A) primary-site DBDs can initiate oligomerization, and they can do so with any DBD and regardless of the bound DNA sequence. (B) Secondary-site DBDs can join an oligomer containing primary-site DBDs. Oligomerization in turn stabilizes the activated conformation and facilitates attachment of additional DBDs, enabling DNA cleavage acceleration (A-B) and/or sequence-specificity expansion (B). To differentiate the distinct subunits, active & stabilized DBDs within the oligomer are shaded differently, although all are presumed to maintain equal activity. (C) Secondary-site DBDs cannot undergo oligomerization by themselves, and higher order species are not observed, although it is possible that transient oligomerzation occurs, but is undetectable under the experimental reaction conditions. The discussion section provides further mechanistic details.