Allosteric equilibrium model of SgrAI filamentation and activation.
SgrAI bound to its primary recognition sequence (DBD, pink, blue) is in equilibrium between a low-activity conformation (the T state, pink) and a high-activity conformation (the R state, blue). The T state structure is missing the second Mg2+ ion in the active site (dotted circle encircling the letter B in the pink box) and does not form filaments. The R state DBDs assemble into filaments with activated DNA cleavage activity, originating from occupancy of both Mg2+ ions in the active site (sites A and B). The conformational change stabilized by contacts between DBDs in the filament results in a shift of residues of SgrAI, which creates a high affinity binding pocket for the site B Mg2+ (right-most arrow within blue box) involving a bridging water molecule (light blue sphere). Mg2+ in site A ligates the nucleophilic water (dark blue sphere), which is responsible for attack on the phosphorus atom at the site of cleavage (left-most arrow within blue box), leading to bond breakage between the phosphorus atom and the O3′ (curved arrow within blue box). All atoms were modeled into and refined against experimental cryo-EM maps, including the water molecules.