The small subunit of the terminase enzyme of Bacillus subtilis bacteriophage SPP1 forms a specialized nucleoprotein complex with the packaging initiation region.

Initiation of SPP1 DNA packaging requires the gene 1 and gene 2 products (G1P and G2P), which are different subunits of the terminase enzyme. G1P specifically recognizes the phage packaging initiation region (pac). The apparent equilibrium constant for the G1P-pac-DNA complex was estimated to be 9 nM. DNase I footprinting experiments reveal that the pac region can be subdivided into three discrete sites (pacL, pacC and pacR). G1P binds co-operatively to the non-adjacent pacL and pacR sites. Several G1P protomers bind to the target sequences which map close to the pac cleavage site (pacC site), but do not overlap with it. G1P interacts in a different fashion with the encapsidated (pacR site) and with the non-encapsidated (pacL site) end of the phage genome. G1P interaction with the intrinsically bent pacL DNA occurs only on one face of the DNA double helix. G1P binding to the pacL and in the pacR region results in a DNA loop. Electron microscopy of purified G1P shows that the protein is an oligomer in solution. G1P binding to the core region of the pacL site could facilitate the formation of a higher-order nucleoprotein structure. This specialized complex would allow the pac DNA to form a loop between binding sites brought together by interaction with G1P. The results presented here suggest that G1P could provide a tool to discriminate the first encapsidated end, which contains pacR, from the non-encapsidated pacL end.