RTP and Tus
A comparison of the Replication Terminator Protein (from Bacillus subtillis) and Tus (from Escerishia coli) provides an interesting insight into how proteins with vastly different structures and mechanisms of action can produce essentially identical effects in their native systems.
Looking at the structures of these two proteins, it is not immediately obvious that they would perfom the same function, specifically, to arrest the progression of the replication fork along the bacterial chromosome at specific sites (termed Ter sites). Furthermore, this arrest-mechanism functions in a polar manner in both organisms, which is perhaps surprising considering the symmetrical characteristics of both proteins.
The structure of Tus is unusual for a DNA-binding protein. It binds Ter DNA as an asymmetrical monomer, which establishes the basis for its polar arrest of the replication fork. Tus has three distinct regions: two α-helical regions and central β-strands which jointly form a large, positively-charged central cleft (Kamada, 1996). The core β-structures embrace 13 base pairs of duplex DNA, and at least 30 other residues make nonspecific contacts with the DNA backbone. The positioning of α-helices in the Tus protein is particularly interesting. Two protrude from both the amino and carboxy domains to clasp the DNA duplex, thereby shielding the interdomain β structures from direct contacts with other proteins (such as the DnaB helicase). The concentration of α-helices on the non-permissive face of Tus is absolutely cruical to the protein's ability to form a locked complex with the Ter site. More about this later!
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