Figure 1. Arrangement of DNA replication terminators in the circular chromosomes of (a) Escherichia coli and (b) Bacillus subtilis. The two replication forks generated at the origin (oriC) move in opposite directions along the DNA and eventually approach one other and fuse within the terminus region diametrically opposed to oriC. The terminus region constitutes a replication fork trap in which the DNA terminators (denoted Ter) are arranged as two opposed groups, with the purple terminators oriented to block movement of the clockwise replication fork and the green terminators oriented to block the anticlockwise fork. The STer region contains additional terminator sites used by B. subtilis only during the stringent response. The approximate chromosomal locations of the genes for the terminator proteins, Tus (terminus utilization substance) in E. coli and RTP (replication terminator protein) in B. subtilis, are marked with arrows. (c) Consensus sequence for the B. subtilis terminators, with the overlapping A and B sites indicated.

Figure 2. Tus–Ter fork arrest complex (Kamada et al., 1996). (a) A view perpendicular to the helical axis of the DNA (red). Tus (terminus utilization substance) is composed of a large N-terminal domain (blue) and a smaller C-terminal domain (green) with an interdomain region (gold) that is composed of two very long strands flanked by three smaller strands. In this view, the ‘passage end’ and the ‘blockage end’ are indicated. (b) A view down the helical axis of the DNA from the blockage end of the fork-arrest complex; this view can be obtained by a 90° leftwards rotation of the view in (a). The L1 loop (indicated) has been implicated in taking part in a specific interaction with the replicative helicase during fork arrest (Henderson et al., 2001; Mulugu et al., 2001), whereas the two bulky -helical domains, suggested sterically to block replisome movement in the alternative model, dominate this ‘helicase eye’ view.

Figure 3. Crystal structure of a replication terminator protein (RTP) dimer bound to DNA (a, b) and a model of the complete RTP–Ter complex (c) (Wilce et al., 2001). (a) A view perpendicular to the helical axis of the DNA. The RTP dimer (green) has its secondary structural elements labelled on one of the RTP monomers. Each monomer has structural homology to other ‘winged-helix’ DNA-binding protein family members, with the 3 helix from each monomer making the most significant base-specific contacts. The long 4 helices from each monomer form the coiled-coil dimerization domain. (b) A view down the helical axis of the DNA; this view can be obtained by a 90° y-axis rotation of the view in (a). (c) A model of the complete RTP–Ter complex based on the crystal structure of the RTP dimer–DNA complex and knowledge of the relative positioning of the two adjacent RTP-binding sites within the Ter DNA. Each dimer is shown as a backbone structure with a surface rendering. The model could explain how the two RTP dimers interact with one another when bound together at the terminator; contact could be mediated by a region comprising portions of the 3 helix and the 2 strand of adjacent RTP molecules – these structural elements are indicated in (b).