Figure 7

Sequence and structural relationships between the T4 clamp loader and those from other branches of life. (a) A sequence similarity dendrogram for the structurally characterized clamp loader subunits. The T4 clamp loader is more similar to yeast clamp loader than to the bacterial clamp loader subunits. Tree calculated using PHYLIP [133] using the neighbor-joining bootstrap criterion. (b) The structure of the T4 clamp loader B position AAA+ module (the gp44 protein; purple) is highly similar to the yeast clamp loader B subunit AAA+ module (the RFC4 protein; salmon). The C_α root mean square deviation (RMSD) is approximately 1.1 and 1.4 Å for the amino- and carboxy-terminal domains of the AAA+ modules, respectively. ATP is shown in spacefilling representation. (c) The A' domain is similar in yeast and T4 clamp loaders. The T4 and yeast A' domains have identical fold topology (the gp62 and RFC1 proteins in purple and salmon, respectively). Additionally, their packing against the E subunit AAA+ module is very similar. (d) A negative stain electron microscopy reconstruction of the P. furiosus clamp loader, clamp and DNA complex [62] reveals the presence of an A' domain. The correspondence of the T4 clamp loader structure (fit to the electron microscopy-derived molecular envelope) with that of the archaeal clamp loader suggests that the P. furiosus clamp loader also has an A' domain. Figure adapted from [60].