Figure 5.

A composite partial molecular model of the sliding clamp docking on an RNAP:promoter complex. The structure of the RB69 sliding clamp [47] has been docked against a Taq RNAP holoenzyme fork junction promoter DNA complex [25]. Evidence from site-specific DNA-protein photochemical cross-linking and DNA footprinting [34] specifies that the sliding clamp abuts RNAP. Gp33 is placed in the model in accordance with the recent determination of its structure in complex with the E. coli β flap and DRII (amino acids 831-1057) by K-A.F. Twist and S.A. Darst [43][K-A.F. Twist, P. Deighan, S. Nechaev, A. Hochschild, E.P. Geiduschek & S.A. Darst, in preparation] and a complete structural model of E. coli RNAP based on a combination of approaches [82]. Placement of the C-end of gp33 in proximity to DNA is consistent with evidence from site-specific DNA-protein cross-linking [34]. The rotational orientation of gp45 is arbitrary, but is likely to be constrained by the interacting RNAP surface and also by the short tether to gp33. The location of the C-end of gp33 on the sliding clamp in the T4 late promoter complex is not known; a C-terminal 11-mer of phage RB69 DNA polymerase from the structure in [47] has not been removed and is barely visible, but its relevance to the late promoter complex is unclear, as discussed in the text. Residues 44-123 of gp55, comprising its RNAP core- and DNA-biding sites, have been modeled based on homology with σ⁷⁰ domain 2 [26] and docked onto the β" subunit coiled-coil. Colors of components are indicated in the Figure. (Images provided by K.-A. Twist and S.A. Darst and reproduced with their permission.)