Fig. 3.

Structure-based alignment of repressor and periplasmic binding proteins. Structure-based alignments were made by using the Dali server at the EMBL (http://www.emblheidelberg.de/Services/index.html) between the liganded "closed" structure of LacI (1lbh; Lewis et al. 1996) and the following proteins: PurR (1wet; Schumacher et al. 1994), TreR (1byk; Hars et al. 1998), RBP (2dri; Mowbray and Cole 1992), ABP (1abe; Newcomer et al. 1981; Quiocho and Vyas 1984), GBP (1glg; Vyas et al. 1988), and ALBP (1rpj; Chaudhuri et al. 1999). Gaps in the sequence of one protein relative to another are indicated with dashes. Dots are used to indicate loops "inserted" on ABP (41–66 and 239–249) that are too long to include on this figure or to indicate where sequence is not shown for simplicity (e.g., LacI 286–325). For the repressor proteins, residues with side chain or backbone contacts within 3.5 Å or hydrophobic contacts within 4.5 Å of the partner monomer are noted. Interactions of the liganded (closed) structure are represented with black text on a gray box; those of the unliganded (open) structure are indicated with white text on a gray box; and those present in both structures are shown as white text on a black box. The open structures used for LacI and PurR are 1efa and 1dbq, respectively (Schumacher et al. 1995; Bell and Lewis 2000). An open structure is not available for TreR. Two structures of closed, inducer-bound LacI are available, 1tlf and 1lbh (Friedman et al. 1995; Lewis et al. 1996). Contacts from both structures are included on this map. (A) Core-to-core contacts in the core N- and C-subdomains. Sites involved in the interfaces of all three repressors are indicated with Roman numerals I–X for the N-subdomain and I–VIII for the C-subdomain. (B) Monomer–monomer contacts between the HTH and core domains for LacI (open) and PurR (closed) are indicated, as well as LacI (closed) contacts between the core C-subdomain and the LHR. The latter are not available for the DNA-bound (open) structure of the protein.