E. coli trp Repressor Forms a Domain-Swapped Array in Aqueous Alcohol
fold (Figure 1A), the trpR dimer itself has been consid-Department of Chemistry and Chemical Biology ered a probable example of quasi-domain swapping 610 Taylor Road (Hakansson and Linse, 2002; Schlunegger et al., 1997). Piscataway, New Jersey 08854 An apparent monomeric homolog of trpR has recently 2 Princeton University been identified (Erzberger et al., 2002). To our knowl-Department of Chemistry edge, the structure we present here is the first example Princeton, New Jersey 08544 of an
... d, extended 3D network formed by domain swapping. The smallest functional unit of trpR is the dimer (Joa-Summary chimiak et al., 1983a), but higher order association is well documented. When bound to tandem DNA sites, The E. coli trp repressor (trpR) homodimer recognizes trpR dimers associate in a 2-fold symmetric manner its palindromic DNA binding site through a pair of flexithrough a limited, predominantly hydrophobic interacble helix-turn-helix (HTH) motifs displayed on an intertion between flexible N-terminal arms and a concave twined helical core. Flexible N-terminal arms mediate surface adjacent to and involving the HTH (Figure 1B) association between dimers bound to tandem DNA (Lawson and Carey, 1993). TrpR dimers also associate sites. The 2.5 A ˚X-ray structure of trpR crystallized in in the absence of DNA, yielding predominantly tetramers 30% (v/v) isopropanol reveals a substantial conformabut also higher order species (Fernando and Royer, tional rearrangement of HTH motifs and N-terminal 1992; Martin et al., 1994). Biochemical, mutational, and arms, with the protein appearing in the unusual form structural evidence support the hypothesis first put forof an ordered 3D domain-swapped supramolecular ward by Royer that dimer-dimer interactions in the abarray. Small angle X-ray scattering measurements sence of DNA involve N-terminal arm contacts similar show that the self-association properties of trpR in to those made on DNA (Chae et al., 1999; Mackintosh solution are fundamentally altered by isopropanol.