A comparative three-dimensional model of the carboxy-terminal domain of the lambda repressor and its use to build intact repressor tetramer models bound to adjacent operator sites

Abstract

A model for residues 93–236 of the λ repressor (1gfx) was predicted, based on the UmuD ′ crystal structure, as part of four intact repressor molecules bound to two adjacent operator sites. The structure of region 136–230 in 1gfx was found to be nearly identical to the independently determined crystal structure of the 132–236 fragment, 1f39, released later by the PDB. Later, two more tetrameric models of the λ repressor tetramer bound to two adjacent operator sites were constructed by us; in one of these, 1j5g, the N-domain and C-domain coordinates and hence monomer-monomer and dimer-dimer interactions are almost the same as in 1gfx, but the structure of the linker region is partly based on the linker region of the LexA dimer in 1jhe; in the other, 1lwq, the crystalline tetramer for region 140–236 has been coopted from the crystal structure deposited in 1kca, the operator DNA and N-domain coordinates of which are same as those in 1gfx and 1j5g, but the linker region is partly based on the LexA dimer structures 1jhe and 1jhh. Monomer-monomer interactions at the same operator site are stabilized by exposed hydrophobic side chains in β-strands while cooperative interactions are mostly confined to β 6 and some adjacent residues in both 1gfx and 1j5g. Mutational data, existence of a twofold axis relating two C-domains within a dimer, and minimization of DNA distortion between adjacent operator sites allow us to roughly position the C-domain with respect to the N-domain for both 1gfx and 1j5g. The study correlates these models with functional, biochemical, biophysical, and immunological data on the repressor in the literature. The oligomerization mode observed in the crystal structure of 132–236 may not exist in the intact repressor bound to the operator since it is shown to contradict several published biochemical data on the intact repressor.