Structural Analysis of Lac Repressor Bound to Allosteric Effectors

Abstract

The lac operon is a model system for understanding how effector molecules regulate transcription and are necessary for allosteric transitions. The crystal structures of the lac repressor bound to inducer and anti-inducer molecules provide a model for how these small molecules can modulate repressor function. The structures of the apo repressor and the repressor bound to effector molecules are compared in atomic detail. All effectors examined here bind to the repressor in the same location and are anchored to the repressor through hydrogen bonds to several hydroxyl groups of the sugar ring. Inducer molecules form a more extensive hydrogen-bonding network compared to anti-inducers and neutral effector molecules. The structures of these effector molecules suggest that the O6 hydroxyl on the galactoside is essential for establishing a water-mediated hydrogen bonding network that bridges the N-terminal and C-terminal sub-domains. The altered hydrogen bonding can account in part for the different structural conformations of the repressor, and is vital for the allosteric transition.

Structural Explanation for Allolactose (lac Operon Inducer) Synthesis by lacZ β-Galactosidase and the Evolutionary Relationship between Allolactose Synthesis and the lac Repressor

“…Residues in the effector binding site were used as distinguishing features. Although a structure of allolactose complexed with lac repressor has not been reported, effector binding has been studied with the lac repressors having isopropyl 1-thio-␤-D-galactopyranoside and oNPG bound (PDB IDs 2P9H and 2PE5, respectively) (36). The Gal moieties of isopropyl 1-thio-␤-D-galactopyranoside and oNPG would define the binding of the Gal moiety of allolactose, whereas the Glc pocket is defined in repressor structures by residues near the thioisopropyl group of isopropyl 1-thio-␤-D-galactopyranoside and the oNP portion of oNPG.…”

Hydrogen Bonds and Hydrophobic Interactions of Porphyrins in Porphyrin-Containing Proteins

“…The directionality of the hydrogen bond is very important since it allows the chemist to control the geometry of the complexes and to design precisely complementary hosts for a given guest. Studies of the structures of small molecules [2,3], surveys of proteins and nucleic acid structures in the Protein Data Bank (PDB) [4][5][6], and calculations based on classical molecular dynamics simulations [7,8] and density functional theory (DFT) [9][10][11] have provided considerable insight into the geometry of hydrogen bonds. In structural studies, however, the presence of hydrogen bonds is most often inferred rather than actually detected [12].…”

Flexibility and Disorder in Gene Regulation: LacI/GalR and Hox Proteins

“…For E. coli LacI, structures of free, DNA-bound, and IPTG-bound protein (14,70), along with molecular dynamics simulations (23,71,72), have been used to study these adaptable regions. The largest changes are found in the linker region and in the N-subdomain interface of LacI (14,23,70). Inducer binding alters the juxtaposition of the LacI N-subdomains to bring them into closer contact (Fig.…”