PDBsum entry 2p9h

Transcription

PDB id: 2p9h

Contents

Protein chains

269 a.a.

Ligands

IPT ×2

Waters ×738

References listed in PDB file

Key reference

Title

Structural analysis of lac repressor bound to allosteric effectors.

Authors

R.Daber, S.Stayrook, A.Rosenberg, M.Lewis.

Ref.

J Mol Biol, 2007, 370, 609-619. [DOI no: 10.1016/j.jmb.2007.04.028]

PubMed id

17543986

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.

Figure 2.
Figure 2. Inducer binding site. (a) The fit of IPTG to the difference electron density where the phases were calculated from the atomic model of the repressor. The inducer and the water molecules were omitted from the structure factor calculations. The difference electron density was contoured at 3.5σ. (b) The binding of the inducer to the repressor. The view is rotated vert, similar 90° from (a) to better illustrate the detailed hydrogen bonding network. The dark blue portions of the structure correspond to residues in the C-terminal domain while the light blue corresponds to the N-terminal portion of the structure. The inducer and the water-mediate hydrogen bonds stabilize this conformation of the repressor. The green broken lines illustrate the water-mediated hydrogen bonding network that links the N-terminal and C-terminal sub-domains.

Figure 3.
Figure 3. The binding of the anti-inducer, ONPF, the repressor in the absence and the presence of the operator. (a) In the presence of DNA, the anti-inducer forms a ternary complex with the repressor primarily by establishing hydrogen bonds between the O2 and O3 hydroxyls of the fucoside and residues R197, N246 and D274 of the repressor and the nitrophenyl group hydrogen bonds to N146. (b) In absence of DNA, the anti-inducer is also bound to the repressor by hydrogen bonding to the fucoside but the nitrophenyl group does not appear to be ordered or adopt the same conformation.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 370, 609-619) copyright 2007.