PDBsum entry 2f78

Gene regulation

PDB id: 2f78

Contents

Protein chains

222 a.a.

Ligands

BEZ ×5

Waters ×588

References listed in PDB file

Key reference

Title

Distinct effector-Binding sites enable synergistic transcriptional activation by benm, A lysr-Type regulator.

Authors

O.C.Ezezika, S.Haddad, T.J.Clark, E.L.Neidle, C.Momany.

Ref.

J Mol Biol, 2007, 367, 616-629. [DOI no: 10.1016/j.jmb.2006.09.090]

PubMed id

17291527

Abstract

BenM, a bacterial transcriptional regulator, responds synergistically to two effectors, benzoate and cis,cis-muconate. CatM, a paralog with overlapping function, responds only to muconate. Structures of their effector-binding domains revealed two effector-binding sites in BenM. BenM and CatM are the first LysR-type regulators to be structurally characterized while bound with physiologically relevant exogenous inducers. The effector complexes were obtained by soaking crystals with stabilizing solutions containing high effector concentrations and minimal amounts of competing ions. This strategy, including data collection with fragments of fractured crystals, may be generally applicable to related proteins. In BenM and CatM, the binding of muconate to an interdomain pocket was facilitated by helix dipoles that provide charge stabilization. In BenM, benzoate also bound in an adjacent hydrophobic region where it alters the effect of muconate bound in the primary site. A charge relay system within the BenM protein appears to underlie synergistic transcriptional activation. According to this model, Glu162 is a pivotal residue that forms salt-bridges with different arginine residues depending on the occupancy of the secondary effector-binding site. Glu162 interacts with Arg160 in the absence of benzoate and with Arg146 when benzoate is bound. This latter interaction enhances the negative charge of muconate bound to the adjacent primary effector-binding site. The redistribution of the electrostatic potential draws two domains of the protein more closely towards muconate, with the movement mediated by the dipole moments of four alpha helices. Therefore, with both effectors, BenM achieves a unique conformation capable of high level transcriptional activation.

Figure 3.

Figure 5.
Figure 5. Schematic representation of the BenM-EBD effector-binding sites. (a) Muconate in the primary site. Hydrogen bonds (between non-hydrogen atoms) to the effector are shown as broken lines. The distance between the O1 of muconate and the Arg146 N^ε atom is also shown (dash-dot). Helices, colored as in Figure 2, are shown as cylinders. β-Strands were omitted for clarity. (b) Benzoate in the secondary site. H1 is a 3[10]-helix associated with both binding sites. (c) Residues implicated in the charge relay postulated to be responsible for synergistic activation.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 367, 616-629) copyright 2007.

Secondary reference #1

Title

Crystallization of the effector-Binding domains of benm and catm, Lysr-Type transcriptional regulators from acinetobacter sp. Adp1.

Authors

T.Clark, S.Haddad, E.Neidle, C.Momany.

Ref.

Acta Crystallogr D Biol Crystallogr, 2004, 60, 105-108.

PubMed id

14684899