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Open AccessArticle

Structures of the Inducer-Binding Domain of Pentachlorophenol-Degrading Gene Regulator PcpR from Sphingobium chlorophenolicum

1
Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA
2
School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA
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Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2014, 15(11), 20736-20752; https://doi.org/10.3390/ijms151120736
Received: 21 August 2014 / Revised: 29 October 2014 / Accepted: 30 October 2014 / Published: 12 November 2014
(This article belongs to the Section Biochemistry)
PcpR is a LysR-type transcription factor from Sphingobium chlorophenolicum L-1 that is responsible for the activation of several genes involved in polychlorophenol degradation. PcpR responds to several polychlorophenols in vivo. Here, we report the crystal structures of the inducer-binding domain of PcpR in the apo-form and binary complexes with pentachlorophenol (PCP) and 2,4,6-trichlorophenol (2,4,6-TCP). Both X-ray crystal structures and isothermal titration calorimetry data indicated the association of two PCP molecules per PcpR, but only one 2,4,6-TCP molecule. The hydrophobic nature and hydrogen bonds of one binding cavity allowed the tight association of both PCP (Kd = 110 nM) and 2,4,6-TCP (Kd = 22.8 nM). However, the other cavity was unique to PCP with much weaker affinity (Kd = 70 μM) and thus its significance was not clear. Neither phenol nor benzoic acid displayed any significant affinity to PcpR, indicating a role of chlorine substitution in ligand specificity. When PcpR is compared with TcpR, a LysR-type regulator controlling the expression of 2,4,6-trichlorophenol degradation in Cupriavidus necator JMP134, most of the residues constituting the two inducer-binding cavities of PcpR are different, except for their general hydrophobic nature. The finding concurs that PcpR uses various polychlorophenols as long as it includes 2,4,6-trichlorophenol, as inducers; whereas TcpR is only responsive to 2,4,6-trichlorophenol. View Full-Text
Keywords: LysR-family; transcription factor; bioremediation; pentachlorophenol; 2,4,6-trichlorophenol LysR-family; transcription factor; bioremediation; pentachlorophenol; 2,4,6-trichlorophenol
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Hayes, R.P.; Moural, T.W.; Lewis, K.M.; Onofrei, D.; Xun, L.; Kang, C. Structures of the Inducer-Binding Domain of Pentachlorophenol-Degrading Gene Regulator PcpR from Sphingobium chlorophenolicum. Int. J. Mol. Sci. 2014, 15, 20736-20752.

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