Structures of the inducer-binding domain of pentachlorophenol-degrading gene regulator PcpR from Sphingobium chlorophenolicum

Robert P Hayes; Timothy W Moural; Kevin M Lewis; David Onofrei; Luying Xun; ChulHee Kang

doi:10.3390/ijms151120736

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Structures of the inducer-binding domain of pentachlorophenol-degrading gene regulator PcpR from Sphingobium chlorophenolicum

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Structures of the inducer-binding domain of pentachlorophenol-degrading gene regulator PcpR from Sphingobium chlorophenolicum

Robert P Hayes, Timothy W Moural, Kevin M Lewis, David Onofrei, Luying Xun and ChulHee Kang

International journal of molecular sciences, Vol.15(11), pp.20736-20752

11/12/2014

DOI: https://doi.org/10.3390/ijms151120736

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https://hdl.handle.net/2376/104948

PMCID: PMC4264193

PMID: 25397598

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Abstract

Protein Structure, Tertiary

Amino Acid Sequence

Transcription Factors - chemistry

Bacterial Proteins - chemistry

Models, Molecular

Molecular Sequence Data

Pentachlorophenol - metabolism

Crystallography, X-Ray

Transcription Factors - metabolism

Sequence Alignment

Sphingomonadaceae - metabolism

Sphingomonadaceae - chemistry

Bacterial Proteins - metabolism

Chlorophenols - metabolism

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.

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Title: Structures of the inducer-binding domain of pentachlorophenol-degrading gene regulator PcpR from Sphingobium chlorophenolicum
Creators: Robert P Hayes - Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA. robert_hayes@wsu.edu
Timothy W Moural - Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA. timothy.moural@email.wsu.edu
Kevin M Lewis - Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA. kevin.lewis@email.wsu.edu
David Onofrei - School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA. david.onofrei@email.wsu.edu
Luying Xun - School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA. luying_xun@vetmed.wsu.edu
ChulHee Kang - Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA. chkang@wsu.edu
Publication Details: International journal of molecular sciences, Vol.15(11), pp.20736-20752
Academic Unit: Chemistry, Department of; Molecular Biosciences, School of
Publisher: Switzerland
Identifiers: 99900546854201842
Language: English
Resource Type: Journal article