Structures of the inducer-binding domain of pentachlorophenol-degrading gene regulator PcpR from Sphingobium chlorophenolicum.
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.
Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA. robert_hayes@wsu.edu.
Robert P
RP
Hayes
Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA. timothy.moural@email.wsu.edu.
Timothy W
TW
Moural
Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA. kevin.lewis@email.wsu.edu.
Kevin M
KM
Lewis
School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA. david.onofrei@email.wsu.edu.
David
D
Onofrei
School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA. luying_xun@vetmed.wsu.edu.
Luying
L
Xun
Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA. chkang@wsu.edu.
ChulHee
C
Kang
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D002733:Chlorophenols / Q000378:metabolism*; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010416:Pentachlorophenol / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D042301:Sphingomonadaceae / Q000737:chemistry* / Q000378:metabolism*; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism
D001426:Bacterial Proteins; D002733:Chlorophenols; D014157:Transcription Factors; D010416:Pentachlorophenol; C024564:2,4,6-trichlorophenol