4RPO

PcpR inducer binding domain (Complex with 2,4,6-trichlorophenol)

Summary for 4RPO

• Entry DOI: 10.2210/pdb4rpo/pdb
• Related: 4RNS 4RPN
• Descriptor: PCP degradation transcriptional activation protein, 2,4,6-trichlorophenol, GLYCEROL, ... (5 entities in total)
• Functional Keywords: lysr family transcriptional regulator, inducer binding domain, transcription
• Biological source: Sphingobium chlorophenolicum
• Total number of polymer chains: 4
• Total formula weight: 102471.66

Authors

Hayes, R.P.,Moural, T.W.,Lewis, K.M.,Onofrei, D.,Xun, L.,Kang, C. (deposition date: 2014-10-30, release date: 2014-11-26, Last modification date: 2023-09-20)

Primary citation

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, 15:20736-20752, 2014

PubMed Abstract: 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.

PubMed: 25397598
DOI: 10.3390/ijms151120736

Experimental method

X-RAY DIFFRACTION (1.95 Å)