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

Hayes RP, Moural TW, Lewis KM, Onofrei D, Xun L, Kang C - Int J Mol Sci (2014)

Bottom Line: 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.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 Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA. robert_hayes@wsu.edu.

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.

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Degradation pathway of pentachlorophenol (PCP) in Sphingobium chlorophenolicum and 2,4,6-TCP in Cupriavidus necator. (A) PCP is converted to maleylacetate through a series of enzymatic transformations. PcpR is responsible for the transcriptional control of PcpA, PcpB and PcpE; and (B) 2,4,6-TCP is converted to maleylacetate through a series of enzymatic transformations. TcpR is responsible for the transcriptional control of TcpX, TcpA, TcpB, TcpC and TcpD.
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ijms-15-20736-f001: Degradation pathway of pentachlorophenol (PCP) in Sphingobium chlorophenolicum and 2,4,6-TCP in Cupriavidus necator. (A) PCP is converted to maleylacetate through a series of enzymatic transformations. PcpR is responsible for the transcriptional control of PcpA, PcpB and PcpE; and (B) 2,4,6-TCP is converted to maleylacetate through a series of enzymatic transformations. TcpR is responsible for the transcriptional control of TcpX, TcpA, TcpB, TcpC and TcpD.

Mentions: The mechanism of microbial degradation of polychlorophenols has been extensively studied over the past several decades with the goal of developing effective bioremediation strategies. Accordingly, genetic organization, biochemical characterization and structural analysis have been conducted for the enzymes involved in the degradation of pentachlorophenol (PCP) in Sphingobium chlorophenolicum L-1 [1,2,3,4,5,6] and 2,4,6-trichlorophenol (2,4,6-TCP) in Cupriavidus necator JMP134 [7,8,9]. In S. chlorophenolicum, PCP is converted to maleylacetate by the concerted actions of a monooxygenase (PcpB) [3], a quinone reductase (PcpD) [3,5], a reductive dechlorinase (PcpC) [10], a ring cleavage 1,2-dioxygenase (PcpA) [1,2,6], and a chloromaleylacetate reductase (PcpE) [4]. Maleylacetate is further channeled to the tricarboxylic acid (TCA) cycle for complete mineralization (Figure 1A). PcpR is responsible for the transcriptional control of PcpA, PcpB, and PcpE, however, PcpC is constitutively produced [4]. The degradation pathway of 2,4,6-TCP to chloromaleylacetate in C. necator involves a two-component flavin-diffusible monoxygenase system (TcpX and TcpA), a quinone reductase (TcpB), a ring-cleaving dioxygenase (TcpC), and a chloromaleylacetate reductase (TcpD) [7]. The produced maleylacetate is also channeled to the TCA cycle for complete mineralization. TcpR is responsible for the transcriptional control of all these proteins (Figure 1B) [8].


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

Hayes RP, Moural TW, Lewis KM, Onofrei D, Xun L, Kang C - Int J Mol Sci (2014)

Degradation pathway of pentachlorophenol (PCP) in Sphingobium chlorophenolicum and 2,4,6-TCP in Cupriavidus necator. (A) PCP is converted to maleylacetate through a series of enzymatic transformations. PcpR is responsible for the transcriptional control of PcpA, PcpB and PcpE; and (B) 2,4,6-TCP is converted to maleylacetate through a series of enzymatic transformations. TcpR is responsible for the transcriptional control of TcpX, TcpA, TcpB, TcpC and TcpD.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4264193&req=5

ijms-15-20736-f001: Degradation pathway of pentachlorophenol (PCP) in Sphingobium chlorophenolicum and 2,4,6-TCP in Cupriavidus necator. (A) PCP is converted to maleylacetate through a series of enzymatic transformations. PcpR is responsible for the transcriptional control of PcpA, PcpB and PcpE; and (B) 2,4,6-TCP is converted to maleylacetate through a series of enzymatic transformations. TcpR is responsible for the transcriptional control of TcpX, TcpA, TcpB, TcpC and TcpD.
Mentions: The mechanism of microbial degradation of polychlorophenols has been extensively studied over the past several decades with the goal of developing effective bioremediation strategies. Accordingly, genetic organization, biochemical characterization and structural analysis have been conducted for the enzymes involved in the degradation of pentachlorophenol (PCP) in Sphingobium chlorophenolicum L-1 [1,2,3,4,5,6] and 2,4,6-trichlorophenol (2,4,6-TCP) in Cupriavidus necator JMP134 [7,8,9]. In S. chlorophenolicum, PCP is converted to maleylacetate by the concerted actions of a monooxygenase (PcpB) [3], a quinone reductase (PcpD) [3,5], a reductive dechlorinase (PcpC) [10], a ring cleavage 1,2-dioxygenase (PcpA) [1,2,6], and a chloromaleylacetate reductase (PcpE) [4]. Maleylacetate is further channeled to the tricarboxylic acid (TCA) cycle for complete mineralization (Figure 1A). PcpR is responsible for the transcriptional control of PcpA, PcpB, and PcpE, however, PcpC is constitutively produced [4]. The degradation pathway of 2,4,6-TCP to chloromaleylacetate in C. necator involves a two-component flavin-diffusible monoxygenase system (TcpX and TcpA), a quinone reductase (TcpB), a ring-cleaving dioxygenase (TcpC), and a chloromaleylacetate reductase (TcpD) [7]. The produced maleylacetate is also channeled to the TCA cycle for complete mineralization. TcpR is responsible for the transcriptional control of all these proteins (Figure 1B) [8].

Bottom Line: 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.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 Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA. robert_hayes@wsu.edu.

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.

Show MeSH
Related in: MedlinePlus