Biodegradation of pyrene by pseudomonas sp. JPN2 and its initial degrading mechanism study by combining the catabolic nahAc gene and structure-based analyses

Jin, Jingnan; Yao, Jun; Zhang, Qingye; Liu, Jianli

doi:10.1016/j.chemosphere.2016.08.113

Cited by 35 publications

(10 citation statements)

References 40 publications

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“…Distinctions observed in the amino acid residues of active site among dioxygenases may briefly explain differences in substrate specificity and catalytic efficiency of the enzymes from various sources 34 , 35 . So far, many aromatic-hydrocarbon degraders from the genus Pseudomonas have been reported to have displayed diverse PAH-degradation ability, and their metabolism mechanisms have been elucidated 6 , 19 , 21 , 36 – 38 . The amino acid sequences of RHD alpha subunit from the strain DN1 showed a maximum identify of 93.92% with that from other Pseudomonas strains ( https://blast.ncbi.nlm.nih.gov/Blast.cgi , see Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1

Xue

Tian

Pan

et al. 2021

Sci Rep

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Pseudomonas aeruginosa DN1 can efficiently utilize fluoranthene as its sole carbon source, and the initial reaction in the biodegradation process is catalyzed by a ring-hydroxylating dioxygenase (RHD). To clarify the binding interaction of RHD with fluoranthene in the strain DN1, the genes encoding alpha subunit (RS30940) and beta subunit (RS05115) of RHD were functionally characterized through multi-technique combination such as gene knockout and homology modeling as well as molecular docking analysis. The results showed that the mutants lacking the characteristic alpha subunit and/or beta subunit failed to degrade fluoranthene effectively. Based on the translated protein sequence and Ramachandran plot, 96.5% of the primary amino-acid sequences of the alpha subunit in the modeled structure of the RHD were in the permitted region, 2.3% in the allowed region, but 1.2% in the disallowed area. The catalytic mechanism mediated by key residues was proposed by the simulations of molecular docking, wherein the active site of alpha subunit constituted a triangle structure of the mononuclear iron atom and the two oxygen atoms coupled with the predicted catalytic ternary of His217-His222-Asp372 for the dihydroxylation reaction with fluoranthene. Those amino acid residues adjacent to fluoranthene were nonpolar groups, and the C7-C8 positions on the fluoranthene ring were estimated to be the best oxidation sites. The distance of C7-O and C8-O was 3.77 Å and 3.04 Å respectively, and both of them were parallel. The results of synchronous fluorescence and site-directed mutagenesis confirmed the roles of the predicted residues during catalysis. This binding interaction could enhance our understanding of the catalytic mechanism of RHDs and provide a solid foundation for further enzymatic modification.

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Section: Resultsmentioning

confidence: 99%

Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1

Xue

Tian

Pan

et al. 2021

Sci Rep

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“…Distinctions observed in the amino acid residues of active site among dioxygenases may brie y explain differences in substrate speci city and catalytic e ciency of the enzymes from various sources 34,35 . So far, many aromatic-hydrocarbon degraders from the genus Pseudomonas have been reported to have displayed diverse PAH-degradation ability, and their metabolism mechanisms have been elucidated 6,19,21,[36][37][38] . The amino acid sequences of the alpha subunit of RHD from the strain DN1 showed a maximum identify of 93.92 % with that from other Pseudomonas strains (https://blast.ncbi.nlm.nih.gov/Blast.cgi, see Supplementary Fig.…”

Section: Structural Exploration Of Active Center Of Alpha Subunitmentioning

confidence: 99%

Binding Interaction of a Ring-hydroxylating Dioxygenase with Fluoranthene in Pseudomonas aeruginosa DN1

Xue¹,

Tian²,

Pan³

et al. 2021

Preprint

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Pseudomonas aeruginosa DN1 can efficiently utilize fluoranthene as its sole carbon source, and the first step in the biodegradation process is catalyzed by a ring-hydroxylating dioxygenase (RHD). To better understand the binding interaction of RHD with fluoranthene in the strain DN1, the genes encoding alpha subunit (RS30940) and beta subunit (RS05115) of the RHD were functionally characterized using gene knockout approach and homology modeling combined with molecular docking. The results showed that the mutants lacking the characteristic alpha subunit and/or beta subunit failed to degrade fluoranthene effectively. Based on the translated protein sequence and Ramachandran plot, 96.5 % of the primary amino-acid sequences of the alpha subunit in the modeled structure of the RHD were in the permitted region, 2.3 % in the allowed region, but 1.2 % in the disallowed area. The active center of the alpha subunit constituted a triangle structure of the mononuclear iron atom and the two oxygen atoms coupled with a catalytic ternary of His217-His222-Asp372 for the dihydroxylation reaction with fluoranthene. Amino acid residues adjacent to fluoranthene were nonpolar groups, and the C7-C8 positions on the fluoranthene ring were estimated to be the best oxidation sites. The distance of C7-O and C8-O was 3.77 Å and 3.04Å respectively, and both of them were parallel. The results demonstrated that the dihydroxylation reaction was initiated at C7-C8 positions of the fluoranthene ring by RHD in P. aeruginosa DN1, indicating that the binding interaction may be useful for predicting substrate conversion of RHDs.

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“…When the hydrophilic amino acid residue Thr308 of the template 1O7N enzyme was replaced by the hydrophobic amino acid residue Val232 in the target JPN2-NDO enzyme, the hydrophobic interaction at the binding site was enhanced, which was more favourable for the binding of pyrene. 46 Therefore, this study attempted to replace the hydrophilic amino acid residues at the binding site of the NDO enzyme (PDB ID: 1O7G) with hydrophobic amino acid residues to increase the affinity between the target aromatic hydrocarbons and the NDO enzyme (PDB ID: 1O7G), thereby increasing the degradation rate of the target aromatic hydrocarbons naphthalene, anthracene, pyrene and benzo[a]pyrene by the NDO enzyme.…”

Section: Docking Conformation Of the Target Aromatic Hydrocarbons Andmentioning

confidence: 99%

Combined molecular docking, homology modelling and density functional theory studies to modify dioxygenase to efficiently degrade aromatic hydrocarbons

Chu

et al. 2019

RSC Adv.

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Biodegradation of pyrene by pseudomonas sp. JPN2 and its initial degrading mechanism study by combining the catabolic nahAc gene and structure-based analyses

Cited by 35 publications

References 40 publications

Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1

Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1

Binding Interaction of a Ring-hydroxylating Dioxygenase with Fluoranthene in Pseudomonas aeruginosa DN1

Combined molecular docking, homology modelling and density functional theory studies to modify dioxygenase to efficiently degrade aromatic hydrocarbons

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