An integrated approach of bioassay and molecular docking to study the dihydroxylation mechanism of pyrene by naphthalene dioxygenase in Rhodococcus sp. ustb-1

Jin, Jingnan; Yao, Jun; Zhang, Qing-Ye; Yu, Chan; Chen, Peng; Liu, Wenjuan; Peng, Dan-Ning; Choi, Martin M. F.

doi:10.1016/j.chemosphere.2015.02.012

Cited by 24 publications

(11 citation statements)

References 42 publications

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“…That is, the ferredoxin-binding site is served as a restrain on the surface of the oxygenase trimer at the adjacent interface to alpha subunits. A similar signature of depression has been observed between the alpha and beta subunits of naphthalene dioxygenase, con rming that it might be the binding-site for ferredoxin in this hexameric oxygenase 30,47 .…”

Section: Structural Exploration Of Active Center Of Alpha Subunitsupporting

confidence: 66%

“…Homology modeling was accomplished according to the crystal structure of the template 4QUR that is a crystal structure of stachydrine demethylase with molecular weight of approximately 49.8 kDa from Sinorhizobium meliloti 1021 (DOI: 10.2210/pdb4QUR/pdb), which displayed a high structural similarity to the alpha subunit. Then the modeled crystal structure of the alpha subunit was examined by means of Ramachandran plot to analyze the distribution rationality of the amino acid residues 30 . Meanwhile, 3VCA (http://www.rcsb.org/structure/3VCA) from Sinorhizobium meliloti 1021 having an identity of 94.71 % with 4QUR was used to verify the validity of homology modeling of the modeled crystal structure of the alpha subunit 31 .…”

Section: Structural Exploration Of Active Center Of Alpha Subunitmentioning

confidence: 99%

“…To analyze the interaction between uoranthene and the alpha subunit of RHD, the nucleotide sequence of alpha subunit was translated to amino acid sequence by the software DNAStar5.0 30 . The translated protein sequence was used to obtain protein modelling of alpha subunit of RHD by homology modeling.…”

Section: Interaction Analysis Of Uoranthene and Active Center Of Alpha Subunitmentioning

confidence: 99%

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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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Section: Structural Exploration Of Active Center Of Alpha Subunitsupporting

confidence: 66%

Section: Structural Exploration Of Active Center Of Alpha Subunitmentioning

confidence: 99%

Section: Interaction Analysis Of Uoranthene and Active Center Of Alpha Subunitmentioning

confidence: 99%

See 1 more Smart Citation

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

Xue¹,

Tian²,

Pan³

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Homology modeling was accomplished on the basis of the crystal structure of the template 4QUR, a crystal structure of stachydrine demethylase with molecular weight of approximately 49.8 kDa from Sinorhizobium meliloti 1021 ( https://doi.org/10.2210/pdb4QUR/pdb ) that displayed a high structural similarity to the alpha subunit. Then the modeled crystal structure of the alpha subunit was examined by means of Ramachandran plot to analyze the distribution rationality of the amino acid residues 30 . Meanwhile, 3VCA ( http://www.rcsb.org/structure/3VCA ) from Sinorhizobium meliloti 1021 having an identity of 94.71% with 4QUR was used to verify the validity of homology modeling of the modeled crystal structure of the alpha subunit 31 .…”

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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“…However, for monoalkyl phthalate hydrolases, the mechanism of binding and hydrolyzing monoalkyl phthalates (MAPs) has not been elucidated. Fortunately, molecular docking and molecular dynamics simulation have been adopted to analyze the interaction between the enzyme and corresponding substrates [ 29 , 30 , 31 ]. These computational methods could be important approaches to investigate combination of monoalkyl phthalate hydrolase and MAPs, detect the key residues, and resolve the catalytic mechanism.…”

Section: Introductionmentioning

confidence: 99%

Excellent Degradation Performance of a Versatile Phthalic Acid Esters-Degrading Bacterium and Catalytic Mechanism of Monoalkyl Phthalate Hydrolase

Fan¹,

Wang²,

Yan³

et al. 2018

IJMS

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Despites lots of characterized microorganisms that are capable of degrading phthalic acid esters (PAEs), there are few isolated strains with high activity towards PAEs under a broad range of environmental conditions. In this study, Gordonia sp. YC-JH1 had advantages over its counterparts in terms of di(2-ethylhexyl) phthalate (DEHP) degradation performance. It possessed an excellent degradation ability in the range of 20–50 °C, pH 5.0–12.0, or 0–8% NaCl with the optimal degradation condition 40 °C and pH 10.0. Therefore, strain YC-JH1 appeared suitable for bioremediation application at various conditions. Metabolites analysis revealed that DEHP was sequentially hydrolyzed by strain YC-JH1 to mono(2-ethylhexyl) phthalate (MEHP) and phthalic acid (PA). The hydrolase MphG1 from strain YC-JH1 hydrolyzed monoethyl phthalate (MEP), mono-n-butyl phthalate (MBP), mono-n-hexyl phthalate (MHP), and MEHP to PA. According to molecular docking and molecular dynamics simulation between MphG1 and monoalkyl phthalates (MAPs), some key residues were detected, including the catalytic triad (S125-H291-D259) and the residues R126 and F54 potentially binding substrates. The mutation of these residues accounted for the reduced activity. Together, the mechanism of MphG1 catalyzing MAPs was elucidated, and would shed insights into catalytic mechanism of more hydrolases.

show abstract

An integrated approach of bioassay and molecular docking to study the dihydroxylation mechanism of pyrene by naphthalene dioxygenase in Rhodococcus sp. ustb-1

Cited by 24 publications

References 42 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

Excellent Degradation Performance of a Versatile Phthalic Acid Esters-Degrading Bacterium and Catalytic Mechanism of Monoalkyl Phthalate Hydrolase

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