Degradation mechanism of biphenyl and 4-4′-dichlorobiphenyl cis-dihydroxylation by non-heme 2,3 dioxygenases BphA: A QM/MM approach

Zhu, Ledong; Zhou, Jie; Zhang, Ruiming; Tang, Xiaowen; Wang, Junjie; Li, Yanwei; Zhang, Qingzhu; Wang, Wenxing

doi:10.1016/j.chemosphere.2020.125844

Cited by 13 publications

(11 citation statements)

References 56 publications

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“…The QM/MM method has been established to be a reliable tool for exploring the enzymatic reactions, − also including some heme enzymes. − In past decades, the QM/MM approach and improved QM method have been widely employed in the studies of biodegradation of pollutants. − Herein, we performed QM/MM calculations to investigate the peroxygenase mechanism of the oxidation of 4-Cl- o -cresol catalyzed by DHP B.…”

Section: Computational Detailsmentioning

confidence: 99%

Computational Study of the Peroxygenase Mechanism Catalyzed by Hemoglobin Dehaloperoxidase Involved in the Degradation of Chlorophenols

et al. 2022

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The biochemical evidence showed that hemoglobin dehaloperoxidase (DHP B) from Amphitrite Ornata is a multifunctional hemoprotein that catalyzes both dehalogenation and hydroxylation of halophenols via the peroxidase and peroxygenase mechanism, respectively, which sets the basis for the degradation of halophenols. In the peroxygenase mechanism, the reaction was previously suggested to be triggered either by the hydrogen atom abstraction by the FeO center or by the proton abstraction by His55. To illuminate the peroxygenase mechanism of DHP B at the atomistic level, on the basis of the high-resolution crystal structure, computational models were constructed, and a series of quantum mechanical/molecular mechanical calculations have been performed. According to the calculation results, the pathway (Path a) initiated by the H-abstraction by the FeO center is feasible. In another pathway (Path b), His55 can abstract the proton from the hydroxyl group of the substrate (4-Cl-o-cresol) to initiate the reaction; however, its feasibility depends on the prior electron transfer from the substrate to the porphyrin group. The rate-limiting step of Path a is the OH-rebound, which corresponds to an energy barrier of 14.7 kcal/mol at the quartet state. His55 acts as an acid–base catalyst and directly involves in the catalysis. Our mutant study indicates that His55 can be replaced by other titratable residues. These findings may provide useful information for further understanding of the catalytic reaction of DHP B and for the design of enzymes in the degradation of pollutants, in particular, halophenols.

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Section: Computational Detailsmentioning

confidence: 99%

Computational Study of the Peroxygenase Mechanism Catalyzed by Hemoglobin Dehaloperoxidase Involved in the Degradation of Chlorophenols

et al. 2022

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“…There are several advantages of our study over previous studies. Previous research has been restricted to characterizing PCB-degrading bacterial strains ( 13 , 23 , 33 , 34 ), the substrate specificity ( 2 , 14 , 16 , 35 ) or genetic modifications ( 27 , 36 , 37 ) of biphenyl dioxygenase, and investigating PCB-degrading bacterial flora in PCB-polluted natural landscapes ( 8 , 38 – 40 ). Herein, we were able to identify the application model in which the newly constructed recombinant E. coli expressing biphenyl dioxygenase of the B. xenovorans LB400 strain was augmented to the isolated wild-type PCB-degrading bacterial strain.…”

Section: Discussionmentioning

confidence: 99%

Augmentation of an Engineered Bacterial Strain Potentially Improves the Cleanup of PCB Water Pollution

et al. 2021

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“…Such an intermediate might directly reattack the substrate for hydroxylation or dioxygenation akin to the mechanism favored in some past studies. 94,128,143 Alternatively, it might convert to an HO-Fe(V)�O species capable of chemistry requiring a more energetic species. The route taken by any given RO after the initial substrate-coupled activation steps is likely to be controlled by the precise electronic properties and positioning of the substrate, and ultimately, the kinetics of reaction with substrate.…”

Section: ■ Conclusionmentioning

confidence: 99%

“…The strength of this bond is much less than that of the aromatic C−H bond (BDFE = 81.4 kcal/mol, Table S1), but its cleavage still requires a powerful oxidizing intermediate such as an Fe(IV)-oxo, Fe(V)oxo, or perhaps Fe(III)-hydroperoxo. 94,141,143 Direct cleavage of the methyl C−H bond by these species would yield a normal rather than inverse KIE. 144 One intriguing hypothesis for the origin of the inverse KIE on Rieske oxidation is illustrated in Scheme 5.…”

Section: Correlation Of Rieske Monooxygenase Activity With Substrate ...mentioning

confidence: 99%

Contrasting Mechanisms of Aromatic and Aryl-Methyl Substituent Hydroxylation by the Rieske Monooxygenase Salicylate 5-Hydroxylase

et al. 2022

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The hydroxylase component (S5HH) of salicylate-5-hydroxylase catalyzes C5 ring hydroxylation of salicylate but switches to methyl hydroxylation when a C5 methyl substituent is present. The use of 18 O 2 reveals that both aromatic and aryl-methyl hydroxylations result from monooxygenase chemistry. The functional unit of S5HH comprises a nonheme Fe(II) site located 12 Å across a subunit boundary from a one-electron reduced Riesketype iron−sulfur cluster. Past studies determined that substrates bind near the Fe(II), followed by O 2 binding to the iron to initiate catalysis. Stopped-flow-single-turnover reactions (STOs) demonstrated that the Rieske cluster transfers an electron to the iron site during catalysis. It is shown here that fluorine ring substituents decrease the rate constant for Rieske electron transfer, implying a prior reaction of an Fe(III)-superoxo intermediate with a substrate. We propose that the iron becomes fully oxidized in the resulting Fe(III)-peroxo-substrate-radical intermediate, allowing Rieske electron transfer to occur. STO using 5-CD 3 -salicylate-d 8 occurs with an inverse kinetic isotope effect (KIE). In contrast, STO of a 1:1 mixture of unlabeled and 5-CD 3 -salicylate-d 8 yields a normal product isotope effect. It is proposed that aromatic and aryl-methyl hydroxylation reactions both begin with the Fe(III)-superoxo reaction with a ring carbon, yielding the inverse KIE due to sp 2 → sp 3 carbon hybridization. After Rieske electron transfer, the resulting Fe(III)-peroxo-salicylate intermediate can continue to aromatic hydroxylation, whereas the equivalent aryl-methyl intermediate formation must be reversible to allow the substrate exchange necessary to yield a normal product isotope effect. The resulting Fe(III)-(hydro)peroxo intermediate may be reactive or evolve through a high-valent iron intermediate to complete the arylmethyl hydroxylation.

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Degradation mechanism of biphenyl and 4-4′-dichlorobiphenyl cis-dihydroxylation by non-heme 2,3 dioxygenases BphA: A QM/MM approach

Cited by 13 publications

References 56 publications

Computational Study of the Peroxygenase Mechanism Catalyzed by Hemoglobin Dehaloperoxidase Involved in the Degradation of Chlorophenols

Computational Study of the Peroxygenase Mechanism Catalyzed by Hemoglobin Dehaloperoxidase Involved in the Degradation of Chlorophenols

Augmentation of an Engineered Bacterial Strain Potentially Improves the Cleanup of PCB Water Pollution

Contrasting Mechanisms of Aromatic and Aryl-Methyl Substituent Hydroxylation by the Rieske Monooxygenase Salicylate 5-Hydroxylase

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