Catalytic Mechanism for 2,3-Dihydroxybiphenyl Ring Cleavage by Nonheme Extradiol Dioxygenases BphC: Insights from QM/MM Analysis

Abstract

An extradiol-cleaving catecholic dioxygenase, 2,3-dihydroxybiphenyl dioxygenase, plays important roles in the catabolism of biphenyl/polychlorinated biphenyl aromatic contaminants in the environment. To better elucidate the biodegradable pathway, a theoretical investigation of the ringopening degradation of 2,3-dihydroxybiphenyl (DHBP) was performed with the aid of quantum mechanical/molecular mechanical calculations. A quintet state of the DHBP−iron− dioxygen group adducts was found to be the reactive state with a substrate radical−Fe II −superoxo) character. The HOO • species was the reactive oxygen species responsible for the subsequent attack of DHBP. Among the whole reaction energy profile, the first step in proton-coupled electron transfer was determined to be the ratedetermining step with a potential energy barrier of 17.2 kcal/mol, which is close to the experimental value (14.7 kcal/mol). Importantly, the residue His194 shows distinct roles in the catalytic cycle, where it acts as an acid−base catalyst to deprotonate the hydroxyl group of DHBP at an early stage, then stabilizes the negative charge on the dioxygen group, and, at the final stage, promotes the semialdehyde product formation as a proton donor.

N-Nitrosation Mechanism Catalyzed by Non-heme Iron-Containing Enzyme SznF Involving Intramolecular Oxidative Rearrangement

“…The gross spin populations at the dioxygen and the N ω O moieties are −0.9 and −0.8, respectively, which, combined with the 1.32 Å O–O bond length, indicating a typical superoxo character of the dioxygen group in 3 IntA HA which is reduced by an α electron from the N ω O group of the substrate. It is very common among the non-heme iron-containing enzymes such as SDO, 2,3-dihydroxybiphenyl dioxygenase (BphC), and homoprotocatechuate 2,3-dioxygenase (HPCD) that simultaneously binding of the substrate and the dioxygen to the iron center generates Fe II –superoxo species and cationic substrate radical. ,,− , It should be ascribed to that the electron-rich substrates of these enzymes are bound up with the iron center so that they can donate electrons to reduce the dioxygen through the iron center. As shown in Figure a, in 3 IntA HA , the Fe–O bond length is 2.01 Å.…”

“…It is very common among the non-heme iron-containing enzymes such as SDO, 2,3dihydroxybiphenyl dioxygenase (BphC), and homoprotocatechuate 2,3-dioxygenase (HPCD) that simultaneously binding of the substrate and the dioxygen to the iron center generates Fe II −superoxo species and cationic substrate radical. 22,23,[25][26][27][28]38 It should be ascribed to that the electron-rich substrates of these enzymes are bound up with the iron center so that they can donate electrons to reduce the dioxygen through the iron center. As shown in Figure 2a, in 3 IntA HA , the Fe−O bond length is 2.01 Å.…”

“…For an instance, a previous theoretical study indicated that with the superoxo being protonated by a histidine residue in the active site, BphC could lower the energy barrier of the superoxo addition step by 26.5 kcal/mol (Figure S3). 26 A very low-energy barrier of the superoxo addition step was obtained for 2-aminophenol 1,6-dioxygenase (APD) either, 24 which is also capable of protonating superoxo through a histidine (His195) in the active site. However, the active site of SznF around the superoxo binding site consists of two hydrophobic residues (Ile442 and Ile461) (Figure S3), which also limits the catalytic efficiency of SznF in this step.…”

“…Sequential hydrogen bond interactions are formed from the methylated Ν ω (N Me ω ) of l -HMA, through two residues, Tyr459 and Glu398, to the ammonium group of l -HMA in a form of hydrogen bond “wire,” which stabilizes l -HMA at the active site along with a hydrogen bond “network” formed among the carboxylate group of l -HMA, Arg48 and two crystal water molecules (WAT713 and WAT828) . The active center of SznF has a very similar geometric structure as that of the non-heme Fe II - and 2-oxoglutarate (2OG)-dependent oxygenases (Fe II /2OG-dependent oxygenases) − and extradiol aromatic ring-cleaving dioxygenases (EDOs), − in which the cosubstrate 2OG or the catecholic substrate also binds to the iron center as a bidentate ligand. Such a structural similarity implies that these enzymes probably share common reaction steps in their catalytic mechanisms.…”

Multiscale QM/MM modelling of catalytic systems with ChemShell

“…[128][129][130] Environmental chemistry is an increasingly prominent topic for QM/MM simulations, which have been used to investigate biodegradation of pesticides, [131][132][133] plastics, 134,135 and other hazardous pollutants. [136][137][138][139][140][141][142] Feng et al used ChemShell to study the degradation of polyethylene terephthalate (PET), 143 comparing the common features of reactions catalysed by the enzymes IsPETase and IsMHETase and analysing the structural characteristics that affect catalytic activity, pointing the way to the design of more efficient enzymes for plastic recycling.…”