Kinetics and stereochemistry of LinB-catalyzed δ-HBCD transformation: Comparison of in vitro and in silico results

LinB is a haloalkane dehalogenase found in Sphingobium indicum B90A, an aerobic bacterium isolated from contaminated soils of hexachlorocyclohexane (HCH) dumpsites. We showed that this enzyme also converts hexabromocyclododecanes (HBCDs). Here we give new insights in the kinetics and stereochemistry of the enzymatic transformation of δ-HBCD, which resulted in the formation of two pentabromocyclododecanols (PBCDols) as first- (P_1δ, P_2δ) and two tetrabromocyclododecadiols (TBCDdiols) as second-generation products (T_1δ, T_2δ). Enzymatic transformations of δ-HBCD, α₁-PBCDol, one of the transformation products, and α₂-PBCDol, its enantiomer, were studied and modeled with Michaelis-Menten (MM) kinetics. Respective MM-parameters K_M, v_max, k_cat/K_M indicated that δ-HBCD is the best LinB substrate followed by α₂- and α₁-PBCDol. The stereochemistry of these transformations was modeled in silico, investigating respective enzyme-substrate (ES) and enzyme-product (EP) complexes. One of the four predicted ES-complexes led to the PBCDol product P_1δ, identical to α₂-PBCDol with the 1R,2R,5S,6R,9R,10S-configuration. An S_N2-like substitution of bromine at C6 of δ-HBCD by Asp-108 of LinB and subsequent hydrolysis of the alkyl-enzyme led to α₂-PBCDol. Modeling results further indicate that backside attacks at C1, C9 and C10 are reasonable too, selectively binding leaving bromide ions in a halide pocket found in LinB. Docking with α₂-PBCDol, also allowed productive enzyme binding. A TBCD-1,5-diol with the 1S,2S,5R,6R,9S,10R-configuration is the predicted second-generation product T_1δ. In conclusion, in vitro- and in silico findings now allow a detailed description of step-wise enzymatic dehalohydroxylation reactions of δ-HBCD to specific PBCDols and TBCDdiols at Å-resolution and predictions of their stereochemistry.

Stereochemistry of enzymatic transformations of (+)β- and (-)β-HBCD with LinA2--a HCH-degrading bacterial enzyme of Sphingobium indicum B90A

LinA2, a bacterial enzyme expressed in various Sphingomonadaceae, catalyzes the elimination of HCl from hexachlorocyclohexanes (HCHs) and, as discussed here, the release of HBr from certain hexabromocyclododecanes (HBCDs). Both classes of compounds are persistent organic pollutants now regulated under the Stockholm Convention. LinA2 selectively catalyzes the transformation of β-HBCDs; other stereoisomers like α-, γ-, and δ-HBCDs are not converted. The transformation of (-)β-HBCD is considerably faster than that of its enantiomer. Here, we present the XRD crystal structure of 1E,5S,6S,9R,10S-pentabromocyclododecene (PBCDE) and demonstrate that its enantiomer with the 1E,5R,6R,9S,10R-configuration is the only metabolite formed during LinA2-catalyzed dehydrobromination of (-)β-HBCD. Formation of this product can be rationalized by HBr elimination at C5 and C6. A reasonable enzyme-substrate complex with the catalytic dyad His-73 and Asp-25 approaching the hydrogen at C6 and a cationic pocket of Lys-20, Try-42 and Arg-129 binding the leaving bromine at C5 was found from in silico docking experiments. A second PBCDE of yet unknown configuration was obtained from (+)β-HBCD. We predicted its stereochemistry to be 1E,5S,6S,9S,10R-PBCDE from docking experiments. The enzyme-substrate complex obtained from LinA2 and an activated conformation of (+)β-HBCD allows the HBr elimination at C9 and C10 leading to the predicted product. Both modeled enzyme-substrate complexes are in line with 1,2-diaxial HBr eliminations. In conclusion, LinA2, a bacterial enzyme of the HCH-degrading strain Sphingobium indicum B90A was able to stereoselectively convert β-HBCDs. Configurations of both PBCDE metabolites were predicted by molecular docking experiments and confirmed in one case by XRD data.

LinA2, a HCH-converting bacterial enzyme that dehydrohalogenates HBCDs

Hexabromocyclododecanes (HBCDs) and hexachlorocyclohexanes (HCHs) are lipophilic, polyhalogenated hydrocarbons with comparable stereochemistry. Bacterial evolution in HCH-contaminated soils resulted in the development of several Spingomonadaceae which express a series of HCH-converting enzymes. We showed that LinB, a haloalkane dehalogenase from Sphingobium indicum B90A, also transforms various HBCDs besides HCHs. Here we present evidence that LinA2, another dehalogenase from S. indicum also converts certain HBCDs to pentabromocyclododecenes (PBCDEs). Racemic mixtures of α-, β-, γ-HBCDs, a mixture of them, and δ-HBCD, a meso form, were exposed to LinA2. Substantial conversion of (-)β-HBCD was observed, but all other stereoisomers were not transformed significantly. The enantiomeric excess (EE) of β-HBCDs increased up to 60% in 32 h, whereas EE values of α- and γ-HBCDs were not affected. Substrate conversion and product formation were described with second-order kinetic models. One major (P1β) and possibly two minor (P2β, P3β) metabolites were detected. Respective mass spectra showed the characteristic isotope pattern of PBCDEs, the HBr elimination products of HBCDs. Michaelis-Menten parameters KM=0.47 ± 0.07 μM and vmax=0.17 ± 0.01 μmoll(-1)h(-1) were deduced from exposure data with varying enzyme/substrate ratios. LinA2 is more substrate specific than LinB, the latter converted all tested HBCDs, LinA2 only one. The widespread HCH pollution favored the selection and evolution of bacteria converting these compounds. We found that LinA2 and LinB, two of these HCH-converting enzymes expressed in S. indicum B90A, also dehalogenate HBCDs to lower brominated compounds, indicating that structural similarities of both classes of compounds are recognized at the level of substrate-protein interactions.