Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering

Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17

Haloalkane dehalogenases are enzymes with a broad application potential in biocatalysis, bioremediation, biosensing and cell imaging. The new haloalkane dehalogenase DmxA originating from the psychrophilic bacterium Marinobacter sp. ELB17 surprisingly possesses the highest thermal stability (apparent melting temperature Tm,app = 65.9 °C) of all biochemically characterized wild type haloalkane dehalogenases belonging to subfamily II. The enzyme was successfully expressed and its crystal structure was solved at 1.45 Å resolution. DmxA structure contains several features distinct from known members of haloalkane dehalogenase family: (i) a unique composition of catalytic residues; (ii) a dimeric state mediated by a disulfide bridge; and (iii) narrow tunnels connecting the enzyme active site with the surrounding solvent. The importance of narrow tunnels in such paradoxically high stability of DmxA enzyme was confirmed by computational protein design and mutagenesis experiments.

Ancestral Haloalkane Dehalogenases Show Robustness and Unique Substrate Specificity

Ancestral sequence reconstruction (ASR) represents a powerful approach for empirical testing structure-function relationships of diverse proteins. We employed ASR to predict sequences of five ancestral haloalkane dehalogenases (HLDs) from the HLD-II subfamily. Genes encoding the inferred ancestral sequences were synthesized and expressed in Escherichia coli, and the resurrected ancestral enzymes (AncHLD1-5) were experimentally characterized. Strikingly, the ancestral HLDs exhibited significantly enhanced thermodynamic stability compared to extant enzymes (ΔT_m up to 24 °C), as well as higher specific activities with preference for short multi-substituted halogenated substrates. Moreover, multivariate statistical analysis revealed a shift in the substrate specificity profiles of AncHLD1 and AncHLD2. This is extremely difficult to achieve by rational protein engineering. The study highlights that ASR is an efficient approach for the development of novel biocatalysts and robust templates for directed evolution.

Different Structural Origins of the Enantioselectivity of Haloalkane Dehalogenases toward Linear β-Haloalkanes: Open-Solvated versus Occluded-Desolvated Active Sites

The enzymatic enantiodiscrimination of linear β-haloalkanes is difficult because the simple structures of the substrates prevent directional interactions. Herein we describe two distinct molecular mechanisms for the enantiodiscrimination of the β-haloalkane 2-bromopentane by haloalkane dehalogenases. Highly enantioselective DbjA has an open, solvent-accessible active site, whereas the engineered enzyme DhaA31 has an occluded and less solvated cavity but shows similar enantioselectivity. The enantioselectivity of DhaA31 arises from steric hindrance imposed by two specific substitutions rather than hydration as in DbjA.

Regio- and Enantioselective Sequential Dehalogenation of rac-1,3-Dibromobutane by Haloalkane Dehalogenase LinB

The hydrolytic dehalogenation of rac-1,3-dibromobutane catalyzed by the haloalkane dehalogenase LinB from Sphingobium japonicum UT26 proceeds in a sequential fashion: initial formation of intermediate haloalcohols followed by a second hydrolytic step to produce the final diol. Detailed investigation of the course of the reaction revealed favored nucleophilic displacement of the sec-halogen in the first hydrolytic event with pronounced R enantioselectivity. The second hydrolysis step proceeded with a regioselectivity switch at the primary position, with preference for the S enantiomer. Because of complex competition between all eight possible reactions, intermediate haloalcohols formed with moderate to good ee ((S)-4-bromobutan-2-ol: up to 87 %). Similarly, (S)-butane-1,3-diol was formed at a maximum ee of 35 % before full hydrolysis furnished the racemic diol product.

Catalytic electron-transfer oxygenation of substrates with water as an oxygen source using manganese porphyrins

Manganese(V)-oxo-porphyrins are produced by the electron-transfer oxidation of manganese-porphyrins with tris(2,2'-bipyridine)ruthenium(III) ([Ru(bpy)(3)](3+); 2 equiv) in acetonitrile (CH(3)CN) containing water. The rate constants of the electron-transfer oxidation of manganese-porphyrins have been determined and evaluated in light of the Marcus theory of electron transfer. Addition of [Ru(bpy)(3)](3+) to a solution of olefins (styrene and cyclohexene) in CH(3)CN containing water in the presence of a catalytic amount of manganese-porphyrins afforded epoxides, diols, and aldehydes efficiently. Epoxides were converted to the corresponding diols by hydrolysis, and were further oxidized to the corresponding aldehydes. The turnover numbers vary significantly depending on the type of manganese-porphyrin used owing to the difference in their oxidation potentials and the steric bulkiness of the ligand. Ethylbenzene was also oxidized to 1-phenylethanol using manganese-porphyrins as electron-transfer catalysts. The oxygen source in the substrate oxygenation was confirmed to be water by using (18)O-labeled water. The rate constant of the reaction of the manganese(V)-oxo species with cyclohexene was determined directly under single-turnover conditions by monitoring the increase in absorbance attributable to the manganese(III) species produced in the reaction with cyclohexene. It has been shown that the rate-determining step in the catalytic electron-transfer oxygenation of cyclohexene is electron transfer from [Ru(bpy)(3)](3+) to the manganese-porphyrins.

Crystal structure determination and mutagenesis analysis of the ene reductase NCR

The crystal structure of the "ene" nicotinamide-dependent cyclohexenone reductase (NCR) from Zymomonas mobilis (PDB ID: 4A3U) has been determined in complex with acetate ion, FMN, and nicotinamide, to a resolution of 1.95 Å. To study the activity and enantioselectivity of this enzyme in the bioreduction of activated α,β-unsaturated alkenes, the rational design methods site- and loop-directed mutagenesis were applied. Based on a multiple sequence alignment of various members of the Old Yellow Enzyme family, eight single-residue variants were generated and investigated in asymmetric bioreduction. Furthermore, a structural alignment of various ene reductases predicted four surface loop regions that are located near the entrance of the active site. Four NCR loop variants, derived from loop-swapping experiments with OYE1 from Saccharomyces pastorianus, were analysed for bioreduction. The three enzyme variants, P245Q, D337Y and F314Y, displayed increased activity compared to wild-type NCR towards the set of substrates tested. The active-site mutation Y177A demonstrated a clear influence on the enantioselectivity. The loop-swapping variants retained reduction efficiency, but demonstrated decreased enzyme activity compared with the wild-type NCR ene reductase enzyme.

Hydrogen-abstraction reactivity patterns from A to Y: the valence bond way

"Give us insight, not numbers" was Coulson's admonition to theoretical chemists. This Review shows that the valence bond (VB)-model provides insights and some good numbers for one of the fundamental reactions in nature, the hydrogen-atom transfer (HAT). The VB model is applied to over 50 reactions from the simplest H + H(2) process, to P450 hydroxylations and H-transfers among closed-shell molecules; for each system the barriers are estimated from raw data. The model creates a bridge to the Marcus equation and shows that H-atom abstraction by a closed-shell molecule requires a higher barrier owing to the additional promotion energy needed to prepare the abstractor for H-abstraction. Under certain conditions, a closed-shell abstractor can bypass this penalty through a proton-coupled electron transfer (PCET) mechanism. The VB model links the HAT and PCET mechanisms conceptually and shows the consequences that this linking has for H-abstraction reactivity.

Towards quantitative computer-aided studies of enzymatic enantioselectivity: the case of Candida antarctica lipase A

The prospect for consistent computer-aided refinement of stereoselective enzymes is explored by simulating the hydrolysis of enantiomers of an α-substituted ester by wild-type and mutant Candida antarctica lipase A, using several strategies. In particular, we focused on the use of the empirical valence bond (EVB) method in a quantitative screening for enantioselectivity, and evaluate both k(cat) and k(cat)/K(M) of the R and S stereoisomers. We found that an extensive sampling is essential for obtaining converging results. This requirement points towards possible problems with approaches that use a limited conformational sampling. However, performing the proper sampling appears to give encouraging results and to offer a powerful tool for the computer-aided design of enantioselective enzymes. We also explore faster strategies for identifying mutations that will help in augmenting directed-evolution experiments, but these approaches require further refinement.