Kinetic characterization of Rhodococcus ruber DSM 44541 alcohol dehydrogenase A

Structure of the iminium reaction intermediate in an engineered aldolase explains the carboligation activity toward arylated ketones and aldehydes

Two structures of fructose 6-phosphate aldolase, the wild-type and an engineered variant containing five active-site mutations, have been solved by cryoelectron microscopy (cryo-EM). The engineered variant affords production of aldols from aryl substituted ketones and aldehydes. This structure was solved to a resolution of 3.1 Å and contains the critical iminium reaction intermediate trapped in the active site. This provides new information that rationalizes the acquired substrate scope and aids in formulating hypotheses of the chemical mechanism. A Tyr residue (Y131) is positioned for a role as catalytic acid/base during the aldol reaction and the different structures demonstrate mobility of this amino acid residue. Further engineering of this fructose 6-phosphate aldolase (FSA) variant, guided by this new structure, identified additional FSA variants that display improved carboligation activities with 2-hydroxyacetophenone and phenylacetaldehyde.

Structures of lactaldehyde reductase, FucO, link enzyme activity to hydrogen bond networks and conformational dynamics

A group-III iron containing 1,2-propanediol oxidoreductase, FucO, (also known as lactaldehyde reductase) from Escherichia coli was examined regarding its structure-dynamics-function relationships in the catalysis of the NADH-dependent reduction of (2S)-lactaldehyde. Crystal structures of FucO variants in the presence or absence of cofactors have been determined, illustrating large domain movements between the apo and holo enzyme structures. Different structures of FucO variants co-crystallized with NAD⁺ or NADH together with substrate further suggest dynamic properties of the nicotinamide moiety of the coenzyme that are important for the reaction mechanism. Modelling of the native substrate (2S)-lactaldehyde into the active site can explain the stereoselectivity exhibited by the enzyme, with a critical hydrogen bond interaction between the (2S)-hydroxyl and the side-chain of N151, as well as the previously experimentally demonstrated pro-(R) selectivity in hydride transfer from NADH to the aldehydic carbon. Furthermore, the deuterium kinetic isotope effect of hydride transfer suggests that reduction chemistry is the main rate-limiting step for turnover which is not the case in FucO catalysed alcohol oxidation. We further propose that a water molecule in the active site - hydrogen bonded to a conserved histidine (H267) and the 2'-hydroxyl of the coenzyme ribose - functions as a catalytic proton donor in the protonation of the product alcohol. A hydrogen bond network of water molecules and the side-chains of amino acid residues D360 and H267 links bulk solvent to this proposed catalytic water molecule.

Enhancement of solubility of recombinant alcohol dehydrogenase from Rhodococcus ruber using predictive tool

Solubility is one of key factors influencing the heterologous production of recombinant proteins in biotechnology. Among many aggregation-prone proteins, alcohol dehydrogenase (ADH-A) from Rhodococcus ruber (in this work abbreviated RrADH) shows a great potential in processes involved in the biotransformation of natural compounds. As ADH-A is a potentially high value asset in industrial biotransformation processes, improvement of its solubility would be of major commercial benefit. Predictive tools and in silico analysis provide a fast means for improving protein properties, for selecting appropriate changes, and ultimately for saving costs. We have therefore focused on enhancement of the solubility of RrADH using an online accesible predictive tool Aggrescan 3D 2.0. Selected mutations were introduced into the protein amino acid sequence by using site-directed PCR. This led to a 17% increase in the protein solubility of RrADHmut1 and a 98% increase for RrADHmut2. Moreover, the basic kinetics of the enzyme reaction were positively affected, further optimizing the overall performance of the production process.

Facile synthesis of 2-hydroxyacetophenone from racemic styrene oxide catalyzed by engineered enzymes

We describe a system that allows for biocatalyzed in vivo synthesis of α-hydroxy ketones from racemic epoxide starting material by in vivo co-expression of native and engineered epoxide hydrolase and alcohol dehydrogenases. The constructed expression system exploits the host cell metabolism for supply and regeneration of precious nicotinamide dinucleotide coenzyme. Racemic styrene oxide added to growth medium passively enters the cells and is hydrolyzed into (1R)-phenylethane-1,2-diol, which is subsequently oxidized to the acyloin 2-hydroxyacetophenone. Produced 2-hydroxyacetophenone escapes the cells via passive diffusion into the growth medium. Thus, co-expression of potato epoxide hydrolase and engineered alcohol dehydrogenase variants can be employed for robust and facile production of 2-hydroxyacetophenone from racemic styrene oxide.

Recombinant Enzymatic Redox Systems for Preparation of Aroma Compounds by Biotransformation

The aim of this study was to develop immobilized enzyme systems that reduce carbonyl compounds to their corresponding alcohols. The demand for natural aromas and food additives has been constantly growing in recent years. However, it can no longer be met by extraction and isolation from natural materials. One way to increase the availability of natural aromas is to prepare them by the enzymatic transformation of suitable precursors. Recombinant enzymes are currently being used for this purpose. We investigated trans-2-hexenal bioreduction by recombinant Saccharomyces cerevisiae alcohol dehydrogenase (ScADH1) with simultaneous NADH regeneration by recombinant Candida boidinii formate dehydrogenase (FDH). In a laboratory bioreactor with two immobilized enzymes, 88% of the trans-2-hexenal was transformed to trans-2-hexenol. The initial substrate concentration was 3.7 mM. The aldehyde destabilized ScADH1 by eluting Zn²⁺ ions from the enzyme. A fed-batch operation was used and the trans-2-hexenal concentration was maintained at a low level to limit the negative effect of Zn²⁺ ion elution from the immobilized ScADH1. Another immobilized two-enzyme system was used to reduce acetophenone to (S)-1-phenylethanol. To this end, the recombinant alcohol dehydrogenase (RrADH) from Rhodococcus ruber was used. This biocatalytic system converted 61% of the acetophenone to (S)-1-phenylethanol. The initial substrate concentration was 8.3 mM. All enzymes were immobilized by poly-His tag to Ni²⁺, which formed strong but reversible bonds that enabled carrier reuse after the loss of enzyme activity.

Substitution of cysteine-153 ligated to the catalytic zinc in yeast alcohol dehydrogenase with aspartic acid and analysis of mechanisms of related medium chain dehydrogenases

The catalytic zincs in complexes of horse liver and yeast alcohol dehydrogenases (ADH) with NAD⁺ and the substrate analogue, 2,2,2-trifluoroethanol, are ligated to two cysteine residues and one histidine residue from the protein and the oxygen from the alcohol. The zinc facilitates deprotonation of the alcohol and is essential for catalysis. In the yeast apoenzyme, the zinc is coordinated to a nearby glutamic acid, which is displaced by the alcohol in the complex with NAD⁺. Some homologous medium chain dehydrogenases have a cysteine replaced by aspartic or glutamic acid residues. How an aspartic acid would affect catalysis was studied by replacing Cys-153 in Saccharomyces cerevisiae ADH1 by using site-directed mutagenesis. The C153D enzyme was about as stable as the wild-type enzyme, if EDTA was not included in the buffers. The substitution increased affinity for NAD⁺ by 3-fold, but did not affect NADH binding. At pH 7.3, the turnover number for ethanol oxidation (V₁/E_t) decreased by 7-fold and catalytic efficiency decreased 18-fold (V₁/E_tK_b), but turnover for acetaldehyde reduction (V₂/E_t) was the same as for wild-type enzyme and catalytic efficiency decreased 8-fold (V₂/E_tK_p). Deuterium isotope effects of 3.0 on V₁/E_t and 3.8 on V₁/E_tK_b for ethanol oxidation suggest that hydride transfer is more rate-limiting for turnover for the C153D enzyme than by wild-type enzyme. The patterns of pH dependence for V₁/E_tK_b for ethanol oxidation were similar for both enzymes in the pH range from 7 to 9. The C153D substitution decreased binding of trifluoroethanol by 5-fold and of pyrazole by 65-fold. Substrate specificities for C153D and wild-type ADHs for primary alcohols have similar patterns. Efficiency for secondary alcohols decreased only about 4-fold, and efficiencies for 1,2-propanediol and acetone were about the same as for wild-type enzyme. The C153D substitution modestly affects catalysis by altering ligand exchange on the zinc or local structure. Structures and mechanisms for acid-base catalysis in related medium chain dehydrogenases with substitutions of the homologous cysteine are reviewed and analyzed.

From Bugs to Bioplastics: Total (+)-Dihydrocarvide Biosynthesis by Engineered Escherichia coli

The monoterpenoid lactone derivative (+)-dihydrocarvide ((+)-DHCD) can be polymerised to form shape-memory polymers. Synthetic biology routes from simple, inexpensive carbon sources are an attractive, alternative route over chemical synthesis from (R)-carvone. We have demonstrated a proof-of-principle in vivo approach for the complete biosynthesis of (+)-DHCD from glucose in Escherichia coli (6.6 mg L-1 ). The pathway is based on the Mentha spicata route to (R)-carvone, with the addition of an 'ene'-reductase and Baeyer-Villiger cyclohexanone monooxygenase. Co-expression with a limonene synthesis pathway enzyme enables complete biocatalytic production within one microbial chassis. (+)-DHCD was successfully produced by screening multiple homologues of the pathway genes, combined with expression optimisation by selective promoter and/or ribosomal binding-site screening. This study demonstrates the potential application of synthetic biology approaches in the development of truly sustainable and renewable bioplastic monomers.

Generation of novel family of reductases from PCR based library for the synthesis of chiral alcohols and amines

Biocatalysis has shown tremendous potential in the synthesis of drugs and drug intermediates in the last decade. Screening of novel biocatalysts from the natural genome space is the growing trend to replenish the harsh chemical synthetic routes, commonly used in the pharmaceutical and chemical industry. Here, we report a novel ketoreductase (KERD) and a nitrile reductase isolated from the PCR based library generated from the genome of Rhodococcus ruber and Bacillus subtilis, respectively. Both the proteins are hypothetical in nature as there is no putative homology found in the database, although both the enzymes have significant activity towards the synthesis of chiral alcohols and amines. Enzyme activity over a wide range of substrates (aromatic and aliphatic) for both the novel catalysts was observed. From the unique gene sequence to activity over a broad range of substrate and >99% conversion at higher concentrations (100 mM and above) entitles both the hypothetical enzymes as novel. The novel KERD has shown >99% selectivity for the synthesis of (S)-phenylethanol which makes it a potential candidate for industrial catalysis. The novel nitrile reductase has also shown promising activity for the synthesis of (R)-2-phenylethanolamine, which is a difficult moiety to synthesize chemically. In this report, starting from a homology based library, two highly potent whole cell biocatalysts are obtained.

Substitutions of a buried glutamate residue hinder the conformational change in horse liver alcohol dehydrogenase and yield a surprising complex with endogenous 3'-Dephosphocoenzyme A

Glu-267 is highly conserved in alcohol dehydrogenases and buried as a negatively-charged residue in a loop of the NAD coenzyme binding domain. Glu-267 might have a structural role and contribute to a rate-promoting vibration that facilitates catalysis. Substitutions of Glu-267 with histidine or asparagine residues increase the dissociation constants for the coenzymes (NAD⁺ by ∼40-fold, NADH by ∼200-fold) and significantly decrease catalytic efficiencies by 16-1200-fold various substrates and substituted enzymes. The turnover numbers modestly change with the substitutions, but hydride transfer is at least partially rate-limiting for turnover for alcohol oxidation. X-ray structures of the E267H and E267 N enzymes are similar to the apoenzyme (open) conformation of the wild-type enzyme, and the substitutions are accommodated by local changes in the structure. Surprisingly, the E267H and E267 N enzymes have endogenous (from the expression in E. coli) 3'-dephosphocoenzyme A bound in the active site with the ADP moiety in the NAD binding site and the pantethiene sulfhydryl bound to the catalytic zinc. The kinetics and crystallography show that the substitutions of Glu-267 hinder the conformational change, which occurs when wild-type enzyme binds coenzymes, and affect productive binding of substrates.

A Microplate Format Assay for Real-Time Screening for New Aldolases that Accept Aryl-Substituted Acceptor Substrates

Aldolases are potentially important biocatalysts for asymmetric synthesis of polyhydroxylated compounds. Fructose 6-phosphate aldolase (FSA) is of particular interest by virtue of its unusually relaxed dependency on phosphorylated substrates. FSA has been reported to be a promising catalyst of aldol addition involving aryl-substituted acceptors such as phenylacetaldehyde that can react with donor ketones such as hydroxyacetone. Improvement of the low intrinsic activity with bulky acceptor substrates of this type is of great interest but has been hampered by the lack of powerful screening protocols applicable in directed evolution strategies. Here we present a new screen allowing for direct spectrophotometric recording of retro-aldol cleavage. The assay utilizes an aldehyde reductase produced in vitro by directed evolution; it reduces the aldehyde product formed after cleavage of the aldol by FSA. The assay is suitable both for steady-state enzyme kinetics and for real-time activity screening in a 96-well format.