Iterative Saturation Mutagenesis Research Articles

Cloning and Direct Evolution of a Novel 7-O-Glycosyltransferase from Cucurbita moschata and Its Application in the Efficient Biocatalytic Synthesis of Luteolin-7-O-glucoside.

Luteolin-7-O-glucoside(L7G), a glycosylation product of luteolin, is present in a variety of foods, vegetables, and medicinal herbs and is commonly used in dietary supplements due to its health benefits. Meanwhile, luteolin-7-O-glucoside is an indicator component for the quality control of honeysuckle in the pharmacopoeia. However, its low content in plants has hindered its use in animal pharmacological studies and clinical practice. In this study, a novel 7-O-glycosyltransferase CmGT from Cucurbita moschata was cloned, which could efficiently convert luteolin into luteolin-7-O-glucoside under optimal conditions (40 °C and pH 8.5). To further improve the catalytic efficiency of CmGT, a 3D structure of CmGT was constructed, and directed evolution was performed. The mutant CmGT-S16A-T80W was obtained by using alanine scanning and iterative saturation mutagenesis. This mutant exhibited a kcat/Km value of 772 s-1·M-1, which was 3.16-fold of the wild-type enzyme CmGT. Finally, by introducing a soluble tag and UDPG synthesis pathway, the strain BXC was able to convert 1.25 g/L of luteolin into 1.91 g/L of luteolin-7-O-glucoside under optimal conditions, achieving a molar conversion rate of 96% and a space-time yield of 27.08 mg/L/h. This study provides an efficient method for the biosynthesis of luteolin-7-O-glucoside, which holds broad application prospects in the food and pharmaceutical industry.

Switching engineered Vitreoscilla hemoglobin into carbene transferase for enantioselective S[sbnd]H insertion

An attractive strategy for efficiently forming CS bonds is through the use of diazo compounds SH insertion. However, achieving good enantioselective control in this reaction within a biocatalytic system has proven to be challenging. This study aimed to enhance the activity and enantioselectivity of to enable asymmetric SH insertion. The researchers conducted site-saturation mutagenesis (SSM) on 5 amino acid residues located around the iron carbenoid intermediate within a distance of 5 Å, followed by iterative saturation mutagenesis (ISM) of beneficial mutants. Through this process, the beneficial variant VHbSH(P54R/V98W) was identified through screening with 4-(methylmercapto) phenol as the substrate. This variant exhibited up to 4-fold higher catalytic efficiency and 6-fold higher enantioselectivity compared to the wild-type VHb. Computational studies were also conducted to elucidate the detailed mechanism of this asymmetric SH insertion, explaining how active-site residues accelerate this transformation and provide stereocontrol.

Engineering Styrene Oxide Isomerase Towards Enhanced Chemoenzymatic Synthesis of (S)‐Flurbiprofen

AbstractThe conventional synthesis of (S)‐flurbiprofen, a valuable non‐steroidal anti‐inflammatory drug (NSAID), involves inefficient chiral resolution with low‐yielding multiple reaction steps, or asymmetric synthesis with low enantioselectivity and/or regioselectivity. Here, we developed high‐yielding, enantioselective, and sustainable synthesis of (S)‐flurbiprofen via two chemoenzymatic approaches from a simple alkene: (A) enzymatic epoxidation‐isomerization‐oxidation cascade and Pd‐catalyzed arylation; and (B) chemical epoxidation, enzymatic isomerization‐oxidation cascade, and Pd‐catalyzed arylation. Styrene oxide isomerase (SOI)‐catalyzed enantio‐retentive Meinwald rearrangement was the key step in the two pathways, but SOI suffers from low activity. SOI was engineered via two rounds of iterative saturation mutagenesis and screening with a three‐enzyme cascade assay, generating a double‐mutant SOIDM (N99A/D95A) with 5.5‐fold improvement in catalytic efficiency (kcat/KM). In Pathway A, cascade biotransformation of 3‐fluoro‐4‐bromo‐α‐methylstyrene with engineered E. coli strain expressing SOIDM, styrene monooxygenase (SMO) and aldehyde dehydrogenase (ALDH), and subsequent Pd‐catalyzed arylation afforded (S)‐flurbiprofen in 98% yield and 91% ee. In Pathway B, chemical epoxidation (Sharpless dihydroxylation and ring‐closing), cascade conversion using an engineered E. coli strain expressing SOIDM, ALDH and NADH oxidase (NOX), and Pd‐catalyzed arylation produced (S)‐flurbiprofen in 83% yield and 98% ee. Compared to conventional synthesis, the developed methods reduced reaction steps, minimized waste generation and improved enantioselectivity or overall yield.

Engineering of Unspecific Peroxygenases Using a Superfolder-Green-Fluorescent-Protein-Mediated Secretion System in Escherichia coli

Engineering of Unspecific Peroxygenases Using a Superfolder-Green-Fluorescent-Protein-Mediated Secretion System in <i>Escherichia coli</i>

Mutability landscape guided engineering of a promiscuous microbial glycosyltransferase for regioselective synthesis of salidroside and icariside D2

Microbial glycosyltransferases efficiently synthesize glucosides and have garnered increasing interest. However, limited regioselectivity has impeded their broad application, particularly in the pharmaceutical industry. In this study, the UDP-glycosyltransferase YjiC from Bacillus licheniformis (BlYjiC) was engineered to achieve the bidirectional regioselective glycosylation of tyrosol and its derivatives. Initially, site-directed saturation mutagenesis was performed on two newly identified substrate-binding cavities in the acceptor pocket of BlYjiC to provide a comprehensive blueprint of the interplay between mutations and function (mutability landscape). Iterative saturation mutagenesis was performed, guided by the mutability landscape. Two highly regioselective mutants M6 (M112L/I325Y/L70R/Q136E/I67E/M77R) and M2’ (M112D/I62L) were generated, exhibiting >99 % regioselectivity toward the alcoholic and phenolic hydroxyl of tyrosol, respectively, compared with the wild-type (product mixture: 51:49 %). Both mutants exhibited excellent regioselectivity toward several dihydroxy phenolic substrates, offering valuable biocatalysts for the regioselective synthesis of glucosides. Their application was confirmed in a short synthesis of salidroside (3.6 g/L) and icariside D2 (2.4 g/L), which exhibited near-perfect regioselectivity. This study provides valuable insights into future protein engineering of similar enzymes and opens new avenues for their practical applications.

Controlling Monoterpene Isomerization by Guiding Challenging Carbocation Rearrangement Reactions in Engineered Squalene-Hopene Cyclases.

The interconversion of monoterpenes is facilitated by a complex network of carbocation rearrangement pathways. Controlling these isomerization pathways is challenging when using common Brønsted and Lewis acid catalysts, which often produce product mixtures that are difficult to separate. In contrast, natural monoterpene cyclases exhibit high control over the carbocation rearrangement reactions but are reliant on phosphorylated substrates. In this study, we present engineered squalene-hopene cyclases from Alicyclobacillus acidocaldarius (AacSHC) that catalyze the challenging isomerization of monoterpenes with unprecedented precision. Starting from a promiscuous isomerization of (+)-β-pinene, we first demonstrate noticeable shifts in the product distribution solely by introducing single point mutations. Furthermore, we showcase the tuneable cation steering by enhancing (+)-borneol selectivity from 1 % to >90 % (>99 % de) aided by iterative saturation mutagenesis. Our combined experimental and computational data suggest that the reorganization of key aromatic residues leads to the restructuring of the water network that facilitates the selective termination of the secondary isobornyl cation. This work expands our mechanistic understanding of carbocation rearrangements and sets the stage for target-oriented skeletal reorganization of broadly abundant terpenes.

Controlling Monoterpene Isomerization by Guiding Challenging Carbocation Rearrangement Reactions in Engineered Squalene‐Hopene Cyclases

AbstractThe interconversion of monoterpenes is facilitated by a complex network of carbocation rearrangement pathways. Controlling these isomerization pathways is challenging when using common Brønsted and Lewis acid catalysts, which often produce product mixtures that are difficult to separate. In contrast, natural monoterpene cyclases exhibit high control over the carbocation rearrangement reactions but are reliant on phosphorylated substrates. In this study, we present engineered squalene‐hopene cyclases from Alicyclobacillus acidocaldarius (AacSHC) that catalyze the challenging isomerization of monoterpenes with unprecedented precision. Starting from a promiscuous isomerization of (+)‐β‐pinene, we first demonstrate noticeable shifts in the product distribution solely by introducing single point mutations. Furthermore, we showcase the tuneable cation steering by enhancing (+)‐borneol selectivity from 1 % to &gt;90 % (&gt;99 % de) aided by iterative saturation mutagenesis. Our combined experimental and computational data suggest that the reorganization of key aromatic residues leads to the restructuring of the water network that facilitates the selective termination of the secondary isobornyl cation. This work expands our mechanistic understanding of carbocation rearrangements and sets the stage for target‐oriented skeletal reorganization of broadly abundant terpenes.

Surface engineering of cyclodextrin glycosyltransferase reveals structural compactness and rigidity responsible for enhanced organic solvents resistance

Cyclodextrin glycosyltransferase (CGTase) is a preferable biocatalyst for production of cyclodextrin and phenols glycosylated derivatives due to its cost-effective donors and broad range of acceptors. Organic solvents (OSs) are often beneficial for solubilizing hydrophobic substrates and product specificity, but often harmful towards CGTases. Herein, using Paenibacillus macerans CGTase (PmCGTase) as a template and DMSO as a screening solvent, semi-rational engineering was performed at 18 surface residues by a developed high throughput screening method. Using site saturation mutagenesis and iterative saturation mutagenesis, 5 OSs-resistant variants (G539I, G539V, G539I/R146F, G539V/R146A, G539I/R146F/D147N) were obtained. Compared with WT, the best variant G539I/R146F/D147N showed a 79.3 % enhanced residual activity at 30 % DMSO and a 60 % increased t1/2 value at both 40 and 50 °C. In addition, a decreased Km value and an increased kcat value led to 41.9 % higher catalytic efficiency of G539I/R146F/D147N than WT in 15 % DMSO. This variant was also applied to glycosylation of sophoricoside in 20 % DMSO, leading to 26.2 % increased conversion. Molecular dynamics demonstrates that its enhanced OSs resistance may be attributed to the strengthened structural compactness and rigidity. Our results provide guidance for engineering OSs resistance of PmCGTase, which would further improve its application potential.

Enhancement of the substrate specificity of D-amino acid oxidase based on tunnel-pocket engineering.

D-Amino acid oxidase (DAAO) selectively catalyzes the oxidative deamination of D-amino acids, making it one of the most promising routes for synthesizing optically pure L-amino acids, including L-phosphinothricin( L-PPT), a chiral herbicide with significant market potential. However, the native DAAOs that have been reported have low activity against unnatural acid substrate D-PPT. Herein, we designed and screened a DAAO from Rhodotorula taiwanensis (RtwDAAO), and improved its catalytic potential toward D-PPT through protein engineering. A semirational design approach was employed to create a mutation library based on the tunnel-pocket engineering. After three rounds of iterative saturation mutagenesis, the optimal variant M3rd -SHVG was obtained, exhibiting a >2000-fold increase in relative activity. The kinetic parameters showed that M3rd -SHVG improved the substrate binding affinity and turnover number. This is the optimal parameter reported so far. Further, molecular dynamics simulation revealed that the M3rd -SHVG reshapes the tunnel-pocket and corrects the direction of enzyme-substrate binding, allowing efficiently catalyze unnatural substrates. Our strategy demonstrates that the redesign of tunnel-pockets is effective in improving the activity and kinetic efficiency of DAAO, which provides a valuable reference for enzymatic catalysis. With the M3rd -SHVG as biocatalyst, 500 mM D, L-PPT was completely converted and the yield reached 98%. The results laid the foundation for further industrial production.

Structure-Guided Engineering of a Protease to Improve Its Activity under Cold Conditions.

Bacillus proteases commonly exhibit remarkably reduced activity under cold conditions. Herein, we employed a tailored combination of a loop engineering strategy and iterative saturation mutagenesis method to engineer two loops for substrate binding at the entrance of the substrate tunnel of a protease (bcPRO) from Bacillus clausii to improve its activity under cold conditions. The variant MT6 (G95P/A96D/S99W/S101T/P127S/S126T) exhibited an 18.3-fold greater catalytic efficiency than the wild-type (WT) variant at 10 °C. Molecular dynamics simulations and dynamic tunnel analysis indicated that the introduced mutations extended the substrate-binding pocket volume and facilitated extra interactions with the substrate, promoting catalysis through binding in a more favorable conformation. This study provides insights and strategies relevant to improving the activities of proteases and supplies a novel protease with enhanced activity under cold conditions for the food industry to maintain the initial flavor and color of food and reduce energy consumption.

Structure-guided protein engineering to reconstruct the biocatalyst properties for efficient l-3,4-dihydroxyphenylalanine production

Biocatalysis becomes more and more popular but few enzymes can directly catalyze the reaction efficiently. Thus, it is essential to modify the catalyst to satisfy the practical needs. Tyrosinases demonstrate great potential to generate l-3,4-dihydroxyphenylalanine (l-DOPA), the most promising therapeutic drug for Parkinson’s disease, using their monophenolase activity with l-tyrosine as substrate. However, the naturally discovered tyrosinases exhibit poor activities towards l-tyrosine. Here, we proposed a structure-guided mutation strategy (iterative saturation mutagenesis (ISM) based on intra- and inter-functional clusters) to redesign the tyrosinase (baTRY) from Bacillus aryabhattai into a biocatalyst for producing l-DOPA. Firstly, key residues (three clusters including (1) the sites nearby the active center, (2) substrate binding pocket, and (3) water molecule interaction domain) for baTRY’s function were identified by computational structural analysis. Secondly, ISM with the order of cluster 1 (ISM) → cluster 2 (ISM) → cluster 3 (ISM) was developed to reconstruct baTRY’s spatial structure. A highly active variant MT6 (G43R/M61H/A232C/Q214D/V217A/F197W) was created, exhibiting a 11.27-fold higher monophenolase activity than WT. Quantum mechanics and molecular dynamics simulations suggested that the improved catalytic efficiency was attributed to the reduced catalysis energy barrier, the enlarged substrate-binding pocket, and the increased interactions with the substrate and water molecules. Finally, ortho-hydroxylation efficiency of MT6 was tested with 2 mM l-tyrosine as substrate, demonstrating the l-DOPA conversion rate of 90.2% and productivity of 177.6 mg/L/h. This study provided an effective strategy for guiding the engineering of biocatalysis and expanded the applications of biocatalyst on value-added chemicals.

Alternative Active Site Confinement in Squalene–Hopene Cyclase Enforces Substrate Preorganization for Cyclization

Confinement of an enzyme’s active site is critical to the efficiency of chemical reactions and has been recognized as an important tool for catalysis to accelerate reactions by proximity and via specific interactions with the substrate to control the course of the reaction. Despite these benefits, a strongly confined active site is inherently limited to compounds that resemble the native substrate, with only small deviations tolerated. To unlock the potential of modifying the terpene scaffold as building blocks of interest with branched isoprene/terpene motifs, the present study demonstrates a simple structure-guided strategy to create alternative confinement in the squalene–hopene cyclase from Alicyclobacillus acidocaldarius (AacSHC). This strategy aims for proximity and shape complementarity between the protein and substrate to enforce preorganization of geranyl acetone analogs with deviant isoprene patterns. Screening of AacSHC variants affecting the substrate tunnel allowed us to detect starting activity with the AacSHC G600M variant. Structural analysis led to the identification of reduced tunnel radii that resulted in steric interactions and proximity by a decrease in the average distances between the double bond of the substrate’s terminal isoprene unit and the catalytic site. Iterative saturation mutagenesis with SHC variants and screening with the geranyl acetone analog dihydropseudoirone were used to generate complementarity and demonstrated further evolvability. The final variant showed a 1174-fold increase in total turnover number and 111-fold increased catalytic efficiency compared to the wild-type. This approach to create alternative active site confinement demonstrates great potential to overcome limitations in the engineering of biocatalysts and generation of interesting building blocks.

Combined engineering of l-sorbose dehydrogenase and fermentation optimization to increase 2-keto-l-gulonic acid production in Escherichia coli

One-step fermentation to produce 2-keto-l-gulonic acid (2-KLG), the precursor of vitamin C, is a long-term goal. Improvement of the enzyme’s activity through engineering could benefit 2-KLG production. This study aimed to conduct a semi-rational design of l-sorbose dehydrogenase (SDH) through structure-directed, to screen mutants that could enhance the 2-KLG titer. First, the predicted structure of SDH was obtained using AlphaFold2. The key mutation sites in the substrate pocket were identified by Ala scanning. Subsequently, the mutant V336I/V368A was obtained by iterative saturation mutagenesis, which increased the yield of 2-KLG 1.9-fold. Finally, 5.03 g/L of 2-KLG was obtained by a two-stage temperature control fermentation method, and the conversion rate was 50%. Furthermore, experiments showed that knockdown of the l-sorbose-associated phosphotransferase system delays 2-KLG production. The results show that the production of 2-KLG was effectively increased through a combination of SDH engineering and fermentation optimization.

Engineering of Hydroxymandelate Oxidase and Cascade Reactions for High-Yielding Conversion of Racemic Mandelic Acids to Phenylglyoxylic Acids and (R)- and (S)-Phenylglycines

An alcohol oxidase (AOx) for the (S)-enantioselective oxidation of 4-hydroxymandelic acid (4-HMA) to 4-hydroxyphenylglyoxylic acid (4-HPGA) with enhanced activity was developed by directed evolution of hydroxymandelate oxidase (HMO) through three rounds of iterative saturation mutagenesis. The engineered HMO mutant A80G-T159S-T162Q (HMOTM) catalyzed the oxidation of (S)-4-HMA to 4-HPGA with a 23-fold enhancement in catalytic efficiency (kcat/KM). Substrate docking simulation on HMOTM suggested that A80G reoriented FMN, while T159S and T162Q formed hydrogen bonds with the carboxylic group of the substrate, thus facilitating substrate binding and catalysis. (S)-Enantioselective HMOTM was used together with mandelic acid racemase (MR) and catalase (KatE) to achieve high-yielding oxidation of rac-4-HMA to 4-HPGA with either purified enzymes (up to 93% yield and 426 mM) or Escherichia coli (HMC) cells expressing the three enzymes (up to 93% yield and 140 mM). The HMOTM-MR-KatE cascades were applied for the oxidation of seven other substituted MAs, producing the corresponding phenylglyoxylic acids with 90–99% conversions using purified enzymes or whole cells. Efficient conversion of racemic α-hydroxy acids to (S)- or (R)-α-amino acids was achieved by combining HMOTM-MR-KatE with (S)-enantioselective transaminase (EcαTA) or (R)-enantioselective transaminase (DpgAT), together with glutamate dehydrogenase (GluDH). Coupling of E. coli (HMC) with E. coli (E-G) expressing EcαTA and GluDH for one-pot biotransformation of five rac-MAs produced the corresponding (S)-phenylglycines (PGs) in 91–99% ee with 73–98% conversions. Using E. coli (HMC) and E. coli (D-G) expressing DpgAT and GluDH enabled the production of five (R)-PGs with 93–99% ee and 73–98% conversions from the corresponding rac-MAs. The engineered AOx, AOx-MR-KatE cascades, and AOx-MR-Kat-GluDH-(S)- or (R)-TA cascades provide useful tools for highly active and enantioselective oxidation of racemic hydroxyacids and high-yielding conversion of racemic hydroxyacids to ketoacids and enantiopure (S)- or (R)-aminoacids, respectively, which are challenging and useful chemical reactions.

Rationally Controlling Selective Steroid Hydroxylation via Scaffold Sampling of a P450 Family

Many steroids are important pharmaceutically active compounds, while cytochrome P450 monooxygenases (CYPs) are attractive enzymes for applications in steroidal drug synthesis. However, the catalytic efficiency of existing P450s is not routinely high enough, as well as the molecular basis for selectivity control is unclear, which severely restrict their real applications. Here, a 16β steroid-hydroxylase CYP109B4 from Bacillus sonorensis is identified with excellent selectivity and activity. The crystallization and structural analysis of CYP109B4 reveal potential three “hotspot” residues (V84, V292, and S387) responsible for selectivity control. Then, guided by the sequence–function relationships revealed from the mutability landscape construction on the three residues, focused rational iterative site-specific mutagenesis (FRISM) and limited iterative saturation mutagenesis were performed, which provide variant B4-M7 (L240V/S387F/V84L/V292S/I291T/M290F/F294I) with completely switched regioselectivity from 16β to 15β. The subsequent computational analysis uncovers insights into the substrate binding modes in CYP109B4 and its variants, which further confirms the critical role of the “hotspot” residues for selectivity control. Finally, the generality of conserved-“hotspots”-mediated selectivity control is demonstrated by performing scaffold sampling between a panel of CYP109B members. Overall, in addition to the present chemical results, our study provides guidance in rationally designing more excellent P450 biocatalysts for potential practical (industrial) applications.

Discovery of New Phenylacetone Monooxygenase Variants for the Development of Substituted Indigoids through Biocatalysis.

Indigoids are natural pigments obtained from plants by ancient cultures. Romans used them mainly as dyes, whereas Asian cultures applied these compounds as treatment agents for several diseases. In the modern era, the chemical industry has made it possible to identify and develop synthetic routes to obtain them from petroleum derivatives. However, these processes require high temperatures and pressures and large amounts of solvents, acids, and alkali agents. Thus, enzyme engineering and the development of bacteria as whole-cell biocatalysts emerges as a promising green alternative to avoid the use of these hazardous materials and consequently prevent toxic waste generation. In this research, we obtained two novel variants of phenylacetone monooxygenase (PAMO) by iterative saturation mutagenesis. Heterologous expression of these two enzymes, called PAMOHPCD and PAMOHPED, in E. coli was serendipitously found to produce indigoids. These interesting results encourage us to characterize the thermal stability and enzyme kinetics of these new variants and to evaluate indigo and indirubin production in a whole-cell system by HPLC. The highest yields were obtained with PAMOHPCD supplemented with L-tryptophan, producing ~3000 mg/L indigo and ~130.0 mg/L indirubin. Additionally, both enzymes could oxidize and produce several indigo derivatives from substituted indoles, with PAMOHPCD being able to produce the well-known Tyrian purple. Our results indicate that the PAMO variants described herein have potential application in the textile, pharmaceutics, and semiconductors industries, prompting the use of environmentally friendly strategies to obtain a diverse variety of indigoids.

Focused mutagenesis in non-catalytic cavity for improving catalytic efficiency of 3-ketosteroid-Δ1-dehydrogenase

Non-catalytic sites are commonly present in many enzymes, but how to classify and modulate such sites for activity improvement is not well-explored. Herein a non-catalytic cavity in the 3-ketosteroid-Δ1-dehydrogenase (Δ1-KstD) from Mycobacterium smegmatis (MsKstD1), which could competitively bind to substrate to form non-catalytic complex, was predicted next to substrate tunnel by the CAVER/molecular dynamics. Based on that, a rational design was performed by Focused Site-directed Iterative Saturation Mutagenesis (FSISM) for blocking the non-catalytic cavity to enhance substrate enter active site to improve the Δ1-dehydrogenation activity of MsKstD1. We obtained the best quadruple mutant (H132M\\L113F\\V419W\\M51L) with 10-fold higher specific activity toward hydrocortisone than that of wild type enzyme. The Δ1-dehydrogenation space time yield toward hydrocortisone reached 36.0 g/L/h to produce prednisolone. This work displays how to combine focused mutagenesis with computational analysis to effectively identify and modify non-catalytic cavity to enhance enzyme activity for efficient production of Δ1-3-ketosteroid.

Going Beyond the Local Catalytic Activity Space of Chitinase Using a Simulation-Based Iterative Saturation Mutagenesis Strategy

Going Beyond the Local Catalytic Activity Space of Chitinase Using a Simulation-Based Iterative Saturation Mutagenesis Strategy

Engineering the Activity of Old Yellow Enzyme NemR-PS for Efficient Reduction of (E/Z)-Citral to (S)-Citronellol

The cascade catalysis of old yellow enzyme, alcohol dehydrogenase and glucose dehydrogenase has become a promising approach for one pot, two-step reduction of (E/Z)-citral to (S)-citronellol, serving as a chiral alcohol with rose fragrance. During the multi-enzymatic cascade catalysis, old yellow enzyme is responsible for the reduction of the conjugated C=C and the introduction of the chiral center, requiring high activity and (S)-enantioselectiviy. Herein, to improve the activity of the old yellow enzyme from Providencia stuartii (NemR-PS) with strict (S)-enantioselectivity, the semi-rational design on its substrate binding pocket was performed through a combination of homology modeling, molecular docking analysis, alanine scanning and iterative saturation mutagenesis. The NemR-PS variant D275G/F351A with improved activity was obtained and then purified for characterization, obeying the substrate inhibition kinetics. Compared with the wild type, the parameters Ki and Kcat/Km were increased from 39.79 mM and 2.09 s−1mM−1 to 128.50 mM and 5.01 s−1mM−1, respectively. Moreover, the variant D275G/F351A maintained strict (S)-enantioselectivity, avoiding the trade-off effect between activity and enantioselectivity. Either the enzyme NemR-PS or the variant D275G/F351A was co-expressed with alcohol dehydrogenase from Yokenella sp. WZY002 (YsADH) and glucose dehydrogenase from Bacillus megaterium (BmGDHM6). In contrast to the whole-cell biocatalyst co-expressing NemR-PS, that co-expressing the variant D275G/F351A shortened the reaction time from 36 h to 12 h in the reduction of 400 mM (E/Z)-citral. In the manner of substrate constant feeding, the accumulated product concentration reached up to 500 mM and completely eliminate the residual intermediate and by-product, suggesting the effectiveness of protein engineering and substrate engineering to improve catalytic efficiency.

Coevolutionary analysis reveals a distal amino acid residue pair affecting the catalytic activity of GH5 processive endoglucanase from Bacillus subtilis BS-5.

EG5C-1, processive endoglucanase from Bacillus subtilis, is a typical bifunctional cellulase with endoglucanase and exoglucanase activities. The engineering of processive endoglucanase focuses on the catalytic pocket or carbohydrate-binding module tailoring based on sequence/structure information. Herein, a computational strategy was applied to identify the desired mutants in the enzyme molecule by evolutionary-coupling analysis; subsequently, four residue pairs were selected as evolutionary mutational hotspots. Based on iterative-saturation mutagenesis and subsequent enzymatic activity analysis, a superior mutant K51T/L93T has been identified away from the active center. This variant had increased specific activity from 4170 U/µmol of wild-type (WT) to 5678 U/µmol towards carboxymethyl cellulose-Na and an increase towards the substrate Avicel from 320 U/µmol in WT to 521 U/µmol. In addition, kinetic measurements suggested that superior mutant K51T/L93T had a high substrate affinity (Km ) and a remarkable improvement in catalytic efficiency (kcat /Km ). Furthermore, molecular dynamics simulations revealed that the K51T/L93T mutation altered the spatial conformation at the active site cleft, enhancing the interaction frequency between active site residues and substrate, and improving catalytic efficiency and substrate affinity. The current studies provided some perspectives on the effects of distal residue substitution, which might assist in the engineering of processive endoglucanase or other glycoside hydrolases.