Insight into the significant roles of the Trp372 and flexible loop in directing the catalytic direction and substrate specificity in AGE superfamily enzymes

Enhancement of isomerization activity and thermostability of cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus using semi-rational design

Cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus (CsCE) is crucial for lactulose production; however, its low isomerization activity and poor thermostability limit its industrial application. Herein, four single-point mutants (S70D, F171W, S173L, and L354F) with significantly improved isomerization activity were obtained using a computer-aided semi-rational design, and combined mutants were introduced. The isomerization specific activities of the mutants CsCE-F171W/S173L/L354F and CsCE-S70D/F171W/S173L/L354F were 2.10 and 2.05 times higher than that of wild-type CsCE, respectively. Enzymatic properties revealed that the mutant CsCE-F171W/S173L/L354F demonstrated a 2.50-fold increase in t1/2 at 80 °C and a 2.70-fold improvement in kcat, while the mutant CsCE-S70D/F171W/S173L/L354F exhibited a 2.91-fold increase in t1/2 at 80 °C and a 3.19-fold improvement in kcat. Three-dimensional structural analysis suggested that conformational changes in the flexible ring induced by mutation could enhance isomerization activity, while increased structural rigidity, hydrophobic contacts, van der Waals forces, and favorable electrostatic potentials may promote thermostability. These findings provide novel insights into the molecular modification of CsCE and significantly enhance its potential for industrial applications.

Unlocking Loop Geometric Remodeling Redirects Aldo-Keto Reductase from Substrate Promiscuity to 3-Keto-Deoxynivalenol Specificity

Aldo-keto reductase is responsible for the formation of nontoxic 3-epi-deoxynivalenol (3-epi-DON) from 3-keto-DON, which is an enzymatic detoxification manner to completely eliminate the toxicity of mycotoxin DON against health and environmental threats. Therefore, unlocking the facilitated substrate specificity of aldo-keto reductase for 3-keto-DON has become a critical challenge for advanced catalytic performance. In this endeavor, a loop-based engineering strategy was developed for aldo-keto reductase AKR13B3 from Devosia A6-243 to catalyze 3-keto-DON. A 31.9-fold switch from a disfavored substrate to the preferred one was produced along with a significant 37.9-fold increase in catalytic efficiency. Kinetic parameter determinations, structural analyses, and molecular simulations were employed to elucidate the molecular mechanisms underlying these enhancements in catalytic activity and substrate specificity. Overall, our work presents a feasible scheme for designing aldo-keto reductases with exceptional substrate specificity and catalytic activity, holding great promise for developing enzymatic detoxification agents.

Advances and prospects on production of lactulose and epilactose by cellobiose 2-epimerases: A review

Lactulose and epilactose are nondigestible disaccharides with a wide range of applications in clinical medicine, nutrition, and the food industry due to their health-benefiting properties. Their chemical synthesis typically involves stringent catalytic conditions and intricate reaction procedures, resulting in elevated production costs and challenges in product separation. Cellobiose 2-epimerases (CEs) facilitate the isomerization and epimerization of lactose to produce lactulose and epilactose directly, without the need for co-substrates. This enzymatic process offers advantages such as mild reaction conditions, straightforward operation, high conversion efficiency, and reduced by-product formation. Recently, numerous CE genes have been identified and characterized, with their enzymatic properties undergoing extensive analysis. This review consolidates information on the properties of CEs from various sources and examines their catalytic mechanisms based on crystal structure data. Additionally, the current research progress in the enzymatic synthesis of lactulose and epilactose is comprehensively reviewed. The future direction of CE research is discussed, highlighting the potential for large-scale production of lactulose and epilactose through environmentally sustainable enzymatic methods.

Rational Design of Loop Dynamics for a Barrel-Shaped Enzyme by Introducing Disulfide Bonds

Loop dynamics redesign is an important strategy to manipulate protein function. Cellobiose 2-epimerase (CE) and other members of its superfamily are widely used for diverse industrial applications. The structural feature of the loops connecting barrel helices contributes greatly to the differences in their functional characteristics. Inspired by the in-silico mutation with molecular dynamics (MD) simulation analysis, we propose a strategy for identifying disulfide bond mutation candidates based on the prediction of protein flexibility and residue-residue interaction. The most beneficial mutant with the newly introduced disulfide bond would simultaneously improve both its thermostability and its reaction propensity to the targeting isomerization product. The ratio of the isomerization/epimerization catalytic rate was improved from 4:103 to 9:22. MD simulation and binding free energy calculations were applied to provide insights into molecular recognition upon mutations. The comparative analysis of enzyme/substrate binding modes indicates that the altered catalytic reaction pathway is due to less efficient binding of the native product. The key residue responsible for the observed phenotype was identified by energy decomposition and was further confirmed by the mutation experiment. The rational design of the key loop region might be a promising strategy to alter the catalytic behavior of all (α/α)6-barrel-like proteins.

Computer-aided design of novel cellobiose 2-epimerase for efficient synthesis of lactulose using lactose

Cellobiose 2-epimerase (CE) is ideally suited to synthesize lactulose from lactose, but the poor thermostability and catalytic efficiency restrict enzymatic application. Herein, a non-characterized CE originating from Caldicellulosiruptor morganii (CmCE) was discovered in the NCBI database. Then, a smart mutation library was constructed based on FoldX ΔΔG calculation and modeling structure analysis, from which a positive mutant D226G located within the α₈/α₉ loop exhibited longer half-lives at 65-75 °C as well as lower K_m and higher k_cat/K_m values compared with CmCE. Molecular modeling demonstrated that the improvement of D226G was largely attributed to the rigidification of the flexible loop, the compactness of the catalysis pocket and the increment of substrate-binding capability. Finally, the yield of synthesizing lactulose catalyzed by D226G reached 45.5%, higher than the 35.9% achieved with CmCE. The disclosed effect of the flexible loop on enzymatic stability and catalysis provides insight to redesign efficient CEs to biosynthesize lactulose.

Lactulose production from lactose isomerization by chemo-catalysts and enzymes: Current status and future perspectives

Lactulose, a semisynthetic nondigestive disaccharide with versatile applications in the food and pharmaceutical industries, has received increasing interest due to its significant health-promoting effects. Currently, industrial lactulose production is exclusively carried out by chemical isomerization of lactose via the Lobry de Bruyn-Alberda van Ekenstein (LA) rearrangement, and much work has been directed toward improving the conversion efficiency in terms of lactulose yield and purity by using new chemo-catalysts and integrated catalytic-purification systems. Lactulose can also be produced by an enzymatic route offering a potentially greener alternative to chemo-catalysis with fewer side products. Compared to the controlled trans-galactosylation by β-galactosidase, directed isomerization of lactose with high isomerization efficiency catalyzed by the most efficient lactulose-producing enzyme, cellobiose 2-epimerase (CE), has gained much attention in recent decades. To further facilitate the industrial translation of CE-based lactulose biotransformation, numerous studies have been reported on improving biocatalytic performance through enzyme mediated molecular modification. This review summarizes recent developments in the chemical and enzymatic production of lactulose. Related catalytic mechanisms are also highlighted and described in detail. Emerging techniques that aimed at advancing lactulose production, such as the boronate affinity-based technique and molecular biological techniques, are reviewed. Finally, perspectives on challenges and opportunities in lactulose production and purification are also discussed.

Insight into the potential factors influencing the catalytic direction in cellobiose 2-epimerase by crystallization and mutagenesis

Cellobiose 2-epimerase (CE) is commonly recognized as an epimerase as most CEs mainly exhibit an epimerization activity towards disaccharides. In recent years, several CEs have been found to possess bifunctional epimerization and isomerization activities. They can convert lactose into lactulose, a high-value disaccharide that is widely used in the food and pharmaceutical industries. However, the factors that determine the catalytic direction in CEs are still not clear. In this study, the crystal structures of three newly discovered CEs, CsCE (a bifunctional CE from Caldicellulosiruptor saccharolyticus), StCE (a bifunctional CE from Spirochaeta thermophila DSM 6578) and BtCE (a monofunctional CE from Bacillus thermoamylovorans B4166), were determined at 1.54, 2.05 and 1.80 Å resolution, respectively, in order to search for structural clues to their monofunctional/bifunctional properties. A comparative analysis of the hydrogen-bond networks in the active pockets of diverse CEs, YihS and mannose isomerase suggested that the histidine corresponding to His188 in CsCE is uniquely required to catalyse isomerization. By alignment of the apo and ligand-bound structures of diverse CEs, it was found that bifunctional CEs tend to have more flexible loops and a larger entrance around the active site, and that the flexible loop 148-181 in CsCE displays obvious conformational changes during ligand binding. It was speculated that the reconstructed molecular interactions of the flexible loop during ligand binding helped to motivate the ligands to stretch in a manner beneficial for isomerization. Further site-directed mutagenesis analysis of the flexible loop in CsCE indicated that the residue composition of the flexible loop did not greatly impact epimerization but affects isomerization. In particular, V177D and I178D mutants showed a 50% and 80% increase in isomerization activity over the wild type. This study provides new information about the structural characteristics involved in the catalytic properties of CEs, which can be used to guide future molecular modifications.