Discovery, characterization and mechanism of a Microbacterium esterase for key d-biotin chiral intermediate synthesis.

Esterases are crucial biocatalysts in chiral compound synthesis. Herein, a novel esterase EstSIT01 belonging to family V was identified from Microbacterium chocolatum SIT101 through genome mining and phylogenetic analysis. EstSIT01 demonstrated remarkable efficiency in asymmetrically hydrolyzing meso-dimethyl ester [Dimethyl cis-1,3-Dibenzyl-2-imidazolidine-4,5-dicarboxyate], producing over 99% yield and 99% enantiomeric excess (e.e.) for (4S, 5R)-monomethyl ester, a crucial chiral intermediate during the synthesis of d-biotin. Notably, the recombinant E. coli expressing EstSIT01 exhibited over 40-fold higher activity than that of the wild strain. EstSIT01 displays a preference for short-chain p-NP esters. The optimal temperature and pH were 45 °C and 10.0, with Km and kcat values of 0.147 mmol/L and 5.808 s- 1, respectively. Molecular docking and MD simulations suggest that the high stereoselectivity for meso-diester may attribute to the narrow entrance tunnel and unique binding pocket structure. Collectively, EstSIT01 holds great potential for preparing chiral carboxylic acids and esters.

Structural Insights of a cis-Epoxysuccinate Hydrolase Facilitate the Development of Robust Biocatalysts for the Production of l-(+)-Tartrate.

l-(+)-Tartaric acid plays important roles in various industries, including pharmaceuticals, foods, and chemicals. cis-Epoxysuccinate hydrolases (CESHs) are crucial for converting cis-epoxysuccinate to l-(+)-tartrate in the industrial production process. There is, however, a lack of detailed structural and mechanistic information on CESHs, limiting the discovery and engineering of these industrially relevant enzymes. In this study, we report the crystal structures of RoCESH and KoCESH-l-(+)-tartrate complex. These structures reveal the key amino acids of the active pocket and the catalytic triad residues and elucidate a dynamic catalytic process involving conformational changes of the active site. Leveraging the structural insights, we identified a robust BmCESH (550 ± 20 U·mg-1) with sustained catalytic activity even at a 3 M substrate concentration. After six batches of transformation, immobilized cells with overexpressed BmCESH maintained 69% of their initial activity, affording an overall productivity of 200 g/L/h. These results provide valuable insights into the development of high-efficiency CESHs and the optimization of biotransformation processes for industrial uses.

Engineering the Substrate Specificity of a P450 Dimerase Enables the Collective Biosynthesis of Heterodimeric Tryptophan-Containing Diketopiperazines.

Heterodimeric tryptophan-containing diketopiperazines (HTDKPs) are an important class of bioactive secondary metabolites. Biosynthesis offers a practical opportunity to access their bioactive structural diversity, however, it is restricted by the limited substrate scopes of the HTDKPs-forming P450 dimerases. Herein, by genome mining and investigation of the sequence-product relationships, we unveiled three important residues (F387, F388 and E73) in these P450s that are pivotal for selecting different diketopiperazine (DKP) substrates in the upper binding pocket. Engineering these residues in NasF5053 significantly expanded its substrate specificity and enabled the collective biosynthesis, including 12 self-dimerized and at least 81 cross-dimerized HTDKPs. Structural and molecular dynamics analysis of F387G and E73S revealed that they control the substrate specificity via reducing steric hindrance and regulating substrate tunnels, respectively.

Facile immobilization of his-tagged Microbacterial esterase on Ni-SBA-15 with enhanced stability for efficient synthesis of key chiral intermediate of d-biotin.

A series of nickel-incorporated SBA-15 mesoporous molecular sieves (Ni-SBA-15) were prepared as support for the immobilization of his-tagged recombinant Microbacterium esterase. The Ni-SBA-15 could strongly and specific absorb the his-tagged esterase from cell disrupted supernatant. It was found that the nickel amount in Ni-SBA-15 has dramatic influence on the activity and thermo-stability of immobilized enzyme, while the kinds of nickel precursor had little effect on enzyme stability. The morphology, chemical composition and structure of the best support NiCl2-SBA-15 (Ni-SBA-15 prepared from NiCl2 precursor) were characterized by various spectroscopy techniques. The immobilized esterase retained full activity of free esterase and showed high immobilized yield (> 90%) with higher thermo-stability, pH stability and organic solvent resistance compared with free enzyme. The optimum reaction temperature increased from 35 to 40 °C and the optimal reaction pH moved from 10.0 to 8.0 after enzyme immobilization. The immobilized esterase exhibited excellent storage stability and keeping 92% of the initial activity after 30 days' storage at 25 °C. In addition, the immobilized esterase had excellent reusability for the synthesis of key chiral intermediate of d-biotin and the substrate conversion could still keep 100% after 13 cycles continuously. Finally, optical pure (4S, 5R)-hemiester was obtained in 80.8% isolated yield and 99% purity in the gram preparative scale.

High specific immobilization of His-tagged recombinant Microbacterium esterase by Ni-NTA magnetic chitosan microspheres for efficient synthesis of key chiral intermediate of d-biotin.

The novel Ni-NTA-functionalized magnetic chitosan microspheres (MCS-NTA-Ni) were prepared via amino functionalization of MCS with epichlorohydrin and ethylenediamine, followed by the introduction of the aldehyde groups and NTA in turn, and nickel (II) ions were chelated in the end. MCS-NTA-Ni contained numerous long-armed NTA-Ni surface groups, ensuring high enzyme loading and providing more space and flexibility to attach enzymes and maintain their activity. This microsphere can have highly selective adsorption of his-tagged recombinant protein. The his-tagged recombinant Microbacterium esterase of E. coli BL21 (DE3)/pET21a-EstSIT01 was first immobilized on MCS-NTA-Ni by affinity fixation, giving high immobilization yield (90.1%) and enzyme loading (120 mg/g). Compared with free esterase, the immobilized esterase was found to exhibit higher pH stability and thermal stability. In addition, the immobilized esterase had excellent reusability for the synthesis of key chiral intermediate of d-biotin and the substrate conversion could still keep 100% after 8 cycles continuously.

Efficient Biosynthesis of Vanillin from Isoeugenol by Recombinant Isoeugenol Monooxygenase from Pseudomonas nitroreducens Jin1.

Currently, the biotechnological preparation of fragrances using natural materials attracted growing attention. Enzymatic synthesis of vanillin from isoeugenol by recombinant isoeugenol monooxygenase from Pseudomonas nitroreducens Jin1 was systematically investigated herein. With series of work on the construction of recombinant E. coli over-expressing isoeugenol monooxygenase, optimization of the culture conditions for enzyme production and reaction process for converting isoeugenol into vanillin, an increase of 22-fold in the enzyme activity (2050 U/L) was obtained, and the conversion was significantly increased at high substrate concentration with the aid of magnetic chitosan membrane for product isolation in situ. Under optimal conditions, the product concentration and space-time yield reached 252 mM and 115 g/L/d, respectively, and vanillin was obtained in 82.3% yield and > 99% purity in the gram preparative scale. The developed bioprocess showed application potential for efficient preparation of vanillin from inexpensive natural resources.

Efficient synthesis of Ibrutinib chiral intermediate in high space-time yield by recombinant E. coli co-expressing alcohol dehydrogenase and glucose dehydrogenase.

The production of (S)-N-boc-3-hydroxy piperidine (NBHP) via asymmetric bioreduction of 1-boc-3-piperidinone with reductase is impeded by the need for expensive coenzymes NAD(P)H. In order to regenerate the coenzyme in situ, the gene of alcohol dehydrogenase from Thermoanaerobacter brockii and glucose dehydrogenase from Bacillus subtilis were ligated into the multiple cloning sites of pRSFDuet-1 plasmid to construct the recombinant Escherichia BL21 (DE3) that co-expressing alcohol dehydrogenase and glucose dehydrogenase. Different culture conditions including the medium composition, inducer and pH etc were systematically investigated to improve the enzyme production. The enzyme activity was increased more than 11-fold under optimal culture condition, from 12.7 to 139.8 U L-1. In the further work, the asymmetric reduction of 1-boc-3-piperidinone by whole cells of recombinant E. coli was systematic optimized to increase the substrate concentration and reaction efficiency. At last, S-NBHP (>99% ee) was prepared at 500 mM substrate concentration without external addition of cofactors. The conversion of S-NBHP reached 96.2% within merely 3 h, corresponding a high space-time yield around 774 g L-1 d-1. All these results demonstrated the potential of recombinant E. coli BL21 (DE3) coupled expressing alcohol dehydrogenase and glucose dehydrogenase for efficient synthesis of S-NBHP.

Efficient Biocatalytic Synthesis of Chiral Chemicals.

Chiral chemicals are a group of important chiral synthons for the synthesis of a series of pharmaceuticals, agrochemicals, and fine chemicals. In past decades, a number of biocatalytic approaches have been developed for the green and effective synthesis of various chiral chemicals. However, the practical application of these biocatalytic processes is still hindered by the lack of highly efficient and robust biocatalysts, which usually results in the low volumetric productivity and high cost of the bioprocesses. Further step forward of biocatalysis in industrial application strongly requires the development of versatile and highly efficient biocatalysts, aiming to increase the process efficiency and facilitate the downstream processing. Recently, the fast growth of genome sequences in the database in post-genomic era offers great opportunities for accessing numerous biocatalysts with practical application potential, and the so-called genome mining approach provides time-effective and highly specific strategy for the fast identification of target enzymes with desired properties and outperforms the traditional screening of soil samples for microbial enzyme producers of interest. A number of biocatalytic processes with industrial application potential were developed thereafter. Further development of protein engineering strategies, process optimization, and cooperative work between biologists, organic chemists, and engineers is expected to make biocatalysis technology the first choice approach for the eco-friendly, highly efficient, and cost-effective synthesis of chiral chemicals in the near future.

A novel D-mandelate dehydrogenase used in three-enzyme cascade reaction for highly efficient synthesis of non-natural chiral amino acids.

A novel NAD(+)-dependent D-mandelate dehydrogenase was identified from Lactobacillus brevis (LbDMDH). After purified to homogeneity, the optimum pH and temperature for oxidation of D-mandelate were pH 10.0 and 40 °C, and the Km and kcat were 1.1 mM and 355 s(-1) respectively. Employing the LbDMDH together with a mandelate racemase from Pseudomonas putida and a leucine dehydrogenase (EsLeuDH) from Exiguobacterium sibiricum, we established a three-step one-pot domino reaction system for preparing chiral L-phenylglycine from racemic mandelic acid with internal cofactor recycling. Under the optimum conditions, 30.4 g rac-mandelic acid (0.2 M) at 1L scale had been converted into chiral L-phenylglycine, with 96.4% conversion, 86.5% isolation yield, >99% eep and 50.4 gL(-1)d(-1) space-time yield.

Crystal structures of Pseudomonas putida esterase reveal the functional role of residues 187 and 287 in substrate binding and chiral recognition.

A recombinant carboxylesterase (rPPE) from Pseudomonas putida ECU1011 was previously cloned and engineered to give a potential application for resolving chiral α-hydroxy acids including mandelic acids and derivatives. Two variants rPPEW187H and rPPED287A showed a ∼100-fold increase in activity towards rac-2-acetoxy-2-(2'-chlorophenyl) acetate (rac-AcO-CPA), but rPPED287A had a significant decrease in enantioselectivity (E=8.7) compared to rPPEW187H and the wild-type rPPE (rPPEWT) (E>200). Here we report the crystal structures of rPPEWT and rPPEW187H, both by themselves and in complex with the substrate, to elucidate the structural basis of this phenomenon. An inactive mutation of nucleophile residue S159A was introduced to obtain the structure of rPPES159A/W187H complexed with (S)-AcO-CPA. The structural analysis reveals that the side chain of residue Asp287 in rPPEWT would have a potential steric conflict with (S)-AcO-CPA when the substrate binds at the active site of the enzyme. However, the mutation W187H could facilitate the relocation of Asp287, while D287A directly eliminates the hindrance of Asp287, both of which offer sufficient space for the binding and hydrolysis of substrate. Moreover, Asp287 generates one site of the "three-point attachment model" as a hydrogen-bond donor that determines the excellent enantioselectivity of rPPE in chiral recognition, and D287A would obviously destroy the hydrogen bond and result in the low enantioselectivity of rPPED287A.

A thermostable and organic-solvent tolerant esterase from Pseudomonas putida ECU1011: catalytic properties and performance in kinetic resolution of α-hydroxy acids.

A novel esterase, rPPE01, from Pseudomonas putida ECU1011 was heterologously expressed in Escherichia coli and identified for enzymatic resolution of hydroxy acids via O-deacetylation. α-Acetoxy carboxylates were converted with approximately 50% yield and excellent enantioselectivity (E>200) at a substrate concentration of 100 mM. The half-lives of rPPE01 were 14 days at 50°C and 30 days at 30°C, indicating the enzyme has relatively high thermostability. Another remarkable advantage of rPPE01 is that both the activity and thermostability were enhanced significantly in the presence of hydrophobic alkanes and ethers. rPPE01 retained 159% of its initial activity after incubation with 50% (v/v) n-heptane at 30°C for 60 days. The attractive organic-solvent tolerance, good thermostability and high enantioselectivity towards α-acetoxy carboxylates endow rPPE01 with the potential of practical application for the production of enantiopure hydroxy acids.