Discovery,Biocatalytic Exploration and Structural Analysis of a 4-Ethylphenol Oxidase from Gulosibacter chungangensis

The vanillyl-alcohol oxidase (VAO) family is a rich source of biocatalysts for the oxidative bioconversion of phenolic compounds. Through genome mining and sequence comparisons, we found that several family members lack a generally conserved catalytic aspartate. This finding led us to study a VAO-homolog featuring a glutamate residue in place of the common aspartate. This 4-ethylphenol oxidase from Gulosibacter chungangensis (Gc4EO) shares 42 % sequence identity with VAO from Penicillium simplicissimum, contains the same 8α-N³-histidyl-bound FAD and uses oxygen as electron acceptor. However, Gc4EO features a distinct substrate scope and product specificity as it is primarily effective in the dehydrogenation of para-substituted phenols with little generation of hydroxylated products. The three-dimensional structure shows that the characteristic glutamate side chain creates a closely packed environment that may limit water accessibility and thereby protect from hydroxylation. With its high thermal stability, well defined structural properties and high expression yields, Gc4EO may become a catalyst of choice for the specific dehydrogenation of phenolic compounds bearing small substituents.     

Biocatalytic Potential of the Epoxide Hydrolase from Agrobacterium radiobacter AD1 and a Mutant with Enhanced Enantioselectivity

Optically pure epoxides are useful synthons for a variety of biologically active compounds. The epoxide hydrolase obtained from Agrobacterium radiobacter AD1 hydrolyses racemic aryl epoxides with moderate and aliphatic epoxides with low enantioselectivity. The three‐dimensional structure of this enzyme indicates that two tyrosine residues interact with the epoxide oxygen. Mutating one of these, tyrosine 215, to a phenylalanine (Y215F) resulted in an enzyme with increased enantioselectivity towards aryl epoxides. The relatively strong decrease in activity towards the remaining enantiomers makes this enzyme a much better biocatalyst than the wild‐type enzyme for the preparation of optically pure (S)‐styrene oxide derivatives.     

Insights into Sequence–Activity Relationships amongst Baeyer–Villiger Monooxygenases as Revealed by the Intragenomic Complement of Enzymes from Rhodococcus jostii RHA1

The Rhodococcus jostii RHA1 genome encodes a number of enzymes that can be exploited as biocatalysts. Study of the substrate spectrum and enantioselectivity of Baeyer–Villiger monooxygenases from R. jostii allowed the identification of short amino acid sequences specific to groups displaying certain catalytic characteristics. The gel illustrates the substrate acceptance spectra and selectivities of the different proteins.

     

Biocatalytic kinetic resolution of rac‐1‐phenylethanol and rac‐2‐pentanol in hexane medium: ACYL donor and water content effects

The kinetic resolutions of rac‐1‐phenylethanol and rac‐2‐pentanol by transesterification with vinyl esters catalysed by a commercial immobilised Candida antarctica lipase B were successfully carried out in hexane medium. This enzyme showed very high enantioselectivity for both substrates. The influence of the water content of the medium on the synthetic activity, selectivity and enantioselectivity of the enzyme was analysed, with the optimal amount of water about 100 ppm. Our results also showed that the activity per gram enzymatic derivate of CaLB was slightly higher with butyl butyrate as acyl donor.     

Structural and Catalytic Characterization of Pichia stipitis OYE 2.6, a Useful Biocatalyst for Asymmetric Alkene Reductions

We have probed Pichia stipitis CBS 6054 Old Yellow Enzyme 2.6 (OYE 2.6) by several strategies including X‐ray crystallography, ligand binding and catalytic assays using the wild‐type as well as libraries of site‐saturation mutants. The alkene reductase crystallized in space group P 6₃ 2 2 with unit cell dimensions of 127.1×123.4 Å and its structure was solved to 1.5 Å resolution by molecular replacement. The protein environment surrounding the flavin mononucleotide (FMN) cofactor was very similar to those of other OYE superfamily members; however, differences in the putative substrate binding site were also observed. Substrate analog complexes were analyzed by both UV‐Vis titration and X‐ray crystallography to provide information on possible substrate binding interactions. In addition, four active site residues were targeted for site saturation mutagenesis (Thr 35, Ile 113, His 188, His 191) and each library was tested against three representative Baylis–Hillman adducts. Thr 35 could be replaced by Ser with no change in activity; other amino acids (Ala, Cys, Leu, Met, Gln and Val) resulted in diminished catalytic efficiency. The Ile 113 replacement library yielded a range of catalytic activities, but had very little impact on stereoselectivity. Finally, the two His residues (188 and 191) were essentially intolerant of substitutions with the exception of the His 191 Asn mutant, which did show significant catalytic ability. Structural comparisons between OYE 2.6 and Saccharomyces pastorianus OYE1 suggest that the key interactions between the substrate hydroxymethyl groups and the side‐chain of Thr 35 and/or Tyr 78 play an important role in making OYE 2.6 an (S)‐selective alkene reductase.     

重组真菌腈水解酶的发酵工艺条件及生物催化特性初探【需加急】

对产真菌腈水解酶的重组大肠杆菌的培养基种类、培养基成分、诱导剂种类和浓度、诱导条件、p H和温度进行了系统考察。摇瓶发酵优化结果显示:以甘油作为主要碳源,蛋白胨和酵母膏作为主要氮源,并添加微量元素的SOC培养基作为发酵培养基,最适接种量为0.5%;较优的诱导剂诱导条件为:采用0.5 mmol/L的IPTG诱导12 h,发酵p H=7.5,诱导温度25℃时产酶效果最佳。经过优化后,重组酶的酶活得到了显著提高,总酶活最高达到了3.84 U/m L,相比初始水平(0.84 U/m L)提高约4倍。5 L发酵罐的放大实验表明,产酶效果良好,总酶活和比酶活均与摇瓶水平基本持平。全细胞催化性质考察研究结果表明,该菌株所产腈水解酶催化反应的最适催化反应温度是45℃,最适反应p H约为7.2。     

Biocatalytic and Structural Properties of a Highly Engineered Halohydrin Dehalogenase

Two highly engineered halohydrin dehalogenase variants were characterized in terms of their performance in dehalogenation and epoxide cyanolysis reactions. Both enzyme variants outperformed the wild‐type enzyme in the cyanolysis of ethyl (S)‐3,4‐epoxybutyrate, a conversion yielding ethyl (R)‐4‐cyano‐3‐hydroxybutyrate, an important chiral building block for statin synthesis. One of the enzyme variants, HheC2360, displayed catalytic rates for this cyanolysis reaction enhanced up to tenfold. Furthermore, the enantioselectivity of this variant was the opposite of that of the wild‐type enzyme, both for dehalogenation and for cyanolysis reactions. The 37‐fold mutant HheC2360 showed an increase in thermal stability of 8 °C relative to the wild‐type enzyme. Crystal structures of this enzyme were elucidated with chloride and ethyl (S)‐3,4‐epoxybutyrate or with ethyl (R)‐4‐cyano‐3‐hydroxybutyrate bound in the active site. The observed increase in temperature stability was explained in terms of a substantial increase in buried surface area relative to the wild‐type HheC, together with enhanced interfacial interactions between the subunits that form the tetramer. The structures also revealed that the substrate binding pocket was modified both by substitutions and by backbone movements in loops surrounding the active site. The observed changes in the mutant structures are partly governed by coupled mutations, some of which are necessary to remove steric clashes or to allow backbone movements to occur. The importance of interactions between substitutions suggests that efficient directed evolution strategies should allow for compensating and synergistic mutations during library design.     

Structural Characterization and Extended Substrate Scope Analysis of Two Mg2+-Dependent O-Methyltransferases from Bacteria**

Oxygen-directed methylation is a ubiquitous tailoring reaction in natural product pathways catalysed by O-methyltransferases (OMTs). Promiscuous OMT biocatalysts are thus a valuable asset in the toolkit for sustainable synthesis and optimization of known bioactive scaffolds for drug development. Here, we characterized the enzymatic properties and substrate scope of two bacterial OMTs from Desulforomonas acetoxidans and Streptomyces avermitilis and determined their crystal structures. Both OMTs methylated a wide range of catechol-like substrates, including flavonoids, coumarins, hydroxybenzoic acids, and their respective aldehydes, an anthraquinone and an indole. One enzyme also accepted a steroid. The product range included pharmaceutically relevant compounds such as (iso)fraxidin, iso(scopoletin), chrysoeriol, alizarin 1-methyl ether, and 2-methoxyestradiol. Interestingly, certain non-catechol flavonoids and hydroxybenzoic acids were also methylated. This study expands the knowledge on substrate preference and structural diversity of bacterial catechol OMTs and paves the way for their use in (combinatorial) pathway engineering.     

微囊藻毒素降解酶MlrA的结构功能分析

MlrA（亦称microcystinase）是微囊藻毒素（microcystins, MCs）细菌降解途径中负责催化起始反应的关键蛋白酶,其结构特征与底物水解机制尚未明确。使用折叠识别法构建MlrA分子模型,通过分子对接和定点突变分析了酶-底物的结合方式与相互作用,结合蛋白重组表达对酶活性影响机制等进行了探究。结果表明MlrA是定位于细菌细胞质膜的整合膜蛋白,主要由8个跨膜α-螺旋（TM1~8）组成,功能结构域ABI（TM4~7）形成向周质空间开放的底物反应空腔。MlrA催化残基（E172、H205、H260和N264）位于膜内,其侧链投射至反应腔内部。微囊藻毒素LR （MC-LR）采用β-发夹构型与酶结合并将易裂键暴露于水分子附近,其水解机制为E172和H205通过一般碱催化将水分子去质子化激活,对Adda-Arg肽键羰基碳进行亲核攻击;接着H260和N264构成氧阴离子穴以稳定过渡态氧阴离子;最后H205或E172催化胺离去基团发生质子化,使四面体氧阴离子中间体崩解。此外,MlrA不是金属蛋白酶,无法与金属离子（Ⅱ）配位结合,菲咯啉类化合物使酶分子发生非特异性解折叠而失活,EDTA对底物结合位点具有竞争作用。本研究揭示了MlrA的属性与水解机制,为进一步探索MCs微生物降解机理提供一定参考依据。     

Effect of Glycosylation on the Biocatalytic Properties of Hydroxynitrile Lyase from the Passion Fruit,Passiflora edulis: A Comparison of Natural and Recombinant Enzymes

A hydroxynitrile lyase from the passion fruit Passiflora edulis (PeHNL) was isolated from the leaves and showed high stability in biphasic co‐organic solvent systems for cyanohydrin synthesis. Cyanohydrins are important building blocks for the production of fine chemicals and pharmaceuticals. Thus, to enhance production yields of PeHNL for industrial applications, we cloned and expressed recombinant PeHNL in Escherichia coli BL21(DE3) and Pichia pastoris GS115 cells without a signal peptide sequence. The aim of this study is to determine the effect of N‐glycosylation on enzyme stability and catalytic properties in microbial expression systems. PeHNL from leaves (PeHNL‐N) and that expressed in P. pastoris (PeHNL‐P) were glycosylated, whereas that expressed in E. coli (PeHNL‐E) was not. The enzymes PeHNL‐N and PeHNL‐P showed much better thermostability, pH stability, and organic solvent tolerance than the deglycosylated enzyme PeHNL‐E and the deglycosylated mutant N105Q from P. pastoris (PeHNL‐P‐N105Q). The glycosylated PeHNL‐P also efficiently performed transcyanation of (R)‐mandelonitrile with a 98 % enantiomeric excess in a biphasic system with diisopropyl ether. These data demonstrate the efficacy of these methods for improving enzyme expression and stability for industrial application through N‐glycosylation.     

LICRED: A Versatile Drop‐In Vector for Rapid Generation of Redox‐Self‐Sufficient Cytochrome P450s

Cytochromes P450 (P450s) are a family of haem‐containing oxidases with considerable potential as tools for industrial biocatalysis. Organismal genomes are revealing thousands of gene sequences that encode P450s of as yet unknown function, the exploitation of which will require high‐throughput tools for their isolation and characterisation. In this report, a ligationindependent cloning vector “LICRED” is described that enables the high‐throughput generation of libraries of redox‐self‐sufficient P450s by fusing a range of P450 haem domains to the reductase of P450RhF (RhF‐Red) in a robust and generically applicable way. Cloning and expression of fusions of RhF‐Red with the haem domains of P450cam and P450‐XplA resulted in soluble, active, redox‐self‐sufficient, chimeric enzymes. In vitro studies also revealed that electron transfer from NADPH to haem was primarily intramolecular. The general applicability of the LICRED platform was then demonstrated through the creation of a library of RhF‐Red fusion constructs by using the diverse complement of P450 haem domains identified in the genome of Nocardia farcinica. The resultant fusion‐protein library was then screened against a panel of substrates; this revealed chimeric enzymes competent for the hydroxylation of testosterone and methyltestosterone, and the dealkylation of 7‐ethoxycoumarin.     

Rhodococcus sp. SHZ-1腈水合酶的诱导表达和稳定性研究

Inducing expression and the reaction characteristic of nitrile hydratase (NHase) from Rhodococcus sp.SHZ-1 were investigated. The results showed that the expression of NHase was greatly enhanced with the cooperation of acrylonitrile and ammonium chloride as inducer in the medium and the specific activity of NHase was increased of 44%. Then the temperature, pH, concentration of acrylonitrile and acrylamide were evaluated, which affected the activity and reaction characteristic of NHase. It was found that the temperature and concentration of acrylamide were the most important factors for the catalyzation of NHase. The optimal catalysis temperature of NHase from Rhodococcus sp. SHZ-1 was 30℃, and the activation energy of the hydration of NHase was 90.2kJ·mol-1 in the temperature range from 5℃ to 30℃. Km of NHase was 0.095mol.L-1 using acrylonitrile(AN)as substrate, and NHase activity was inhibited seriously when acrylonitrile concentration was up to 40g·L-1, the substrate inhibition constant Ki is 0.283mol·L-1. Moreover, the NHase from Rhodococcus sp. SHZ-1 had very strong tolerance to acrylamide, in which the final concentration of acrylamide reached to 642g·L-1 and the residual activity of NHase still maintained 8.6% of the initial enzyme activity.     

BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic Experiments

The development of novel enzymes for biocatalytic processes requires knowledge on substrate profile and selectivity; this can be derived from databases and from publications. Often, these sources lack time‐course data for the substrate or product, and an unambiguous link between experiment and enzyme sequence. The lack of integrated, original data hampers the comprehensive analysis of enzyme kinetics and the evaluation of sequence–function relationships. In order to accelerate enzyme engineering, BioCatNet integrates protein sequence, protein structure, and experimental data for a given enzyme family. BioCatNet explicitly assigns the enzyme sequence to the experimental data, which consists of information on reaction conditions and time‐course data. BioCatNet facilitates the consistent documentation of reaction conditions, the archiving of time‐course data, and the efficient exchange of experimental data among collaborators. Data integration is demonstrated for three case studies by using the TEED (Thiamine diphosphate‐dependent Enzymes Engineering Database).     

Diphenylene Iodonium Is a Noncovalent MAO Inhibitor: A Biochemical and Structural Analysis

Diphenylene iodonium (DPI) is known for its inhibitory activities against many flavin- and heme-dependent enzymes, and is often used as an NADPH oxidase inhibitor. We probed the efficacy of DPI on two well-known drug targets, the human monoamine oxidases MAO A and B. UV-visible spectrophotometry and steady-state kinetics experiments demonstrate that DPI acts as a competitive and reversible MAO inhibitor with K_i values of 1.7 and 0.3 μM for MAO A and MAO B, respectively. Elucidation of the crystal structure of human MAO B bound to the inhibitor revealed that DPI binds deeply in the active-site cavity to establish multiple hydrophobic interactions with the surrounding side chains and the flavin. These data prove that DPI is a genuine MAO inhibitor and that the inhibition mechanism does not involve a reaction with the reduced flavin. This binding and inhibitory activity against the MAOs, two major reactive oxygen species (ROS)-producing enzymes, will have to be carefully considered when interpreting experiments that rely on DPI for target validation and chemical biology studies on ROS functions.     

Catalytic and Spectroscopic Properties of the Halotolerant Soluble Methane Monooxygenase Reductase from Methylomonas methanica MC09

The soluble methane monooxygenase receives electrons from NADH via its reductase MmoC for oxidation of methane, which is itself an attractive C1 building block for a future bioeconomy. Herein, we present biochemical and spectroscopic insights into the reductase from the marine methanotroph Methylomonas methanica MC09. The presence of a flavin adenine dinucleotide (FAD) and [2Fe2S] cluster as its prosthetic group were revealed by reconstitution experiments, iron determination and electron paramagnetic resonance spectroscopy. As a true halotolerant enzyme, MmoC still showed 50 % of its specific activity at 2 M NaCl. We show that MmoC produces only trace amounts of superoxide, but mainly hydrogen peroxide during uncoupled turnover reactions. The characterization of a highly active reductase is an important step for future biotechnological applications of a halotolerant sMMO.     

Kinetic Resolution of α‐Bromoamides: Experimental and Theoretical Investigation of Highly Enantioselective Reactions Catalyzed by Haloalkane Dehalogenases

Haloalkane dehalogenases from five sources were heterologously expressed in Escherichia coli, isolated, and tested for their ability to achieve kinetic resolution of racemic α‐bromoamides, which are important intermediates used in the preparation of bioactive compounds. To explore the substrate scope, fourteen α‐bromoamides, with different Cα‐ and N‐substituents, were synthesized. Catalytic activity towards eight substrates was found, and for five of these compounds the conversion proceeded with a high enantioselectivity (E value >200). In all cases, the (R)‐α‐bromoamide is the preferred substrate. Conversions on a preparative scale with a catalytic amount of enzyme (enzyme:substrate ratio less 1:50 w/w) were all completed within 17–46 h and optically pure α‐bromoamides and α‐hydroxyamides were isolated with good yields (31–50%). Substrate docking followed by molecular dynamics simulations indicated that the high enantioselectivity results from differences in the percentage of the time in which the substrate enantiomers are bound favourably for catalysis. For the preferred (R)‐substrates, the angle between the attacking aspartate oxygen atom of the enzyme, the attacked carbon atom of the substrate, and the displaced halogen atom, is more often in the optimal range (>157°) for reactivity. This can explain the observed enantioselectivity of LinB dehalogenase in a kinetic resolution experiment.     

Screening,Molecular Cloning,and Biochemical Characterization of an Alcohol Dehydrogenase from Pichia pastoris Useful for the Kinetic Resolution of a Racemic β‐Hydroxy‐β‐trifluoromethyl Ketone

The stereoselective synthesis of chiral 1,3‐diols with the aid of biocatalysts is an attractive tool in organic chemistry. Besides the reduction of diketones, an alternative approach consists of the stereoselective reduction of β‐hydroxy ketones (aldols). Thus, we screened for an alcohol dehydrogenase (ADH) that would selectively reduce a β‐hydroxy‐β‐trifluoromethyl ketone. One potential starting material for this process is readily available by aldol addition of acetone to 2,2,2‐trifluoroacetophenone. Over 200 strains were screened, and only a few yeast strains showed stereoselective reduction activities. The enzyme responsible for the reduction of the β‐hydroxy‐β‐trifluoromethyl ketone was identified after purification and subsequent MALDI‐TOF mass spectrometric analysis. As a result, a new NADP⁺‐dependent ADH from Pichia pastoris (PPADH) was identified and confirmed to be capable of stereospecific and diastereoselective reduction of the β‐hydroxy‐β‐trifluoromethyl ketone to its corresponding 1,3‐diol. The gene encoding PPADH was cloned and heterologously expressed in Escherichia coli BL21(DE3). To determine the influence of an N‐ or C‐terminal His‐tag fusion, three different recombinant plasmids were constructed. Interestingly, the variant with the N‐terminal His‐tag showed the highest activity; consequently, this variant was purified and characterized. Kinetic parameters and the dependency of activity on pH and temperature were determined. PPADH shows a substrate preference for the reduction of linear and branched aliphatic aldehydes. Surprisingly, the enzyme shows no comparable activity towards ketones other than the β‐hydroxy‐β‐trifluoromethyl ketone.