Structure and Biocatalytic Scope of Coclaurine N‐Methyltransferase

Benzylisoquinoline alkaloids (BIAs) are a structurally diverse family of plant secondary metabolites, which have been exploited to develop analgesics, antibiotics, antitumor agents, and other therapeutic agents. Biosynthesis of BIAs proceeds via a common pathway from tyrosine to (S)‐reticulene at which point the pathway diverges. Coclaurine N‐methyltransferase (CNMT) is a key enzyme in the pathway to (S)‐reticulene, installing the N‐methyl substituent that is essential for the bioactivity of many BIAs. In this paper, we describe the first crystal structure of CNMT which, along with mutagenesis studies, defines the enzymes active site architecture. The specificity of CNMT was also explored with a range of natural and synthetic substrates as well as co‐factor analogues. Knowledge from this study could be used to generate improved CNMT variants required to produce BIAs or synthetic derivatives.     

A Synthetic Adenylation‐Domain‐Based tRNA‐Aminoacylation Catalyst

The incorporation of non‐proteinogenic amino acids represents a major challenge for the creation of functionalized proteins. The ribosomal pathway is limited to the 20–22 proteinogenic amino acids while nonribosomal peptide synthetases (NRPSs) are able to select from hundreds of different monomers. Introduced herein is a fusion‐protein‐based design for synthetic tRNA‐aminoacylation catalysts based on combining NRPS adenylation domains and a small eukaryotic tRNA‐binding domain (Arc1p‐C). Using rational design, guided by structural insights and molecular modeling, the adenylation domain PheA was fused with Arc1p‐C using flexible linkers and achieved tRNA‐aminoacylation with both proteinogenic and non‐proteinogenic amino acids. The resulting aminoacyl‐tRNAs were functionally validated and the catalysts showed broad substrate specificity towards the acceptor tRNA. Our strategy shows how functional tRNA‐aminoacylation catalysts can be created for bridging the ribosomal and nonribosomal worlds. This opens up new avenues for the aminoacylation of tRNAs with functional non‐proteinogenic amino acids.     

Inverting the Regioselectivity of the Berberine Bridge Enzyme by Employing Customized Fluorine‐Containing Substrates

Fluorine is commonly applied in pharmaceuticals to block the degradation of bioactive compounds at a specific site of the molecule. Blocking of the reaction center of the enzyme‐catalyzed ring closure of 1,2,3,4‐tetrahydrobenzylisoquinolines by a fluoro moiety allowed redirecting the berberine bridge enzyme (BBE)‐catalyzed transformation of these compounds to give the formation of an alternative regioisomeric product namely 11‐hydroxy‐functionalized tetrahydroprotoberberines instead of the commonly formed 9‐hydroxy‐functionalized products. Alternative strategies to change the regioselectivity of the enzyme, such as protein engineering, were not applicable in this special case due to missing substrate–enzyme interactions. Medium engineering, as another possible strategy, had clear influence on the regioselectivity of the reaction pathway, but did not lead to perfect selectivity. Thus, only substrate tuning by introducing a fluoro moiety at one potential reactive carbon center switched the reaction to the formation of exclusively one regioisomer with perfect enantioselectivity.     

Enzymatic Synthesis of Acylphloroglucinol 3‐C‐Glucosides from 2‐O‐Glucosides using a C‐Glycosyltransferase from Mangifera indica

A green and cost‐effective process for the convenient synthesis of acylphloroglucinol 3‐C‐glucosides from 2‐O‐glucosides was exploited using a novel C‐glycosyltransferase (MiCGTb) from Mangifera indica. Compared with previously characterized CGTs, MiCGTb exhibited unique de‐O‐glucosylation promiscuity and high regioselectivity toward structurally diverse 2‐O‐glucosides of acylphloroglucinol and achieved high yields of C‐glucosides even with a catalytic amount of uridine 5′‐diphosphate (UDP). These findings demonstrate for the first time the significant potential of a single‐enzyme approach to the synthesis of bioactive C‐glucosides from both natural and unnatural acylphloroglucinol 2‐O‐glucosides.     

Identification of HcgC as a SAM‐Dependent Pyridinol Methyltransferase in [Fe]‐Hydrogenase Cofactor Biosynthesis

Previous retrosynthetic and isotope‐labeling studies have indicated that biosynthesis of the iron guanylylpyridinol (FeGP) cofactor of [Fe]‐hydrogenase requires a methyltransferase. This hypothetical enzyme covalently attaches the methyl group at the 3‐position of the pyridinol ring. We describe the identification of HcgC, a gene product of the hcgA‐G cluster responsible for FeGP cofactor biosynthesis. It acts as an S‐adenosylmethionine (SAM)‐dependent methyltransferase, based on the crystal structures of HcgC and the HcgC/SAM and HcgC/S‐adenosylhomocysteine (SAH) complexes. The pyridinol substrate, 6‐carboxymethyl‐5‐methyl‐4‐hydroxy‐2‐pyridinol, was predicted based on properties of the conserved binding pocket and substrate docking simulations. For verification, the assumed substrate was synthesized and used in a kinetic assay. Mass spectrometry and NMR analysis revealed 6‐carboxymethyl‐3,5‐dimethyl‐4‐hydroxy‐2‐pyridinol as the reaction product, which confirmed the function of HcgC.     

A Self‐Sacrificing N‐Methyltransferase Is the Precursor of the Fungal Natural Product Omphalotin

Research on ribosomally synthesized and posttranslationally modified peptides (RiPPs) has led to an increasing understanding of biosynthetic mechanisms, mostly drawn from bacterial examples. In contrast, reports on RiPPs from fungal producers, apart from the amanitins and phalloidins, are still scarce. The fungal cyclopeptide omphalotin A carries multiple N‐methylations on the peptide backbone, a modification previously known only from nonribosomal peptides. Mining the genome of the omphalotin‐producing fungus for a precursor peptide led to the identification of two biosynthesis genes, one encoding a methyltransferase OphMA that catalyzes the automethylation of its C‐terminus, which is then released and cyclized by the protease OphP. Our findings suggest a novel biosynthesis mechanism for a RiPP in which a modifying enzyme bears its own precursor peptide.     

Investigation of Alkyne Regioselectivity in the Ni‐Catalyzed Benzannulation of Cyclobutenones

A Ni‐catalyzed benzannulation reaction of cyclobutenones and alkynes provides a rapid synthesis of heavily substituted phenols. The regioselectivity of this reaction can be modulated by variation of substituents on the alkyne. Though the incorporation of Lewis basic donors provides modest selectivities, the use of aryl substituents can provide high levels of regiocontrol. Finally, alkynylboronates derived from alkyl‐substituted acetylenes provide both high yields and regioselectivities. This study suggests that alkynes bearing one sp²‐ and one sp³‐based substituent can undergo benzannulation with high levels of regiocontrol whereby the sp³‐based group is incorporated ortho‐to the phenolic OH.     

Donor Promiscuity of a Thermostable Transketolase by Directed Evolution: Efficient Complementation of 1‐Deoxy‐d‐xylulose‐5‐phosphate Synthase Activity

Enzymes catalyzing asymmetric carboligation reactions typically show very high substrate specificity for their nucleophilic donor substrate components. Structure‐guided engineering of the thermostable transketolase from Geobacillus stearothermophilus by directed in vitro evolution yielded new enzyme variants that are able to utilize pyruvate and higher aliphatic homologues as nucleophilic components for acyl transfer instead of the natural polyhydroxylated ketose phosphates or hydroxypyruvate. The single mutant H102T proved the best hit toward 3‐methyl‐2‐oxobutyrate as donor, while the double variant H102L/H474S showed highest catalytic efficiency toward pyruvate as donor. The latter variant was able to complement the auxotrophic deficiency of Escherichia coli cells arising from a deletion of the dxs gene, which encodes for activity of the first committed step into the terpenoid biosynthesis, offering the chance to employ a growth selection test for further enzyme optimization.     

The Interplay between a Multifunctional Dehydratase Domain and a C‐Methyltransferase Effects Olefin Shift in Ambruticin Biosynthesis

The olefin shift is an important modification during polyketide biosynthesis. Particularly for type I cis‐AT PKS, little information has been gained on the enzymatic mechanisms involved. We present our in vitro investigations on the olefin shift occurring during ambruticin biosynthesis. The unique, multifunctional domain AmbDH4 catalyzes consecutive dehydration, epimerization, and enoyl isomerization. The resulting 3‐enethioate is removed from the equilibrium by α‐methylation catalyzed by the highly specific C‐methyltransferase AmbM. This thermodynamically unfavorable overall process is enabled by the high, concerted substrate specificity of the involved enzymes. AmbDH4 shows close relationship to DH domains and initial mechanistic studies suggest that the olefin shift occurs via a similar proton‐shuttling mechanism as previously described for EI domains from trans‐AT‐PKS.     

Solvent Choice and Kinetic Isotope Effects (KIEs) Dramatically Alter Regioselectivity in the Directed ortho Metalation (DoM) of 1,5‐Dichloro‐2,4‐dimethoxybenzene

The regioselective formation of the 6‐lithio derivative of 1,5‐dichloro‐2,4‐dimethoxybenzene (i.e., 12 ) by directed ortho metalation (DoM) with nBuLi in THF is described. Although literature reports suggest direct deprotonation at C6, a series of time‐course and labelling studies has revealed that deprotonation rather occurs exclusively at C3 followed by isomerization of the anion to C6. By contrast, when DoM was performed in Et₂O, deprotonation again occurred selectively at C3, but now no isomerization occurs, and electrophilic capture produces the regioisomer of that produced in THF. In these labeling studies, it has been found that deuterium has an enormous kinetic isotope effect (KIE) that suppresses not only the original DoM reaction at C3 when deuterium is present there, but also suppresses isomerization to C6 when the label is at that site. Remarkably, this “protecting‐group” role of the deuterium is unique to THF; in ether, full deprotonation of the deuterium at C3 was observed.     

Gram‐Scale Synthesis of Chiral Cyclopropane‐Containing Drugs and Drug Precursors with Engineered Myoglobin Catalysts Featuring Complementary Stereoselectivity

Engineered hemoproteins have recently emerged as promising systems for promoting asymmetric cyclopropanations, but variants featuring predictable, complementary stereoselectivity in these reactions have remained elusive. In this study, a rationally driven strategy was implemented and applied to engineer myoglobin variants capable of providing access to 1‐carboxy‐2‐aryl‐cyclopropanes with high trans‐(1R,2R) selectivity and catalytic activity. The stereoselectivity of these cyclopropanation biocatalysts complements that of trans‐(1S,2S)‐selective variants developed here and previously. In combination with whole‐cell biotransformations, these stereocomplementary biocatalysts enabled the multigram synthesis of the chiral cyclopropane core of four drugs (Tranylcypromine, Tasimelteon, Ticagrelor, and a TRPV1 inhibitor) in high yield and with excellent diastereo‐ and enantioselectivity (98–99.9% de; 96–99.9% ee). These biocatalytic strategies outperform currently available methods to produce these drugs.     

A Hybrid Ring‐Opening Metathesis Polymerization Catalyst Based on an Engineered Variant of the β‐Barrel Protein FhuA

A β‐barrel protein hybrid catalyst was prepared by covalently anchoring a Grubbs–Hoveyda type olefin metathesis catalyst at a single accessible cysteine amino acid in the barrel interior of a variant of β‐barrel transmembrane protein ferric hydroxamate uptake protein component A (FhuA). Activity of this hybrid catalyst type was demonstrated by ring‐opening metathesis polymerization of a 7‐oxanorbornene derivative in aqueous solution.     

NMR Studies of Active‐Site Properties of Human Carbonic Anhydrase II by Using 15N‐Labeled 4‐Methylimidazole as a Local Probe and Histidine Hydrogen‐Bond Correlations

By using a combination of liquid and solid‐state NMR spectroscopy, ¹⁵N‐labeled 4‐methylimidazole (4‐MI) as a local probe of the environment has been studied: 1) in the polar, wet Freon CDF₃/CDF₂Cl down to 130 K, 2) in water at pH 12, and 3) in solid samples of the mutant H64A of human carbonic anhydrase II (HCA II). In the latter, the active‐site His64 residue is replaced by alanine; the catalytic activity is, however, rescued by the presence of 4‐MI. For the Freon solution, it is demonstrated that addition of water molecules not only catalyzes proton tautomerism but also lifts its quasidegeneracy. The possible hydrogen‐bond clusters formed and the mechanism of the tautomerism are discussed. Information about the imidazole hydrogen‐bond geometries is obtained by establishing a correlation between published ¹H and ¹⁵N chemical shifts of the imidazole rings of histidines in proteins. This correlation is useful to distinguish histidines embedded in the interior of proteins and those at the surface, embedded in water. Moreover, evidence is obtained that the hydrogen‐bond geometries of His64 in the active site of HCA II and of 4‐MI in H64A HCA II are similar. Finally, the degeneracy of the rapid tautomerism of the neutral imidazole ring His64 reported by Shimahara et al. (J. Biol. Chem.­ 2007 , 282, 9646) can be explained with a wet, polar, nonaqueous active‐site conformation in the inward conformation, similar to the properties of 4‐MI in the Freon solution. The biological implications for the enzyme mechanism are discussed.     

Engineering the Donor Selectivity of D‐Fructose‐6‐Phosphate Aldolase for Biocatalytic Asymmetric Cross‐Aldol Additions of Glycolaldehyde

D ‐Fructose‐6‐phosphate aldolase (FSA) is a unique catalyst for asymmetric cross‐aldol additions of glycolaldehyde. A combination of a structure‐guided approach of saturation mutagenesis, site‐directed mutagenesis, and computational modeling was applied to construct a set of FSA variants that improved the catalytic efficiency towards glycolaldehyde dimerization up to 1800‐fold. A combination of mutations in positions L107, A129, and A165 provided a toolbox of FSA variants that expand the synthetic possibilities towards the preparation of aldose‐like carbohydrate compounds. The new FSA variants were applied as highly efficient catalysts for cross‐aldol additions of glycolaldehyde to N‐carbobenzyloxyaminoaldehydes to furnish between 80–98 % aldol adduct under optimized reaction conditions. Donor competition experiments showed high selectivity for glycolaldehyde relative to dihydroxyacetone or hydroxyacetone. These results demonstrate the exceptional malleability of the active site in FSA, which can be remodeled to accept a wide spectrum of donor and acceptor substrates with high efficiency and selectivity.     

Unraveling the Mechanism and Regioselectivity of the B12‐Dependent Reductive Dehalogenase PceA

PceA is a cobalamin‐dependent reductive dehalogenase that catalyzes the dechlorination of perchloroethylene to trichloroethylene and then to cis‐dichloroethylene as the sole final product. The reaction mechanism and the regioselectivity of this enzyme are investigated by using density functional calculations. Four different substrates, namely, perchloroethylene, trichloroethylene, cis‐dichloroethylene, and chlorotheylene, have been considered and were found to follow the same reaction mechanism pattern. The reaction starts with the reduction of Co^II to Co^I through a proton‐coupled electron transfer process, with the proton delivered to a Tyr246 anion. This is followed by concerted C?Cl bond heterolytic cleavage and proton transfer from Tyr246 to the substrate carbon atom, generating a Co^III?Cl intermediate. Subsequently, a one‐electron transfer leads to the formation of the Co^II?Cl product, from which the chloride and the dehalogenated product can be released from the active site. The substrate reactivity follows the trend perchloroethylene>trichloroethylene?cis‐dichloroethylene?chlorotheylene. The barriers for the latter two substrates are significantly higher compared with those for perchloroethylene and trichloroethylene, implying that PceA does not catalyze their degradation. In addition, the formation of cis‐dichloroethylene has a lower barrier by 3.8 kcal mol^?1 than the formation of trans‐dichloroethylene and 1,1‐dichloroethylene, reproducing the regioselectivity. These results agree quite well with the experimental findings, which show cis‐dichloroethylene as the sole product in the PceA‐catalyzed dechlorination of perchloethylene and trichloroethylene.     

Structural Characterization of O‐ and C‐Glycosylating Variants of the Landomycin Glycosyltransferase LanGT2

The structures of the O‐glycosyltransferase LanGT2 and the engineered, C? C bond‐forming variant LanGT2S8Ac show how the replacement of a single loop can change the functionality of the enzyme. Crystal structures of the enzymes in complex with a nonhydrolyzable nucleotide‐sugar analogue revealed that there is a conformational transition to create the binding sites for the aglycon substrate. This induced‐fit transition was explored by molecular docking experiments with various aglycon substrates.