Nickel(II)‐Mediated Reversible Thiolate/Disulfide Conversion as a Mimic for a Key Step of the Catalytic Cycle of Methyl‐Coenzyme M Reductase

According to the well‐accepted mechanism, methyl‐coenzyme M reductase (MCR) involves Ni‐mediated thiolate‐to‐disulfide conversion that sustains its catalytic cycle of methane formation in the energy saving pathways of methanotrophic microbes. Model complexes that illustrate Ni‐ion mediated reversible thiolate/disulfide transformation are unknown. In this paper we report the synthesis, crystal structure, spectroscopic properties and redox interconversions of a set of Ni^II complexes comprising a tridentate N₂S donor thiol and its analogous N₄S₂ donor disulfide ligands. These complexes demonstrate reversible Ni^II‐thiolate/Ni^II‐disulfide (both bound and unbound disulfide‐S to Ni^II) transformations via thiyl and disulfide monoradical anions that resemble a primary step of MCR's catalytic cycle.     

Targeting the Substrate Binding Site of E. coli Nitrile Reductase QueF by Modeling,Substrate and Enzyme Engineering

Nitrile reductase QueF catalyzes the reduction of 2‐amino‐5‐cyanopyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₀) to 2‐amino‐5‐aminomethylpyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₁) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non‐natural substrates. Various structural analogues of the natural substrate preQ₀ were synthesized and screened with wild‐type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non‐natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild‐type and mutant nitrile reductase.     

β‐Amyrin Biosynthesis: The Methyl‐30 Group of (3S)‐2,3‐Oxidosqualene Is More Critical to Its Correct Folding To Generate the Pentacyclic Scaffold than the Methyl‐24 Group

Oxidosqualene cyclases catalyze the transformation of oxidosqualene ( 1 ) into numerous cyclic triterpenes. Enzymatic reactions of 24‐noroxidosqualene ( 8 ) and 30‐noroxidosqualene ( 9 ) with Euphorbia tirucalli β‐amyrin synthase were conducted to examine the role of the branched methyl groups of compound 1 in the β‐amyrin biosynthesis. Substrate 8 almost exclusively afforded 30‐nor‐β‐amyrin (>95.5 %), which was produced through a normal cyclization pathway, along with minor products (<4.5 %). However, a lack of the Me‐30 group (analogue 9 ) resulted in significantly high production of premature cyclization products, including 6/6/6/5‐fused tetracyclic and 6/6/6/6/5‐fused pentacyclic skeletons (64.6 %). In addition, the fully cyclized product (35.4 %) having the 6/6/6/6/6‐fused pentacycle was produced; however, the normally cyclized product, 29‐nor‐β‐amyrin was present in only 18.6 % of these products. The conversion yield of substrate 8 possessing a Z‐Me group at the terminus was approximately twofold greater than that of compound 9 with an E‐Me group. Thus, the Me‐30 group is essential for the correct folding of a chair–chair–chair–boat–boat conformation of compound 1 for the production of the β‐amyrin scaffold, whereas the Me‐24 group exerts little influence on the normal polycyclization cascade. Here, we show that the Me‐30 group plays critical roles in constructing the ordered architecture of a chair–chair–chair–boat–boat structure, in facilitating the ring‐expansion reactions, and in performing the final deprotonation reaction at the correct position.     

Lanosterol Biosynthesis: The Critical Role of the Methyl‐29 Group of 2,3‐Oxidosqualene for the Correct Folding of this Substrate and for the Construction of the Five‐Membered D Ring

Lanosterol synthase catalyzes the polycyclization reaction of (3S)‐2,3‐oxidosqualene ( 1 ) into tetracyclic lanosterol 2 by folding 1 in a chair‐boat‐chair‐chair conformation. 27‐Nor‐ and 29‐noroxidosqaulenes ( 7 and 8 , respectively) were incubated with this enzyme to investigate the role of the methyl groups on 1 for the polycyclization cascade. Compound 7 afforded two enzymatic products, namely, 30‐norlanosterol ( 12 ) and 26‐normalabaricatriene ( 13 ; 12 / 13 9:1), which were produced through the normal chair‐boat‐chair‐chair conformation and an atypical chair‐chair‐boat conformation, respectively. Compound 8 gave two products 14 and 15 ( 14 / 15 4:5), which were generated by the normal and the unusual polycyclization pathways through a chair‐chair‐boat‐chair conformation, respectively. It is remarkable that the twist‐boat structure for the B‐ring formation was changed to an energetically favored chair structure for the generation of 15 . Surprisingly, 14 and 15 consisted of a novel 6,6,6,6‐fused tetracyclic ring system, thus differing from the 6,6,6,5‐fused lanosterol skeleton. Together with previous results, we conclude that the methyl‐29 group is critical to the correct folding of 1 , with lesser contributions from the other branched methyl groups, such as methyl‐26, ‐27, and ‐28. Furthermore, we demonstrate that the methyl‐29 group has a crucial role in the formation of the five‐membered D ring of the lanosterol scaffold.     

Myoglobin Reconstituted with Ni Tetradehydrocorrin as a Methane‐Generating Model of Methyl‐coenzyme M Reductase

Myoglobin reconstituted with Ni tetradehydrocorrin was investigated as a model of F430‐containing methyl‐coenzyme M reductase, which catalyzes anaerobic methane generation. The Ni^II tetradehydrocorrin complex has a Ni^II/Ni^I redox potential of ?0.34 V vs. SHE and EPR spectroscopy indicates the formation of a Ni^I species upon reduction by dithionite. This redox potential is approximately 0.31 V more positive than that of F430. The Ni^I tetradehydrocorrin moiety is bound to the apo‐form of myoglobin to yield the reconstituted protein. Methane gas is generated in the reaction of the model with methyl iodide in the presence of the reconstituted protein under reductive conditions, whereas the Ni^I complex itself does not produce methane gas. This is the first example of a protein‐based functional model of F430‐containing methyl‐coenzyme M reductase.     

Efforts Toward the Direct Experimental Characterization of Enzyme Microenvironments: Tyrosine100 in Dihydrofolate Reductase

State secrets : Site‐specific deuteration and FTIR studies reveal that Tyr100 in dihydrofolate reductase plays an important role in catalysis, with a strong electrostatic coupling occuring between Tyr100 and the charge that develops in the hydride‐transfer transition state (see picture, NADP⁺ purple, Tyr100 green). However, relaying correlated motions that facilitate catalysis from distal sites of the protein to the hydride donor may also be involved.

     

Stereoselective Hydrogenation of Olefins Using Rhodium‐Substituted Carbonic Anhydrase—A New Reductase

One useful synthetic reaction missing from nature's toolbox is the direct hydrogenation of substrates using hydrogen. Instead nature uses cofactors like NADH to reduce organic substrates, which adds complexity and cost to these reductions. To create an enzyme that can directly reduce organic substrates with hydrogen, researchers have combined metal hydrogenation catalysts with proteins. One approach is an indirect link where a ligand is linked to a protein and the metal binds to the ligand. Another approach is direct linking of the metal to protein, but nonspecific binding of the metal limits this approach. Herein, we report a direct hydrogenation of olefins catalyzed by rhodium(I) bound to carbonic anhydrase (CA‐[Rh]). We minimized nonspecific binding of rhodium by replacing histidine residues on the protein surface using site‐directed mutagenesis or by chemically modifying the histidine residues. Hydrogenation catalyzed by CA‐[Rh] is slightly slower than for uncomplexed rhodium(I), but the protein environment induces stereoselectivity favoring cis‐ over trans‐stilbene by about 20:1. This enzyme is the first cofactor‐independent reductase that reduces organic molecules using hydrogen. This catalyst is a good starting point to create variants with tailored reactivity and selectivity. This strategy to insert transition metals in the active site of metalloenzymes opens opportunities to a wider range of enzyme‐catalyzed reactions.     

One‐Pot Enzymatic Synthesis of Merochlorin A and B

The polycycles merochlorin A and B are complex halogenated meroterpenoid natural products with significant antibacterial activities and are produced by the marine bacterium Streptomyces sp. strain CNH‐189. Heterologously produced enzymes and chemical synthesis are employed herein to fully reconstitute the merochlorin biosynthesis in vitro. The interplay of a dedicated type III polyketide synthase, a prenyl diphosphate synthase, and an aromatic prenyltransferase allow formation of a highly unusual aromatic polyketide‐terpene hybrid intermediate which features an unprecedented branched sesquiterpene moiety from isosesquilavandulyl diphosphate. As supported by in vivo experiments, this precursor is furthermore chlorinated and cyclized to merochlorin A and isomeric merochlorin B by a single vanadium‐dependent haloperoxidase, thus completing the remarkably efficient pathway.     

Catalytic Asymmetric Inverse‐Electron‐Demand Oxa‐Diels–Alder Reaction of In Situ Generated ortho‐Quinone Methides with 3‐Methyl‐2‐Vinylindoles

The first catalytic asymmetric inverse‐electron‐demand (IED) oxa‐Diels–Alder reaction of ortho‐quinone methides, generated in situ from ortho‐hydroxybenzyl alcohols, has been established. By selecting 3‐methyl‐2‐vinylindoles as a class of competent dienophiles, this approach provides an efficient strategy to construct an enantioenriched chroman framework with three adjacent stereogenic centers in high yields and excellent stereoselectivities (up to 99 % yield, >95:5 d.r., 99.5:0.5 e.r.). The utilization of ortho‐hydroxybenzyl alcohols as precursors of dienes and 3‐methyl‐2‐vinylindoles as dienophiles, as well as the hydrogen‐bonding activation mode of the substrates met the challenges of a catalytic asymmetric IED oxa‐Diels–Alder reaction.     

Synthesis of a Phosphonate‐Linked Aminoglycoside–Coenzyme A Bisubstrate and Use in Mechanistic Studies of an Enzyme Involved in Aminoglycoside Resistance

Just five steps! The synthesis of a phosphonate‐linked aminoglycoside‐coenzyme A derivative (see scheme) that includes a Michael addition in water has been realized in just five steps.

     

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.     

Active Intermediates in Copper Nitrite Reductase Reactions Probed by a Cryotrapping‐Electron Paramagnetic Resonance Approach

Redox active metalloenzymes catalyse a range of biochemical processes essential for life. However, due to their complex reaction mechanisms, and often, their poor optical signals, detailed mechanistic understandings of them are limited. Here, we develop a cryoreduction approach coupled to electron paramagnetic resonance measurements to study electron transfer between the copper centers in the copper nitrite reductase (CuNiR) family of enzymes. Unlike alternative methods used to study electron transfer reactions, the cryoreduction approach presented here allows observation of the redox state of both metal centers, a direct read‐out of electron transfer, determines the presence of the substrate/product in the active site and shows the importance of protein motion in inter‐copper electron transfer catalyzed by CuNiRs. Cryoreduction‐EPR is broadly applicable for the study of electron transfer in other redox enzymes and paves the way to explore transient states in multiple redox‐center containing proteins (homo and hetero metal ions).     

Flavoenzyme‐Catalyzed Formation of Disulfide Bonds in Natural Products

Nature provides a rich source of compounds with diverse chemical structures and biological activities, among them, sulfur‐containing metabolites from bacteria and fungi. Some of these compounds bear a disulfide moiety that is indispensable for their bioactivity. Specialized oxidoreductases such as GliT, HlmI, and DepH catalyze the formation of this disulfide bridge in the virulence factor gliotoxin, the antibiotic holomycin, and the anticancer drug romidepsin, respectively. We have examined all three enzymes by X‐ray crystallography and activity assays. Despite their differently sized substrate binding clefts and hence, their diverse substrate preferences, a unifying reaction mechanism is proposed based on the obtained crystal structures and further supported by mutagenesis experiments.     

A Promiscuous De Novo Retro‐Aldolase Catalyzes Asymmetric Michael Additions via Schiff Base Intermediates

Recent advances in computational design have enabled the development of primitive enzymes for a range of mechanistically distinct reactions. Here we show that the rudimentary active sites of these catalysts can give rise to useful chemical promiscuity. Specifically, RA95.5‐8, designed and evolved as a retro‐aldolase, also promotes asymmetric Michael additions of carbanions to unsaturated ketones with high rates and selectivities. The reactions proceed by amine catalysis, as indicated by mutagenesis and X‐ray data. The inherent flexibility and tunability of this catalyst should make it a versatile platform for further optimization and/or mechanistic diversification by directed evolution.     

Formation of High‐Valent Iron–Oxo Species in Superoxide Reductase: Characterization by Resonance Raman Spectroscopy

Superoxide reductase (SOR), a non‐heme mononuclear iron protein that is involved in superoxide detoxification in microorganisms, can be used as an unprecedented model to study the mechanisms of O₂ activation and of the formation of high‐valent iron–oxo species in metalloenzymes. By using resonance Raman spectroscopy, it was shown that the mutation of two residues in the second coordination sphere of the SOR iron active site, K₄₈ and I₁₁₈, led to the formation of a high‐valent iron–oxo species when the mutant proteins were reacted with H₂O₂. These data demonstrate that these residues in the second coordination sphere tightly control the evolution and the cleavage of the O? O bond of the ferric iron hydroperoxide intermediate that is formed in the SOR active site.     

Structure and Mechanism of an Aspartimide‐Dependent Peptide Ligase in Human Legumain

Peptide ligases expand the repertoire of genetically encoded protein architectures by synthesizing new peptide bonds, energetically driven by ATP or NTPs. Here, we report the discovery of a genuine ligase activity in human legumain (AEP) which has important roles in immunity and tumor progression that were believed to be due to its established cysteine protease activity. Defying dogma, the ligase reaction is independent of the catalytic cysteine but exploits an endogenous energy reservoir that results from the conversion of a conserved aspartate to a metastable aspartimide. Legumain’s dual protease–ligase activities are pH‐ and thus localization controlled, dominating at acidic and neutral pH, respectively. Their relevance includes reversible on–off switching of cystatin inhibitors and enzyme (in)activation, and may affect the generation of three‐dimensional MHC epitopes. The aspartate–aspartimide (succinimide) pair represents a new paradigm of coupling endergonic reactions in ATP‐scarce environments.