Protein‐Templated Peptide Ligation

Molecular templates bind particular reactants, thereby increasing their effective concentrations and accelerating the corresponding reaction. This concept has been successfully applied to a number of chemical problems with a strong focus on nucleic acid templated reactions. We present the first protein‐templated reaction that allows N‐terminal linkage of two peptides. In the presence of a protein template, ligation reactions were accelerated by more than three orders of magnitude. The templated reaction is highly selective and proved its robustness in a protein‐labeling reaction that was performed in crude cell lysate.     

Quantum Mechanics/Molecular Mechanics Studies on the Mechanism of Action of Cofactor Pyridoxal 5′‐Phosphate in Ornithine 4,5‐Aminomutase

A computational study was performed on the experimentally elusive cyclisation step in the cofactor pyridoxal 5′‐phosphate (PLP)‐dependent D ‐ornithine 4,5‐aminomutase (OAM)‐catalysed reaction. Calculations using both model systems and a combined quantum mechanics/molecular mechanics approach suggest that regulation of the cyclic radical intermediate is achieved through the synergy of the intrinsic catalytic power of cofactor PLP and the active site of the enzyme. The captodative effect of PLP is balanced by an enzyme active site that controls the deprotonation of both the pyridine nitrogen atom (N1) and the Schiff‐base nitrogen atom (N2). Furthermore, electrostatic interactions between the terminal carboxylate and amino groups of the substrate and Arg297 and Glu81 impose substantial “strain” energy on the orientation of the cyclic intermediate to control its trajectory. In addition the “strain” energy, which appears to be sensitive to both the number of carbon atoms in the substrate/analogue and the position of the radical intermediates, may play a key role in controlling the transition of the enzyme from the closed to the open state. Our results provide new insights into several aspects of the radical mechanism in aminomutase catalysis and broaden our understanding of cofactor PLP‐dependent reactions.     

Isotope Probing of the UDP‐Apiose/UDP‐Xylose Synthase Reaction: Evidence of a Mechanism via a Coupled Oxidation and Aldol Cleavage

The C‐branched sugar d ‐apiose (Api) is essential for plant cell‐wall development. An enzyme‐catalyzed decarboxylation/pyranoside ring‐contraction reaction leads from UDP‐α‐d ‐glucuronic acid (UDP‐GlcA) to the Api precursor UDP‐α‐d ‐apiose (UDP‐Api). We examined the mechanism of UDP‐Api/UDP‐α‐d ‐xylose synthase (UAXS) with site‐selectively ²H‐labeled and deoxygenated substrates. The analogue UDP‐2‐deoxy‐GlcA, which prevents C‐2/C‐3 aldol cleavage as the plausible initiating step of pyranoside‐to‐furanoside conversion, did not give the corresponding Api product. Kinetic isotope effects (KIEs) support an UAXS mechanism in which substrate oxidation by enzyme‐NAD⁺ and retro‐aldol sugar ring‐opening occur coupled in a single rate‐limiting step leading to decarboxylation. Rearrangement and ring‐contracting aldol addition in an open‐chain intermediate then give the UDP‐Api aldehyde, which is intercepted via reduction by enzyme‐NADH.     

Cationic Reverse Micelles Create Water with Super Hydrogen‐Bond‐Donor Capacity for Enzymatic Catalysis: Hydrolysis of 2‐Naphthyl Acetate by α‐Chymotrypsin

Reverse micelles (RMs) are very good nanoreactors because they can create a unique microenvironment for carrying out a variety of chemical and biochemical reactions. The aim of the present work is to determine the influence of different RM interfaces on the hydrolysis of 2‐naphthyl acetate (2‐NA) by α‐chymotrypsin (α‐CT). The reaction was studied in water/benzyl‐n‐hexadecyldimethylammonium chloride (BHDC)/benzene RMs and, its efficiency compared with that observed in pure water and in sodium 1,4‐bis‐2‐ethylhexylsulfosuccinate (AOT) RMs. Thus, the hydrolysis rates of 2‐NA catalyzed by α‐CT were determined by spectroscopic measurements. In addition, the method used allows the joint evaluation of the substrate partition constant K_p between the organic and the micellar pseudophase and the kinetic parameters: catalytic rate constant k_cat, and the Michaelis constant K_M of the enzymatic reaction. The effect of the surfactant concentration on the kinetics parameters was determined at constant W₀=[H₂O]/[surfactant], and the variation of W₀ with surfactant constant concentration was investigated. The results show that the classical Michaelis–Menten mechanism is valid for α‐CT in all of the RMs systems studied and that the reaction takes place at both RM interfaces. Moreover, the catalytic efficiency values k_cat/K_M obtained in the RMs systems are higher than that reported in water. Furthermore, there is a remarkable increase in α‐CT efficiency in the cationic RMs in comparison with the anionic system, presumably due to the unique water properties found in these confined media. The results show that in cationic RMs the hydrogen‐bond donor capacity of water is enhanced due to its interaction with the cationic interface. Hence, entrapped water can be converted into “super‐water” for the enzymatic reaction studied in this work.     

Structural Basis and Enzymatic Mechanism of the Biosynthesis of C9‐ from C10‐Monoterpenoid Indole Alkaloids

Cutting carbons : The three‐dimensional structure of polyneuridine aldehyde esterase (PNAE) gives insight into the enzymatic mechanism of the biosynthesis of C₉‐ from C₁₀‐monoterpenoid indole alkaloids (see scheme). PNAE is a very substrate‐specific serine esterase. It harbors the catalytic triad S87‐D216‐H244, and is a new member of the α/β‐fold hydrolase superfamily. Its novel function leads to the diversification of alkaloid structures.

     

Extended Reaction Scope of Thiamine Diphosphate Dependent Cyclohexane‐1,2‐dione Hydrolase: From CC Bond Cleavage to CC Bond Ligation

ThDP‐dependent cyclohexane‐1,2‐dione hydrolase (CDH) catalyzes the C? C bond cleavage of cyclohexane‐1,2‐dione to 6‐oxohexanoate, and the asymmetric benzoin condensation between benzaldehyde and pyruvate. One of the two reactivities of CDH was selectively knocked down by mutation experiments. CDH‐H28A is much less able to catalyze the C? C bond formation, while the ability for C? C bond cleavage is still intact. The double variant CDH‐H28A/N484A shows the opposite behavior and catalyzes the addition of pyruvate to cyclohexane‐1,2‐dione, resulting in the formation of a tertiary alcohol. Several acyloins of tertiary alcohols are formed with 54–94 % enantiomeric excess. In addition to pyruvate, methyl pyruvate and butane‐2,3‐dione are alternative donor substrates for C? C bond formation. Thus, the very rare aldehyde–ketone cross‐benzoin reaction has been solved by design of an enzyme variant.     

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.     

Mechanistic Studies of the Radical S‐Adenosylmethionine Enzyme DesII with TDP‐D‐Fucose

DesII is a radical S‐adenosylmethionine (SAM) enzyme that catalyzes the C4‐deamination of TDP‐4‐amino‐4,6‐dideoxyglucose through a C3 radical intermediate. However, if the C4 amino group is replaced with a hydroxy group (to give TDP‐quinovose), the hydroxy group at C3 is oxidized to a ketone with no C4‐dehydration. It is hypothesized that hyperconjugation between the C4 C? N/O bond and the partially filled p orbital at C3 of the radical intermediate modulates the degree to which elimination competes with dehydrogenation. To investigate this hypothesis, the reaction of DesII with the C4‐epimer of TDP‐quinovose (TDP‐fucose) was examined. The reaction primarily results in the formation of TDP‐6‐deoxygulose and likely regeneration of TDP‐fucose. The remainder of the substrate radical partitions roughly equally between C3‐dehydrogenation and C4‐dehydration. Thus, changing the stereochemistry at C4 permits a more balanced competition between elimination and dehydrogenation.     

Enzyme‐Regulated Activation of DNAzyme: A Novel Strategy for a Label‐Free Colorimetric DNA Ligase Assay and Ligase‐Based Biosensing

The DNA nick repair catalyzed by DNA ligase is significant for fundamental life processes, such as the replication, repair, and recombination of nucleic acids. Here, we have employed ligase to regulate DNAzyme activity and developed a homogeneous, colorimetric, label‐free and DNAzyme‐based strategy to detect DNA ligase activity. This novel strategy relies on the ligation‐trigged activation or production of horseradish peroxidase mimicking DNAzyme that catalyzes the generation of a color change signal; this results in a colorimetric assay of DNA ligase activity. Using T4 DNA ligase as a model, we have proposed two approaches to demonstrate the validity of the DNAzyme strategy. The first approach utilizes an allosteric hairpin‐DNAzyme probe specifically responsive to DNA ligation; this approach has a wide detection range from 0.2 to 40 U mL^?1 and a detection limit of 0.2 U mL^?1. Furthermore, the approach was adapted to probe nucleic acid phosphorylation and single nucleotide mismatch. The second approach employs a “split DNA machine” to produce numerous DNAzymes after being reassembled by DNA ligase; this greatly enhances the detection sensitivity by a signal amplification cascade to achieve a detection limit of 0.01 U mL^?1.     

CaII Binding Regulates and Dominates the Reactivity of a Transition‐Metal‐Ion‐Dependent Diesterase from Mycobacterium tuberculosis

The diesterase Rv0805 from Mycobacterium tuberculosis is a dinuclear metallohydrolase that plays an important role in signal transduction by controlling the intracellular levels of cyclic nucleotides. As Rv0805 is essential for mycobacterial growth it is a promising new target for the development of chemotherapeutics to treat tuberculosis. The in vivo metal‐ion composition of Rv0805 is subject to debate. Here, we demonstrate that the active site accommodates two divalent transition metal ions with binding affinities ranging from approximately 50 nm for Mn^II to about 600 nm for Zn^II. In contrast, the enzyme GpdQ from Enterobacter aerogenes, despite having a coordination sphere identical to that of Rv0805, binds only one metal ion in the absence of substrate, thus demonstrating the significance of the outer sphere to modulate metal‐ion binding and enzymatic reactivity. Ca^II also binds tightly to Rv0805 (K_d≈40 nm ), but kinetic, calorimetric, and spectroscopic data indicate that two Ca^II ions bind at a site different from the dinuclear transition‐metal‐ion binding site. Ca^II acts as an activator of the enzymatic activity but is able to promote the hydrolysis of substrates even in the absence of transition‐metal ions, thus providing an effective strategy for the regulation of the enzymatic activity.     

Didehydroaspartate Modification in Methyl‐Coenzyme M Reductase Catalyzing Methane Formation

All methanogenic and methanotrophic archaea known to date contain methyl‐coenzyme M reductase (MCR) that catalyzes the reversible reduction of methyl‐coenzyme M to methane. This enzyme contains the nickel porphinoid F₄₃₀ as a prosthetic group and, highly conserved, a thioglycine and four methylated amino acid residues near the active site. We describe herein the presence of a novel post‐translationally modified amino acid, didehydroaspartate, adjacent to the thioglycine as revealed by mass spectrometry and high‐resolution X‐ray crystallography. Upon chemical reduction, the didehydroaspartate residue was converted into aspartate. Didehydroaspartate was found in MCR I and II from Methanothermobacter marburgensis and in MCR of phylogenetically distantly related Methanosarcina barkeri but not in MCR I and II of Methanothermobacter wolfeii, which indicates that didehydroaspartate is dispensable but might have a role in fine‐tuning the active site to increase the catalytic efficiency.     

Structure and Mechanism of the Caseinolytic Protease ClpP1/2 Heterocomplex from Listeria monocytogenes

Listeria monocytogenes is a devastating bacterial pathogen. Its virulence and intracellular stress tolerance are supported by caseinolytic protease P (ClpP), an enzyme that is conserved among bacteria. L. monocytogenes expresses two ClpP isoforms that are only distantly related by sequence and differ in catalysis, oligomerization, active‐site composition, and N‐terminal interaction sites for associated AAA⁺ chaperones. The crystal structure of the ClpP1/2 heterocomplex from L. monocytogenes was solved, and in combination with biochemical studies, it provides insights into the mode of action. The results demonstrate that structural interlocking of LmClpP1 with LmClpP2 leads to the formation of a tetradecamer, aligns all 14 active sites, and enhances proteolytic activity. Furthermore, the catalytic center was identified as being responsible for the transient stability of ClpPs.     

Solution‐State 17O Quadrupole Central‐Transition NMR Spectroscopy in the Active Site of Tryptophan Synthase

Oxygen is an essential participant in the acid–base chemistry that takes place within many enzyme active sites, yet has remained virtually silent as a probe in NMR spectroscopy. Here, we demonstrate the first use of solution‐state ¹⁷O quadrupole central‐transition NMR spectroscopy to characterize enzymatic intermediates under conditions of active catalysis. In the 143 kDa pyridoxal‐5′‐phosphate‐dependent enzyme tryptophan synthase, reactions of the α‐aminoacrylate intermediate with the nucleophiles indoline and 2‐aminophenol correlate with an upfield shift of the substrate carboxylate oxygen resonances. First principles calculations suggest that the increased shieldings for these quinonoid intermediates result from the net increase in the charge density of the substrate–cofactor π‐bonding network, particularly at the adjacent α‐carbon site.     

A 3.3 Å‐Resolution Structure of Hyperthermophilic Respiratory Complex III Reveals the Mechanism of Its Thermal Stability

Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc₁ complex (Complex III) from thermophilic bacteria, little is known about the adaptations of this macromolecular machine to hyperthermophilic environments. In this study, we purified the cytochrome bc₁ complex of Aquifex aeolicus, one of the most extreme thermophilic bacteria known, and determined its structure with and without an inhibitor at 3.3 Å resolution. Several residues unique for thermophilic bacteria were detected that provide additional stabilization for the structure. An extra transmembrane helix at the N‐terminus of cyt. c₁ was found to greatly enhance the interaction between cyt. b and cyt. c₁, and to bind a phospholipid molecule to stabilize the complex in the membrane. These results provide the structural basis for the hyperstability of the cytochrome bc₁ complex in an extreme thermal environment.     

Substrate‐Dependent Stereospecificity of Tyl‐KR1: An Isolated Polyketide Synthase Ketoreductase Domain from Streptomyces fradiae

The stereospecificity of an enzymatic reaction depends on the way in which a substrate and its enantiomer bind to the active site. These binding modes cannot be easily predicted. We have studied the stereospecificity and stereoselectivity of the ketoreductase domain Tyl‐KR1 of the tylactone polyketide synthase from Streptomyces fradiae by analysing the stereochemical outcome of the reduction of five different keto ester substrates. The absolute configuration of the Tyl‐KR1 reduction products was determined by using vibrational circular dichroism (VCD) spectroscopy combined with quantum chemical calculations. The conversion of only one of the tested substrates, 2‐methyl‐3‐oxovaleric acid N‐acetylcysteamine thioester, afforded the expected anti‐(2R,3R) configuration of the α‐methyl‐β‐hydroxyl ester product, representing the stereochemistry observed for the physiological polyketide product tylactone. For all other substrates, which were modified with respect to the type of ester and/or the chain length (C₄ instead of C₅), the opposite configuration (anti‐(2S,3S)) was obtained with significant enantio‐ and diastereoselectivity. Inversion of both stereocentres suggests completely different binding modes invoked by only minor modifications of the substrate structure.