Molecular evolution of B<Subscript>6</Subscript> enzymes: Binding of pyridoxal-5'-phosphate and Lys41Arg substitution turn ribonuclease A into a model B<Subscript>6</Subscript> protoenzyme

Background  

The pyridoxal-5'-phosphate (PLP)-dependent or vitamin B₆-dependent enzymes that catalyze manifold reactions in the metabolism of amino acids belong to no fewer than four evolutionarily independent protein families. The multiple evolutionary origin and the essential mechanistic role of PLP in these enzymes argue for the cofactor having arrived on the evolutionary scene before the emergence of the respective apoenzymes and having played a dominant role in the molecular evolution of the B₆ enzyme families. Here we report on an attempt to re-enact the emergence of a PLP-dependent protoenzyme. The starting protein was pancreatic ribonuclease A (RNase), in which active-site Lys41 or Lys7 readily form a covalent adduct with PLP.     

Role of the pyridine nitrogen in pyridoxal 5'-phosphate catalysis: activity of three classes of PLP enzymes reconstituted with deazapyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (PLP; vitamin B(6))-catalyzed reactions have been well studied, both on enzymes and in solution, due to the variety of important reactions this cofactor catalyzes in nitrogen metabolism. Three functional groups are central to PLP catalysis: the C4' aldehyde, the O3' phenol, and the N1 pyridine nitrogen. In the literature, the pyridine nitrogen has traditionally been assumed to be protonated in enzyme active sites, with the protonated pyridine ring providing resonance stabilization of carbanionic intermediates. This assumption is certainly correct for some PLP enzymes, but the structures of other active sites are incompatible with protonation of N1, and, consequently, these enzymes are expected to use PLP in the N1-unprotonated form. For example, aspartate aminotransferase protonates the pyridine nitrogen for catalysis of transamination, while both alanine racemase and O-acetylserine sulfhydrylase are expected to maintain N1 in the unprotonated, formally neutral state for catalysis of racemization and β-elimination. Herein, kinetic results for these three enzymes reconstituted with 1-deazapyridoxal 5'-phosphate, an isosteric analogue of PLP lacking the pyridine nitrogen, are compared to those for the PLP enzyme forms. They demonstrate that the pyridine nitrogen is vital to the 1,3-prototropic shift central to transamination, but not to reactions catalyzed by alanine racemase or O-acetylserine sulfhydrylase. Not all PLP enzymes require the electrophilicity of a protonated pyridine ring to enable formation of carbanionic intermediates. It is proposed that modulation of cofactor electrophilicity plays a central role in controlling reaction specificity in PLP enzymes.     

Pyridoxal-5'-phosphate-dependent catalytic antibodies

Cofactors--i.e., metal ions and coenzymes--extend the catalytic scope of enzymes and might have been among the first biological catalysts. They may be expected to efficiently extend the catalytic potential of antibodies. Monoclonal antibodies (MAbs) against Nalpha-phosphopyridoxyl-L-lysine were screened for 1) binding of 5'-phosphopyridoxyl amino acids, 2) binding of the planar Schiff base of pyridoxal-5'-phosphate (PLP) and amino acids, the first intermediate of all PLP-dependent reactions, and 3) catalysis of the PLP-dependent alpha, beta-elimination reaction with beta-chloro-D/L-alanine. Antibody 15A9 fulfilled all criteria and was also found to catalyze the cofactor-dependent transamination reaction of hydrophobic D-amino acids and oxo acids (k'cat = 0.42 min(-1) with D-alanine at 25 degrees C). No other reactions with either D- or L-amino acids were detected. PLP markedly contributes to catalytic efficacy-it is a 10(4) times more efficient acceptor of the amino group than pyruvate. The antibody ensures reaction specificity, stereospecificity, and substrate specificity, and further accelerates the transamination reaction (k'cat(Ab)/k'cat(PLP) = 5 x 10(3)). The successive screening steps simulate the selection criteria that might have been operative in the evolution of protein-assisted pyridoxal catalysis.     

Radical stabilization is crucial in the mechanism of action of lysine 5,6-aminomutase: role of tyrosine-263α as revealed by electron paramagnetic resonance spectroscopy

Adenosylcobalamin- and pyridoxal-5'-phosphate-dependent lysine 5,6-aminomutase utilizes free radical intermediates to mediate 1,2-amino group rearrangement, during which an elusive high-energy aziridincarbinyl radical is proposed to be central in the mechanism of action. Understanding how the enzyme participates in stabilizing any of the radical intermediates is fundamentally significant. Y263F mutation abolished the enzymatic activity. With isotope-edited EPR methods, the roles of the Tyr263α residue in the putative active site are revealed. The Tyr263α residue stabilizes a radical intermediate, which most likely is the aziridincarbinyl radical, either by acting as a spin-relay device or serving as an anchor for the pyridine ring of pyridoxal-5'-phosphate through aromatic π-stacking interactions during spin transfer. The Tyr263α residue also protects the radical intermediate from interception by molecular oxygen. This study supports the proposed reaction mechanism, including the aziridincarbinyl radical, which has eluded detection for more than two decades.     

Synthesis and structure-activity relationships of o-sulfonamido-arylhydrazides as inhibitors of LL-diaminopimelate aminotransferase (LL-DAP-AT)

Recently, LL-diaminopimelate aminotransferase (LL-DAP-AT), a pyridoxal-5'-phosphate (PLP)-dependent enzyme, was reported to catalyze a key step in the biosynthesis of L-lysine in plants and Chlamydia. Previous screening of a 29,201-compound library against LL-DAP-AT identified an o-sulfonamidoarylhydrazide as a reversible inhibitor with IC(50)～ 5 μM. Structure-activity relationship (SAR) studies based on this lead compound identified key structural features essential for enzyme inhibition and led to slightly improved inhibitors. Preliminary studies on the mode of inhibition of LL-DAP-AT by this class of compounds are also reported.     

Tyrosine decarboxylase

We have developed a highly sensitive and rapid spectrophotometric assay for tyrosine decarboxylase that can be applied to determining pyridoxal-5'-phosphate. In the assay, tyramine, a product of tyrosine decarboxylation, reacts with 2,4,6-trinitrobenzenesulfonic acid to give a product soluble in toluene whereas tyrosine does not. We determined the amount of tyramine produced enzymatically by reading the absorbance at 340 nm of a toluene extract of the reaction mixture. This method is capable of detecting as low as 2.9 micrograms/mL of the enzyme. Using this method, we find the Km for tyrosine decarboxylase from Streptococcus faecalis to be 3.55 X 10(-4)M. We have also developed a specific and extremely sensitive method for determining pyridoxal-5'-phosphate, a cofactor of the enzyme, by using this spectrophotometric assay with apotyrosine decarboxylase.     

RNA-cleaving DNA enzymes with altered regio- or enantioselectivity

In vitro evolution methods were used to obtain DNA enzymes that cleave either a 2',5'-phosphodiester following a D-ribonucleotide or a 3',5'-phosphodiester following an L-ribonucleotide. Both enzymes can operate in an intermolecular reaction format with multiple turnover. The DNA enzyme that cleaves a 2',5'-phosphodiester exhibits a k(cat) of approximately 0.01 min(-1) and catalytic efficiency, k(cat)/K(m), of approximately 10(8) M(-1) min(-1). The enzyme that cleaves an L-ribonucleotide is about 10-fold slower and has a catalytic efficiency of approximately 4 x 10(5) M(-1) min(-1). Both enzymes require a divalent metal cation for their activity and have optimal catalytic rate at pH 7-8 and 35-50 degrees C. In a comparison of each enzyme's activity with either its corresponding substrate that contains an unnatural ribonucleotide or a substrate that instead contains a standard ribonucleotide, the 2',5'-phosphodiester-cleaving DNA enzyme exhibited a regioselectivity of 6000-fold, while the L-ribonucleotide-cleaving DNA enzyme exhibited an enantioselectivity of 40-fold. These molecules demonstrate how in vitro evolution can be used to obtain regio- and enantioselective catalysts that exhibit specificities for nonnatural analogues of biological compounds.     

Occurrence and functions of free D-aspartate and its metabolizing enzymes

D-Aspartate is one of a few D-amino acids that attracted attention at an early date, since it was detected in various tissues of mammals as a protein component. The occurrence of free D-aspartate in nature was recognized a little later, and raised questions about its physiological functions and metabolism. This amino acid has been gradually accepted, based on various experimental observations, to be a physiological substrate of D-aspartate oxidase, whose role had been considered enigmatic since its early discovery in the 1940s. Mammalian enzymes that serve to liberate D-aspartyl residue in proteins have been identified. One enzyme hydrolyzes peptide bond at the amino side of D-aspartyl residue in a dipeptide and another enzyme hydrolyzes that at the carbonyl side of the residue in proteins. The first pyridoxal 5'-phosphate-dependent aspartate racemase has been purified and cloned from a bivalve species. The enzyme supports the high contents of D-aspartate comparable to those of L-aspartate in the bivalve, and the enantiomers are consumed when hypoxia is imposed on the bivalve. In some yeast species, assimilation of D-aspartate has been found to depend on inducible D-aspartate oxidase, which also serves to detoxify acidic D-amino acids.     

Stereospecificity for the hydrogen transfer of pyridoxal enzyme reactions

We have studied the stereospecificities of various pyridoxal 5'-phosphate dependent enzymes for the hydrogen transfer between the C-4' of a bound coenzyme and the C-2 of a substrate in the transamination catalyzed by the enzymes. Prior to our studies, pyridoxal enzymes so far studied were reported to catalyze the hydrogen transfer only on the si-face of the planar imine intermediate formed from substrate and coenzyme. This finding had been considered as the evidence that pyridoxal enzymes have evolved divergently from a common ancestral protein, because identity in the stereospecificity reflects the similarity in the active-site structure, in particular in the geometrical relationship between the coenzyme and the active site base participating in the hydrogen transfer. However, we found that D-amino acid aminotransferase, branched-chain L-amino acid aminotransferase, and 4-amino-4-deoxychorismate lyase catalyze the re-face specific hydrogen transfer, and that amino acid racemases catalyze the nonstereospecific hydrogen transfer. These findings suggest the convergent evolution of pyridoxal enzymes. Crystallographical studies have shown that the stereospecificity reflects the active-site structure of the enzymes, and that the enzymes with the same fold exhibit the same stereospecificity. The active site structure with the catalytic base being situated on the specific face of the cofactor has been conserved during the evolution among the pyridoxal enzymes of the same family.     

Evolutionary relationship and application of a superfamily of cyclic amidohydrolase enzymes

Cyclic amidohydrolases belong to a superfamily of enzymes that catalyze the hydrolysis of cyclic C-N bonds. They are commonly found in nucleotide metabolism of purine and pyrimidine. These enzymes share similar catalytic mechanisms and show considerable structural homologies, suggesting that they might have evolved from a common ancestral protein. Homology searches based on common mechanistic properties and three-dimensional protein structures provide clues to the evolutionary relationships of these enzymes. Among the superfamily of enzymes, hydantoinase has been highlighted by its potential for biotechnological applications in the production of unnatural amino acids. The enzymatic process for the production of optically pure amino acids consists of three enzyme steps: hydantoin racemase, hydantoinase, and N-carbamoylase. For efficient industrial application, some critical catalytic properties such as thermostability, catalytic activity, enantioselectivity, and substrate specificity require further improvement. To this end, isolation of new enzymes with desirable properties from natural sources and the optimization of enzymatic processes were attempted. A combination of directed evolution techniques and rational design approaches has made brilliant progress in the redesign of industrially important catalytic enzymes; this approach is likely to be widely applied to the creation of designer enzymes with desirable catalytic properties.     

Comparison of the coupling recoveries of immobilized aspartate aminotransferase

Aspartate aminotransferase (AspAT, EC 2.6.1.1) was bound on CNBr-activated Sepharose and the effects of immobilization on the maximum velocity, biologically active pyridoxal-5'-phosphate (PLP), and transaminationable active centers were studied. By comparing these parameters of soluble and immobilized enzyme the factors decreasing the observed reaction rate upon immobilization were evaluated. Ninety percent of the soluble protein in the coupling mixture was bound to the support. The amount of enzyme-bound PLP of immobilized preparation was 83% of that of the soluble one. The coupling recovery of specific activity was 46%, which was 10%-units lower than that of the transaminationable active centers. This difference depends on the fact that a part of the active centers of immobilized enzyme had lower catalytic rate, due to the enzyme-matrix interactions or internal mass transfer limitations, than the others. The immobilized catalytically active AspAT had 80% of the turnover efficiency of the soluble enzyme. The affinity of the enzyme to its substrates did not significantly change upon immobilization, neither did the pH profile.     

Carbon-carbon bonds by hydrolytic enzymes

Enzymes are efficient catalysts in synthetic chemistry, and their catalytic activity with unnatural substrates in organic reaction media is an area attracting much attention. Protein engineering has opened the possibility to change the reaction specificity of enzymes and allow for new reactions to take place in their active sites. We have used this strategy on the well-studied active-site scaffold offered by the serine hydrolase Candida antarctica lipase B (CALB, EC 3.1.1.3) to achieve catalytic activity for aldol reactions. The catalytic reaction was studied in detail by means of quantum chemical calculations in model systems. The predictions from the quantum chemical calculations were then challenged by experiments. Consequently, Ser105 in CALB was targeted by site-directed mutagenesis to create enzyme variants lacking the nucleophilic feature of the active site. The experiments clearly showed an increased reaction rate when the aldol reaction was catalyzed by the mutant enzymes as compared to the wild-type lipase. We expect that the new catalytic activity, harbored in the stable protein scaffold of the lipase, will allow aldol additions of substrates, which cannot be reached by traditional aldolases.     

Diversity of P450 enzymes in the biosynthesis of natural products

Covering: 1985 to 2012Diverse oxygenation patterns of natural products generated by secondary metabolic pathways in microorganisms and plants are largely achieved through the tailoring reactions catalysed by cytochrome P450 enzymes (P450s). P450s are a large family of oxidative hemoproteins found in all life forms from prokaryotes to humans. Understanding the reactivity and selectivity of these fascinating C-H bond-activating catalysts will advance their use in generating valuable pharmaceuticals and products for medicine, agriculture and industry. A major strength of this P450 group is its set of established enzyme-substrate relationships, the source of the most detailed knowledge on how P450 enzymes work. Engineering microbial-derived P450 enzymes to accommodate alternative substrates and add new functions continues to be an important near- and long-term practical goal driving the structural characterization of these molecules. Understanding the natural evolution of P450 structure-function should accelerate metabolic engineering and directed evolutionary approaches to enhance diversification of natural product structures and other biosynthetic applications.     

Functions of propeptide parts in cysteine proteases

Regulation of proteolytic enzyme activity is an essential requirement for cells and tissues because proteolysis at the wrong time and location may be lethal. Two principal mechanisms to control the activity of proteases have been developed during evolution. The first is the co-evolution of endogenous inhibitors, typically occurring in cellular compartments separated from those containing active enzymes. The second is the fact that proteases are synthesized as inactive or less active precursor molecules. They are activated, in some cases, upon an appropriate signal like acidification, Ca(++) -binding or, in other cases, by limited intra- or intermolecular proteolysis cleaving off an inhibitory peptide. These regulatory proenzyme regions have attracted much attention during the last decade, since it became obvious that they harbour much more information than just triggering activation. In this review we summarize experimental data concerning three functions of propeptides of clan CA family C1 cysteine peptidases (papain family), namely the selectivity of their inhibitory potency, the participation in correct intracellular targeting and assistance in folding of the mature enzyme. Cysteine peptidases of the CA-C1 family include members from the plant kingdom like papain as well as from the animal kingdom like the lysosomal cathepsins L and B. As it will be shown, the functions are determined by certain structural motifs conserved over millions of years after the evolutionary trails have diverged. The function of propeptides of two other important classes of cysteine peptidases - the calpains, clan CA family C4, and the caspases, clan CD family C 14 - are not considered in this review.     

Mechanism of formation of the internal aldimine in pyridoxal 5'-phosphate-dependent enzymes

In this paper we studied the mechanism of formation of the internal aldimine, a common intermediate to most pyridoxal 5'-phosphate (PLP)-dependent enzymes. A large model based on the crystal structure from the human ornithine decarboxylase (ODC) enzyme was constructed and in total accounts for 504 atoms. The reaction mechanism was investigated using the ONIOM methodology (B3LYP/6-31G(d)//AM1), and the final energies were calculated with the M06/6-311++G(2d,2p)//B3LYP/6-31G(d) level of theory. It was demonstrated that the reaction is accomplished in three sequential steps: (i) the nucleophilic attack of Lysine69 to PLP, (ii) the carbinolamine formation, and (iii) a final dehydration step. For the carbinolamine formation, several mechanistic hypotheses were explored, and the preferred pathway assigns a key role for the conserved active site Cys360. The overall reaction is exergonic in -9.1 kcal/mol, and the rate-limiting step is the dehydration step (E(a) = 13.5 kcal/mol). For the first time, we provide an atomistic portrait of this mechanism in an enzymatic environment. Moreover, we were able to assign a novel role to Cys360 in the ODC reaction mechanism that was never proposed.     

Endo-inulinase Stabilization by Pyridoxal Phosphate Modification: A Kinetics, Thermodynamics, and Simulation Approach

The structural and storage and functional thermostabilization of endo-inulinase (EC 3.2.1.7) through semi-rational modification of surface accessible lysine residues by pyridoxal-5'-phosphate (PLP) and ascorbate reduction have been explored. Improved stability was observed on modifications in the absence or presence of inulin, which indicates storage or functional thermostabilization, respectively. Comparisons have been made between non-modified and modified enzyme by the determination of Tm as an indicator of structural stability, temperature-dependent half-lives (t1/2), energy barrier of the inactivation process, and thermodynamic parameters (ΔH, ΔG, and ΔS) in a storage thermostability approach. These parameters coincided well with the observed stabilization of the engineered enzyme. Moreover, relative activities with sucrose and inulin were determined for non-modified and modified endo-inulinases at different temperatures. A comparison of the sucrose-to-inulin ratios of the initial rate of hydrolysis as an indicator of substrate specificity revealed about twofold improvement in inulinase versus sucrose activity by enzyme modification. Molecular dynamics simulations and molecular docking approaches were employed to explain the observed structural and functional thermostabilization of endo-inulinase upon modification. We hypothesize the establishment of intramolecular interactions between the covalently attached PLP-Lys381 and Arg526 and Ser376 residues as a representative of modification-originated intramolecular contacts in the modified enzyme.     

Cryptic functions of enzymes in chemical catalysis

Using a number of examples, this article demonstrates how the functional groups responsible for the catalytic activity of an enzyme must be studied within the context of the enzyme-substrate complex. Very often a substrate will actively cooperate with the enzyme to bring about its own transformation. The so-called cryptic functions of enzymes are considered in the case of seryl proteases which, according to the type of substrate or structural modification introduced in the enzyme, may exhibit esterase, amidase, protease, racemase or dehydratase activity. The cryptic functions may possess a physiological significance which reflects the evolutionary history of the protein. Alternatively they may offer a simple way of exploiting the enzymes as catalysts capable of taking part in the chemical reactions of biotechnological interest but little physiological importance.This work is dedicated to Prof.E. Wünsch (München) at the occasion of his 60^th birthday.     

Assemblage of signaling DNA enzymes with intriguing metal-ion specificities and pH dependences

We report a group of new DNA enzymes that possess a synchronized RNA-cleavage/fluorescence-signaling ability and exhibit wide-ranging metal-ion and pH dependences. These DNA catalysts were derived from a random-sequence DNA pool in a two-stage process: (1) establishment of a catalytic DNA population through repetitive rounds of in vitro selection at pH 4.0, and (2) sequence-diversification and catalytic-activity optimization through five parallel paths of in vitro evolution conducted at pH 3.0, 4.0, 5.0, 6.0, and 7.0, respectively. The deoxyribozymes were evolved to cleave the phosphodiester bond of a single ribonucleotide embedded in DNA and flanked immediately by two deoxyribonucleotides modified with a fluorophore and a quencher, respectively--a setting that synchronizes catalysis with fluorescence signaling. The most dominant catalyst from each pool was examined for metal-ion specificity, catalytic efficiency, pH dependence, and fluorescence-signaling capability. Individual catalysts have different metal-ion requirements and can generate as much as a 12-fold fluorescence enhancement upon RNA cleavage. Most of the DNA enzymes have a pH optimum coinciding with the selection pH and exhibit a rate constant approximating 1 min(-)(1) under optimal reaction conditions. The demonstration of DNA enzymes that are functional under extremely high acidity (such as pH 3 and 4) indicates that DNA has the ability to perform efficient catalysis even under harsh reaction conditions. The isolation of many new signaling DNA enzymes with broad pH optima and metal-ion specificities should facilitate the development of diverse deoxyribozyme-based biosensors.     

Simultaneous determination of water-soluble vitamins in selected food matrices by liquid chromatography/electrospray ionization tandem mass spectrometry

A rapid, simple and sensitive method based on liquid chromatography/tandem mass spectrometry (LC/MS/MS) with an electrospray ionization (ESI) source for the simultaneous analysis of fourteen water-soluble vitamins (B1, B2, two B3 vitamers, B5, five B6 vitamers, B8, B9, B12 and C) in various food matrices, i.e. maize flour, green and golden kiwi and tomato pulp, is presented here. Analytes were separated by ion-suppression reversed-phase liquid chromatography in less than 10 min and detected in positive ion mode. Sensitivity and specificity of this method allowed two important results to be achieved: (i) limits of detection of the analytes at ng g(-1) levels (except for vitamin C); (ii) development of a rapid sample treatment that minimizes analyte exposition to light, air and heat, eliminating any step of extract concentration. Analyte recovery depended on the type of matrix. In particular, recovery of the analytes in maize flour was > or =70%, with the exception of vitamin C, pyridoxal-5'-phosphate and vitamin B9 (ca 40%); with tomato pulp, recovery was > or =64%, except for vitamin C (41%); with kiwi, recovery was > or =73%, except for nicotinamide (ca. 30%).     

High‐throughput droplet‐based microfluidics for directed evolution of enzymes

Natural enzymes have evolved over millions of years to allow for their effective operation within specific environments. However, it is significant to note that despite their wide structural and chemical diversity, relatively few natural enzymes have been successfully applied to industrial processes. To address this limitation, directed evolution (DE) (a method that mimics the process of natural selection to evolve proteins toward a user‐defined goal) coupled with droplet‐based microfluidics allows the detailed analysis of millions of enzyme variants on ultra‐short timescales, and thus the design of novel enzymes with bespoke properties. In this review, we aim at presenting the development of DE over the last years and highlighting the most important advancements in droplet‐based microfluidics, made in this context towards the high‐throughput demands of enzyme optimization. Specifically, an overview of the range of microfluidic unit operations available for the construction of DE platforms is provided, focusing on their suitability and benefits for cell‐based assays, as in the case of directed evolution experimentations.