Protonation of the Binuclear Metal Center within the Active Site of Phosphotriesterase

Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases

Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade N- acyl-L-homoserine lactones (AHLs). In doing so, they play a role in a microbial communication system, quorum sensing, which contributes to pathogenicity and biofilm formation. There is currently great interest in designing quorum quenching ( QQ ) enzymes that can interfere with this communication and be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific targets requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of the MLL GcL, which is highly proficient, thermostable, and has broad substrate specificity. Strikingly, we show that GcL does not only accept a broad range of substrates but is also capable of utilizing different reaction mechanisms that are differentially used in function of the substrate structure or the remodeling of the active site via mutations. Comparison of GcL to other lactonases such as AiiA and AaL demonstrates similar mechanistic promiscuity, suggesting this is a shared feature across lactonases in this enzyme family. Mechanistic promiscuity has previously been observed in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general-acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and an engineering perspective: in addition to optimizing for specific substrates, it is possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes, but also of other mechanistically promiscuous enzymes.

Mechanism of Radical Initiation and Transfer in Class Id Ribonucleotide Reductase Based on Density Functional Theory

Class Id ribonucleotide reductase (RNR) is a newly discovered enzyme, which employs the dimanganese cofactor in the superoxidized state (Mn^III/Mn^IV) as the radical initiator. The dimanganese cofactor of class Id RNR in the reduced state (inactive) is clearly based on the crystal structure of the Fj-β subunit. However, the state of the dimanganese cofactor of class Id RNR in the oxidized state (active) is not known. The X-band EPR spectra have shown that the activated Fj-β subunit exists in two distinct complexes, 1 and 2. In this work, quantum mechanical/molecular mechanical calculations were carried out to study class Id RNR. First, we have determined that complex 2 contains a Mn^III-(μ-oxo)₂-Mn^IV cluster, and complex 1 contains a Mn^III-(μ-hydroxo/μ-oxo)-Mn^IV cluster. Then, based on the determined dimanganese cofactors, the mechanism of radical initiation and transfer in class Id RNR is revealed. The Mn^III-(μ-oxo)₂-Mn^IV cluster in complex 2 has not enough reduction potential to initiate radical transfer directly. Instead, it needs to be monoprotonated into Mn^III-(μ-hydroxo/μ-oxo)-Mn^IV (complex 1) before the radical transfer. The protonation state of μ-oxo can be regulated by changing the protein microenvironment, which is induced by the protein aggregation and separation of β subunits with α subunits. The radical transfer between the cluster of Mn^III-(μ-hydroxo/μ-oxo)-Mn^IV and Trp30 in the radical-transfer chain of the Fj-β subunit (Mn^III/Mn^IV ↔ His100 ↔ Asp194 ↔ Trp30 ↔ Arg99) is a water-mediated tri-proton-coupled electron transfer, which transfers proton from the ε-amino group of Lys71 to the carboxyl group of Glu97 via the water molecule Wat551 and the bridging μ-hydroxo ligand through a three-step reaction. This newly discovered proton-coupled electron-transfer mechanism in class Id RNR is different from those reported in the known Ia-Ic RNRs. The ε-amino group of Lys71, which serves as a proton donor, plays an important role in the radical transfer.

Molecular Dynamics-Derived Descriptor Informs the Impact of Mutation on the Catalytic Turnover Number in Lactonase Across Substrates

Molecular dynamics simulations have been extensively employed to reveal the roles of protein dynamics in mediating enzyme catalysis. However, simulation-derived predictive descriptors that inform the impacts of mutations on catalytic turnover numbers remain largely unexplored. In this work, we report the identification of molecular modeling-derived descriptors to predict mutation effect on the turnover number of lactonase SsoPox with both native and non-native substrates. The study consists of 10 enzyme-substrate complexes resulting from a combination of five enzyme variants with two substrates. For each complex, we derived 15 descriptors from molecular dynamics simulations and applied principal component analysis to rank the predictive capability of the descriptors. A top-ranked descriptor was identified, which is the solvent-accessible surface area (SASA) ratio of the substrate to the active site pocket. A uniform volcano-shaped plot was observed in the distribution of experimental activation free energy against the SASA ratio. To achieve efficient lactonase hydrolysis, a non-native substrate-bound enzyme variant needs to involve a similar range of the SASA ratio to the native substrate-bound wild-type enzyme. The descriptor reflects how well the enzyme active site pocket accommodates a substrate for reaction, which has the potential of guiding optimization of enzyme reaction turnover for non-native chemical transformations.

The evolution of phosphotriesterase for decontamination and detoxification of organophosphorus chemical warfare agents

The organophosphorus chemical warfare agents were initially synthesized in the 1930's and are some of the most toxic compounds ever discovered. The standard means of decontamination are either harsh chemical hydrolysis or high temperature incineration. Given the continued use of chemical warfare agents there are ongoing efforts to develop gentle environmentally friendly means of decontamination and medical counter measures to chemical warfare agent intoxication. Enzymatic decontamination offers the benefits of extreme specificity and mild conditions, allowing their use for both environmental and medical applications. The most promising enzyme for decontamination of the organophosphorus chemical warfare agents is the enzyme phosphotriesterase from Pseudomonas diminuta. However, the catalytic activity of the wild-type enzyme with the chemical warfare agents falls far below that seen with its best substrates, and its stereochemical preference is for the less toxic enantiomer of the chiral phosphorus center found in most chemical warfare agents. Rational design efforts have succeeded in the dramatic improvement of the stereochemical preference of PTE for the more toxic enantiomers. Directed evolution experiments, including site-saturation mutagenesis, targeted error-prone PCR, computational design, and quantitative library analysis, have systematically improved the catalytic activity against the chemical warfare nerve agents. These efforts have resulted in greater than 4-orders of magnitude improvement in catalytic activity and have led to the identification of variants that are highly effective at detoxifying both G-type and V-type nerve agents. The best of these variants have the ability to prevent intoxication when delivered as a post-exposure treatment for VX and as a pre-exposure treatment for G-agent intoxication with observed protective factors up to 60-fold. Combining the best variant, H257Y/L303T, with a PCB polymer coating has enabled the development of a long lasting circulating prophylactic treatment that is highly effective against sarin.

Transition State Analysis of the Reaction Catalyzed by the Phosphotriesterase from Sphingobium sp. TCM1

Organophosphorus flame retardants are stable toxic compounds used in nearly all durable plastic products and are considered major emerging pollutants. The phosphotriesterase from Sphingobium sp. TCM1 ( Sb-PTE) is one of the few enzymes known to be able to hydrolyze organophosphorus flame retardants such as triphenyl phosphate and tris(2-chloroethyl) phosphate. The effectiveness of Sb-PTE for the hydrolysis of these organophosphates appears to arise from its ability to hydrolyze unactivated alkyl and phenolic esters from the central phosphorus core. How Sb-PTE is able to catalyze the hydrolysis of the unactivated substituents is not known. To interrogate the catalytic hydrolysis mechanism of Sb-PTE, the pH dependence of the reaction and the effects of changing the solvent viscosity were determined. These experiments were complemented by measurement of the primary and secondary 18-oxygen isotope effects on substrate hydrolysis and a determination of the effects of changing the p K_a of the leaving group on the magnitude of the rate constants for hydrolysis. Collectively, the results indicated that a single group must be ionized for nucleophilic attack and that a separate general acid is not involved in protonation of the leaving group. The Brønsted analysis and the heavy atom kinetic isotope effects are consistent with an early associative transition state with subsequent proton transfers not being rate limiting. A novel binding mode of the substrate to the binuclear metal center and a catalytic mechanism are proposed to explain the unusual ability of Sb-PTE to hydrolyze unactivated esters from a wide range of organophosphate substrates.

Structural stability, acidity, and halide selectivity of the fluoride riboswitch recognition site

Using static and dynamics DFT methods we show that the Mg(2+)/F(-)/phosphate/water cluster at the center of the fluoride riboswitch is stable by its own and, once assembled, does not rely on any additional factor from the overall RNA fold. Further, we predict that the pKa of the water molecule bridging two Mg cations is around 8.4. We also demonstrate that the halide selectivity of the fluoride riboswitch is determined by the stronger Mg-F bond, which is capable of keeping together the cluster. Replacing F(-) with Cl(-) results in a cluster that is unstable under dynamic conditions. Similar conclusions on the structure and energetics of the cluster in the binding pocket of fluoride-inhibited pyrophosphatase suggest that the peculiarity of fluoride is in its ability to establish much stronger metal-halide bonds.

The protonation states of oxo-bridged Mn(IV) dimers resolved by experimental and computational Mn K pre-edge X-ray absorption spectroscopy

In nature, the protonation of oxo bridges is a commonly encountered mechanism for fine-tuning chemical properties and reaction pathways. Often, however, the protonation states are difficult to establish experimentally. This is of particular importance in the oxygen evolving complex of photosystem II, where identification of the bridging oxo protonation states is one of the essential requirements toward unraveling the mechanism. In order to establish a combined experimental and theoretical protocol for the determination of protonation states, we have systematically investigated a series of Mn model complexes by Mn K pre-edge X-ray absorption spectroscopy. An ideal test case for selective bis-μ-oxo-bridge protonation in a Mn dimer is represented by the system [Mn(IV)2(salpn)2(μ-OHn)2](n+). Although the three species [Mn(IV)2(salpn)2(μ-O)2], [Mn(IV)2(salpn)2(μ-O)(μ-OH)](+) and [Mn(IV)2(salpn)2(μ-OH)2](2+) differ only in the protonation of the oxo bridges, they exhibit distinct differences in the pre-edge region while maintaining the same edge energy. The experimental spectra are correlated in detail to theoretically calculated spectra. A time-dependent density functional theory approach for calculating the pre-edge spectra of molecules with multiple metal centers is presented, using both high spin (HS) and broken symmetry (BS) electronic structure solutions. The most intense pre-edge transitions correspond to an excitation of the Mn 1s core electrons into the unoccupied orbitals of local e(g) character (d(z)(2) and d(xy) based in the chosen coordinate system). The lowest energy experimental feature is dominated by excitations of 1s-α electrons, and the second observed feature is primarily attributed to 1s-β electron excitations. The observed energetic separation is due to spin polarization effects in spin-unrestricted density functional theory and models final state multiplet effects. The effects of spin polarization on the calculated Mn K pre-edge spectra, in both the HS and BS solutions, are discussed in terms of the strength of the antiferromagnetic coupling and associated changes in the covalency of Mn-O bonds. The information presented in this paper is complemented with the X-ray emission spectra of the same compounds published in an accompanying paper. Taken together, the two studies provide the foundation for a better understanding of the X-ray spectroscopic data of the oxygen evolving complex (OEC) in photosystem II.

Catalytic mechanisms for phosphotriesterases

Phosphotriesters are one class of highly toxic synthetic compounds known as organophosphates. Wide spread usage of organophosphates as insecticides as well as nerve agents has lead to numerous efforts to identify enzymes capable of detoxifying them. A wide array of enzymes has been found to have phosphotriesterase activity including phosphotriesterase (PTE), methyl parathion hydrolase (MPH), organophosphorus acid anhydrolase (OPAA), diisopropylfluorophosphatase (DFP), and paraoxonase 1 (PON1). These enzymes differ widely in protein sequence and three-dimensional structure, as well as in catalytic mechanism, but they also share several common features. All of the enzymes identified as phosphotriesterases are metal-dependent hydrolases that contain a hydrophobic active site with three discrete binding pockets to accommodate the substrate ester groups. Activation of the substrate phosphorus center is achieved by a direct interaction between the phosphoryl oxygen and a divalent metal in the active site. The mechanistic details of the hydrolytic reaction differ among the various enzymes with both direct attack of a hydroxide as well as covalent catalysis being found. This article is part of a Special Issue entitled: Chemistry and mechanism of phosphatases, diesterases and triesterases.

Cis-trans isomeric and polymorphic effects on the magnetic properties of water-bridged copper coordination chains

The synthesis and magnetic characterization of vanillin-based Cu(II) mononuclear complexes of formula [Cu(van)(2)(H(2)O)(2)](H(2)O)(x) (van = vanillinate; x = 0, compound 1; x = 2, compounds 2 and 3) were performed. Despite the presence of very similar [Cu(van)(2)(H(2)O)(2)] moieties, the crystal structures exhibit distinct Cu···Cu contacts and display three different through-H-bond exchange-coupling pathways. As a result of the relative positions of the water molecules, the experimental (MAGSUS) exchange-coupling constants are dissimilar, i.e., J(1) = -3.0 cm(-1) (the data have been fitted to the Bleaney-Bowers equation considering a dimer; 2J = -6.0 cm(-1)), J(2) = -4.0 cm(-1) (the data have been fitted to the Bonner-Fischer equation for a chain of monomeric copper(II) units), whereas compound 3 is paramagnetic. Subsequently, the theoretical density functional theory (DFT) and wave function theory-based (DDCI) calculations were carried out to better understand the role of the water molecule as a mediator of the magnetic coupling. The use of localized orbitals allows one to elucidate the role of the H-bonds in generating exchange interactions. Since the exchange-coupling constants are strongly dependent on the mechanisms selectively introduced, the role of the H-bond is demonstrated.

The organophosphate-degrading enzyme from Agrobacterium radiobacter displays mechanistic flexibility for catalysis

The OP (organophosphate)-degrading enzyme from Agrobacterium radiobacter (OpdA) is a binuclear metallohydrolase able to degrade highly toxic OP pesticides and nerve agents into less or non-toxic compounds. In the present study, the effect of metal ion substitutions and site-directed mutations on the catalytic properties of OpdA are investigated. The study shows the importance of both the metal ion composition and a hydrogen-bond network that connects the metal ion centre with the substrate-binding pocket using residues Arg254 and Tyr257 in the mechanism and substrate specificity of this enzyme. For the Co(II) derivative of OpdA two protonation equilibria (pKa1 ~5; pKa2 ~10) have been identified as relevant for catalysis, and a terminal hydroxide acts as the likely hydrolysis-initiating nucleophile. In contrast, the Zn(II) and Cd(II) derivatives only have one relevant protonation equilibrium (pKa ~4-5), and the μOH is the proposed nucleophile. The observed mechanistic flexibility may reconcile contrasting reaction models that have been published previously and may be beneficial for the rapid adaptation of OP-degrading enzymes to changing environmental pressures.

Protonation of a hydroxide anion bridging two divalent magnesium cations in water probed by first-principles metadynamics simulation

The protonation of a hydroxide anion (OH(-)) located between two magnesium cations (Mg(2+)) in aqueous solution has been investigated by first-principles metadynamics simulation. We observe that the complex Mg(2+)-OH(-)-Mg(2+) is stabilized by the coparticipation of the hydroxide anion to the first hydration shells of both the Mg(2+) cations. Contrary to the cases of OH(-) in pure water, the transfer of protons in the presence of the divalent metal ions turns out to be a slow chemical event. This can be ascribed to the decreased proton affinity of the bridging OH(-). Metadynamics simulation, used to overcome the difficulty of the long time scale required by the protonation of the bridging OH(-), has shown that the system possesses a great stability on the reactant state, characterized by a bioctahedral (6,6) solvation structure around the two Mg(2+) cations. The exploration of the free energy landscape shows that this stable bioctahedral configuration converts into a lower coordinated (5,6) structure, leading to a proton transfer from a water molecule belonging to the first solvation shell of the Mg(2+) ion having the lower coordination to the bridging OH(-); the free energy barrier for the protonation reaction is 11 kcal/mol, meaning that the bridging hydroxide is a weak base. During the proton transfer, the bridging OH(-) reverts to an H(2)O molecule, and this breaks the electrostatic coupling of the two Mg(2+) ions, which depart independently with their own hydration shells, one of which is entirely formed by water molecules. The second one carries the newly created OH(-). Our results show that the flexibility in the metal coordination plays a crucial role in both the protonation process of the bridging OH(-) and the separation of the metal cations, providing useful insight into the nature of proton transfer in binuclear divalent metal ions, with several biological implications, such as, for instance, transesterification of catalytic RNA.

Insights into the nitric oxide reductase mechanism of flavodiiron proteins from a flavin-free enzyme

Flavodiiron proteins (FDPs) catalyze reductive scavenging of dioxygen and nitric oxide in air-sensitive microorganisms. FDPs contain a distinctive non-heme diiron/flavin mononucleotide (FMN) active site. Alternative mechanisms for the nitric oxide reductase (NOR) activity consisting of either protonation of a diiron-bridging hyponitrite or "super-reduction" of a diferrous-dinitrosyl by the proximal FMNH(2) in the rate-determining step have been proposed. To test these alternative mechanisms, we examined a deflavinated FDP (deflavo-FDP) from Thermotoga maritima. The deflavo-FDP retains an intact diiron site but does not exhibit multiturnover NOR or O(2) reductase (O(2)R) activity. Reactions of the reduced (diferrous) deflavo-FDP with nitric oxide were examined by UV-vis absorption, EPR, resonance Raman, and FTIR spectroscopies. Anaerobic addition of nitric oxide up to one NO per diferrous deflavo-FDP results in formation of a diiron-mononitrosyl complex characterized by a broad S = (1)/(2 )EPR signal arising from antiferromagnetic coupling of an S = (3)/(2) {FeNO}(7) with an S = 2 Fe(II). Further addition of NO results in two reaction pathways, one of which produces N(2)O and the diferric site and the other of which produces a stable diiron-dinitrosyl complex. Both NO-treated and as-isolated deflavo-FDPs regain full NOR and O(2)R activities upon simple addition of FMN. The production of N(2)O upon addition of NO to the mononitrosyl deflavo-FDP supports the hyponitrite mechanism, but the concomitant formation of a stable diiron-dinitrosyl complex in the deflavo-FDP is consistent with a super-reduction pathway in the flavinated enzyme. We conclude that a diiron-mononitrosyl complex is an intermediate in the NOR catalytic cycle of FDPs.

Characterizations of chloro and aqua Mn(II) mononuclear complexes with amino-pyridine ligands. Comparison of their electrochemical properties with those of Fe(II) counterparts

The solution behavior of mononuclear Mn(II) complexes, namely, [(L(5)(2))MnCl](+) (1), [(L(5)(3))MnCl](+) (2), [(L(5)(2))Mn(OH(2))](2+) (3), [(L(5)(3))Mn(OH(2))](2+) (4), and [(L(6)(2))Mn(OH(2))](2+) (6), with L(5)(2/3) and L(6)(2) being penta- and hexadentate amino-pyridine ligands, is investigated in MeCN using EPR, UV-vis spectroscopies, and electrochemistry. The addition of one chloride ion onto species 6 leads to the formation of the complex [(L(6)(2))MnCl](+) (5) that is X-ray characterized. EPR and UV-vis spectra indicate that structure and redox states of complexes 1-6 are maintained in MeCN solution. Chloro complexes 1, 2, and 5 show reversible Mn(II)/Mn(III) process at 0.95, 1.02, and 1.05 V vs SCE, respectively, whereas solvated complexes 3, 4, and 6 show an irreversible anodic peak around 1.5 V vs SCE. Electrochemical oxidations of 1 and 5 leading to the Mn(III) complexes [(L(5)(2))MnCl](2+) (7) and [(L(6)(2))MnCl](2+) (8) are successful. The UV-vis signatures of 7 and 8 show features associated with chloro to Mn(III) LMCT and d-d transitions. The X-ray characterization of the heptacoordinated Mn(III) species 8 is also reported. The analogous electrochemical generation of the corresponding Mn(III) complex was not possible when starting from 2. The new mixed-valence di-mu-oxo [(L(5)(2))Mn(muO)(2)Mn(L(5)(2))](3+) species (9) can be obtained from 3, whereas the sister [(L(5)(3))Mn(muO)(2)Mn(L(5)(3))](3+) species can not be generated from 4. Such different responses upon oxidations are commented on with the help of comparison with related Mn/Fe complexes and are discussed in relation with the size of the metallacycle formed between the diamino bridge and the metal center (5- vs 6-membered). Lastly, a comparison between redox potentials of the studied Mn(II) complexes with those of Fe(II) analogues is drawn and completed with previously reported data on Mn/Fe isostructural systems. This gives us the opportunity to get some indirect insights into the metal specificity encountered in enzymes among which superoxide dismutase is the archetypal model.

Structural basis for natural lactonase and promiscuous phosphotriesterase activities

Organophosphates are the largest class of known insecticides, several of which are potent nerve agents. Consequently, organophosphate-degrading enzymes are of great scientific interest as bioscavengers and biodecontaminants. Recently, a hyperthermophilic phosphotriesterase (known as SsoPox), from the Archaeon Sulfolobus solfataricus, has been isolated and found to possess a very high lactonase activity. Here, we report the three-dimensional structures of SsoPox in the apo form (2.6 A resolution) and in complex with a quorum-sensing lactone mimic at 2.0 A resolution. The structure also reveals an unexpected active site topology, and a unique hydrophobic channel that perfectly accommodates the lactone substrate. Structural and mutagenesis evidence allows us to propose a mechanism for lactone hydrolysis and to refine the catalytic mechanism established for phosphotriesterases. In addition, SsoPox structures permit the correlation of experimental lactonase and phosphotriesterase activities and this strongly suggests lactonase activity as the cognate function of SsoPox. This example demonstrates that promiscuous activities probably constitute a large and efficient reservoir for the creation of novel catalytic activities.