Exploring the catalytic potential of the 3-His mononuclear nonheme Fe(II) center: discovery and characterization of an unprecedented maltol cleavage activity

Mononuclear nonheme iron enzymes (MNHEs) catalyze a range of very diverse reactions in O₂ metabolism, but they share a common principle active-site organization. To investigate a putative catalytic promiscuity of these enzymatic metal centers, we studied the reactivity of the 3-His ligated metal center of diketone cleaving enzyme (Dke1) toward non-native substrates, with a focus on alternative O₂ dependent reactions. From a screening approach, which aims at eliminating steric factors by including minimal substrate-substructures, three alternative, ‘non-β-dicarbonyl-cleavage’ reactions are identified, among them an unprecedented oxygenation of maltol. Maltol cleavage is characterized by steady state and fast kinetic measurements and shows an O₂ concentration dependent rate determining step k_cat/K_M(O₂) of 0.3 mM^− 1 s^− 1 and a strict coupling of O₂ reduction and substrate oxidation. Furthermore, the catalytic potential of the 3-His metal center for O₂ dependent catechol ring-cleavage and phenylpyruvate oxidation (PP) is demonstrated.     

NO binding to Mn-substituted homoprotocatechuate 2,3-dioxygenase: relationship to O2 reactivity

Iron(II)-containing homoprotocatechuate 2,3-dioxygenase (FeHPCD) activates O₂ to catalyze the aromatic ring opening of homoprotocatechuate (HPCA). The enzyme requires Fe^II for catalysis, but Mn^II can be substituted (MnHPCD) with essentially no change in the steady-state kinetic parameters. Near simultaneous O₂ and HPCA activation has been proposed to occur through transfer of an electron or electrons from HPCA to O₂ through the divalent metal. In O₂ reactions with MnHPCD–HPCA and the 4-nitrocatechol (4NC) complex of the His200Asn (H200N) variant of FeHPCD, this transfer has resulted in the detection of a transient M^III–O₂ ^·? species that is not observed during turnover of the wild-type FeHPCD. The factors governing formation of the M^III–O₂ ^·? species are explored here by EPR spectroscopy using MnHPCD and nitric oxide (NO) as an O₂ surrogate. Both the HPCA and the dihydroxymandelic substrate complexes of MnHPCD bind NO, thus representing the first reported stable MnNO complexes of a nonheme enzyme. In contrast, the free enzyme, the MnHPCD–4NC complex, and the MnH200N and MnH200Q variants with or without HPCA bound do not bind NO. The MnHPCD–ligand complexes that bind NO are also active in normal O₂-linked turnover, whereas the others are inactive. Past studies have shown that FeHPCD and the analogous variants and catecholic ligand complexes all bind NO, and are active in normal turnover. This contrasting behavior may stem from the ability of the enzyme to maintain the approximately 0.8-V difference in the solution redox potentials of Fe^II and Mn^II. Owing to the higher potential of Mn, the formation of the NO adduct or the O₂ adduct requires both strong charge donation from the bound catecholic ligand and additional stabilization by interaction with the active-site His200. The same nonoptimal electronic and structural forces that prevent NO and O₂ binding in MnHPCD variants may lead to inefficient electron transfer from the catecholic substrate to the metal center in variants of FeHPCD during O₂-linked turnover. Accordingly, past studies have shown that intermediate Fe^III species are observed for these mutant enzymes.     

Determinants of substrate specificity and the role of metal in the reactions of ribulosebisphosphate carboxylase/oxygenase

Recent studies have provided a fairly detailed view of the various intermediates involved in the reactions of ribulosebisphosphate carboxylase and the manner in which the catalytically essential metal atom might catalyze their interconversions. A better understanding of how the enzyme distinguishes between its alternate substrates, CO₂ and O₂, has also emerged. The results of these studies should prove useful in anticipating possible ways in which the enzyme's substrate specificity might be manipulated. Together, the techniques that are described constitute a powerful methodology for more refined experimentation aimed at understanding the curious reactivities of ribulosebisphosphate carboxylase.     

A hyperactive cobalt-substituted extradiol-cleaving catechol dioxygenase

Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum (HPCD) has an Fe(II) center in its active site that can be replaced with Mn(II) or Co(II). Whereas Mn-HPCD exhibits steady-state kinetic parameters comparable to those of Fe-HPCD, Co-HPCD behaves somewhat differently, exhibiting significantly higher K_\textM^{\textO ₂} K_{\text{M}}^{{{\text{O}}_{ 2} }} and k _cat. The high activity of Co-HPCD is surprising, given that cobalt has the highest standard M(III/II) redox potential of the three metals. Comparison of the X-ray crystal structures of the resting and substrate-bound forms of Fe-HPCD, Mn-HPCD, and Co-HPCD shows that metal substitution has no effect on the local ligand environment, the conformational integrity of the active site, or the overall protein structure, suggesting that the protein structure does not differentially tune the potential of the metal center. Analysis of the steady-state kinetics of Co-HPCD suggests that the Co(II) center alters the relative rate constants for the interconversion of intermediates in the catalytic cycle but still allows the dioxygenase reaction to proceed efficiently. When compared with the kinetic data for Fe-HPCD and Mn-HPCD, these results show that dioxygenase catalysis can proceed at high rates over a wide range of metal redox potentials. This is consistent with the proposed mechanism in which the metal mediates electron transfer between the catechol substrate and O₂ to form the postulated [M(II)(semiquinone)superoxo] reactive species. These kinetic differences and the spectroscopic properties of Co-HPCD provide new tools with which to explore the unique O₂ activation mechanism associated with the extradiol dioxygenase family.     

Author index to volume 154

Horseradish peroxidase-catalyzed N-demethylation of aminopyrine and dimethylaniline results in generation of free radical intermediates which can interact with glutathione (GSH) to form a glutathione radical. This can either dimerize to yield glutathione disulfide or react with O₂ to form oxygenated products of glutathione. Ethylmorphine is not a substrate in the peroxidase-mediated reaction, and free radical intermediates which react with GSH, are not formed from aminopyrine and dimethylaniline when the horseradish peroxidase/H₂O₂ system is replaced by liver microsomes and NADPH. Therefore, it appears unlikely that formation of free radical intermediates can be responsible for the depletion of GSH observed during N-demethylation of several drugs in isolated liver cells.     

Dioxygenases Without Requirement for Cofactors: Identification of Amino Acid Residues Involved in Substrate Binding and Catalysis, and Testing for Rate-Limiting Steps in the Reaction of 1H-3-Hydroxy-4-oxoquinaldine 2,4-dioxygenase

1H-3-Hydroxy-4-oxoquinaldine 2,4-dioxygenase (Hod), catalyzing cleavage of its heteroaromatic substrate to form carbon monoxide and N-acetylanthranilate, belongs to the α/β hydrolase fold family of enzymes. Analysis of protein variants suggested that Hod has adapted active-site residues of the α/β hydrolase fold for the dioxygenolytic reaction. H251 was recently shown to act as a general base to abstract a proton from the organic substrate. Residue S101, which corresponds to the nucleophile of the catalytic triad of α/β-hydrolases, presumably participates in binding the heteroaromatic substrate. H102 and residues located in the topological region of the triad’s acidic residue appear to influence O₂ binding and reactivity. A tyrosine residue might be involved in the turnover of the ternary complex [HodH⁺–3,4-dioxyquinaldine dianion–O₂]. Absence of viscosity effects and kinetic solvent isotope effects suggests that turnover of the ternary complex, rather than substrate binding, product release, or proton movements, involves the rate-determining step in the reaction catalyzed by Hod.     

New Insight into the Synthesis of Aromatic Azo Compounds Assisted by Surface Plasmon Resonance

The application of surface plasmon resonance (SPR)-assisted catalysis to synthesize aromatic azo compounds was first reported in 2010. The feasibility of SPR-assisted catalytic decomposition of aromatic azo compounds has also been confirmed, both experimentally and theoretically. Compared with traditional chemical synthesis methods, SPR-assisted catalysis has many advantages, such as high efficiency, low energy consumption, and high selectivity. The synthetic route to aromatic azo compounds and the kinetics thereof can be efficiently monitored by Raman spectroscopy. In this way, it has been confirmed that SPR-assisted catalysis occurs on the surface of noble metal nanoparticles (NPs). Mechanistically, the process involves transfer of electrons excited by the incident laser from noble metal NPs to ³O₂ in air to form ²O₂ ^? for the generation of SPR on the surface of the noble metal nanoparticles. The ²O₂ ^? can then react with the metal to form metal oxides or hydroxides, which in turn can react with the substrate molecule. The substrate molecule can gain a proton from a proton donor or lose a proton to form a radical, which can react further. This mechanism accounts for the conversion of 4-aminothiophenol (PATP) into 4, 4-dimercaptoazobenzene (DMAB). The metal oxide or hydroxide formed reacts with PATP in an acid-base neutralization process. PATP radicals (PATP ^· ) are formed by the loss of a proton, and pairing of two PATP ^· leads to the intermediate product DMHAB. Deprotonation DMHAB then gives the final product DMAB.     

NO binding to naphthalene dioxygenase

Nitric oxide (NO) is commonly used as an analogue for dioxygen in structural and spectroscopic studies of oxygen binding and oxygen activation. In this study, crystallographic structures of naphthalene dioxygenase (NDO) in complex with nitric oxide are reported. In the presence of the aromatic substrate indole, NO is bound end-on to the active-site mononuclear iron of NDO. The structural observations correlate well with spectroscopic measurements of NO binding to NDO in solution. However, the end-on binding of NO is in contrast to the recently reported structure of oxygen to the active-site iron of NDO that binds side-on. While NO is a good oxygen analogue with many similarities to O₂, the different binding mode of NO to the active-site iron atom leads to different mechanistic implications. Hence, caution needs to be used in extrapolating NO as an analogue to O₂ binding.     

Dicamba Monooxygenase: Structural Insights into a Dynamic Rieske Oxygenase that Catalyzes an Exocyclic Monooxygenation

Dicamba (2-methoxy-3,6-dichlorobenzoic acid) O-demethylase (DMO) is the terminal Rieske oxygenase of a three-component system that includes a ferredoxin and a reductase. It catalyzes the NADH-dependent oxidative demethylation of the broad leaf herbicide dicamba. DMO represents the first crystal structure of a Rieske non-heme iron oxygenase that performs an exocyclic monooxygenation, incorporating O₂ into a side-chain moiety and not a ring system. The structure reveals a 3-fold symmetric trimer (α₃) in the crystallographic asymmetric unit with similar arrangement of neighboring inter-subunit Rieske domain and non-heme iron site enabling electron transport consistent with other structurally characterized Rieske oxygenases. While the Rieske domain is similar, differences are observed in the catalytic domain, which is smaller in sequence length than those described previously, yet possessing an active-site cavity of larger volume when compared to oxygenases with larger substrates. Consistent with the amphipathic substrate, the active site is designed to interact with both the carboxylate and aromatic ring with both key polar and hydrophobic interactions observed. DMO structures were solved with and without substrate (dicamba), product (3,6-dichlorosalicylic acid), and either cobalt or iron in the non-heme iron site. The substitution of cobalt for iron revealed an uncommon mode of non-heme iron binding trapped by the non-catalytic Co²⁺, which, we postulate, may be transiently present in the native enzyme during the catalytic cycle. Thus, we present four DMO structures with resolutions ranging from 1.95 to 2.2 Å, which, in sum, provide a snapshot of a dynamic enzyme where metal binding and substrate binding are coupled to observed structural changes in the non-heme iron and catalytic sites.     

The metal ion requirements of Arabidopsis thaliana Glx2-2 for catalytic activity

In an effort to better understand the structure, metal content, the nature of the metal centers, and enzyme activity of Arabidopsis thaliana Glx2-2, the enzyme was overexpressed, purified, and characterized using metal analyses, kinetics, and UV–vis, EPR, and ¹H NMR spectroscopies. Glx2-2-containing fractions that were purple, yellow, or colorless were separated during purification, and the differently colored fractions were found to contain different amounts of Fe and Zn(II). Spectroscopic analyses of the discrete fractions provided evidence for Fe(II), Fe(III), Fe(III)–Zn(II), and antiferromagnetically coupled Fe(II)–Fe(III) centers distributed among the discrete Glx2-2-containing fractions. The individual steady-state kinetic constants varied among the fractionated species, depending on the number and type of metal ion present. Intriguingly, however, the catalytic efficiency constant, k _cat/K _m, was invariant among the fractions. The value of k _cat/K _m governs the catalytic rate at low, physiological substrate concentrations. We suggest that the independence of k _cat/K _m on the precise makeup of the active-site metal center is evolutionarily related to the lack of selectivity for either Fe versus Zn(II) or Fe(II) versus Fe(III), in one or more metal binding sites.     

A heme•DNAzyme activated by hydrogen peroxide catalytically oxidizes thioethers by direct oxygen atom transfer rather than by a Compound I-like intermediate

Hemin [Fe(III)-protoporphyrin IX] is known to bind tightly to single-stranded DNA and RNA molecules that fold into G-quadruplexes (GQ). Such complexes are strongly activated for oxidative catalysis. These heme•DNAzymes and ribozymes have found broad utility in bioanalytical and medicinal chemistry and have also been shown to occur within living cells. However, how a GQ is able to activate hemin is poorly understood. Herein, we report fast kinetic measurements (using stopped-flow UV–vis spectrophotometry) to identify the H₂O₂-generated activated heme species within a heme•DNAzyme that is active for the oxidation of a thioether substrate, dibenzothiophene (DBT). Singular value decomposition and global fitting analysis was used to analyze the kinetic data, with the results being consistent with the heme•DNAzyme''s DBT oxidation being catalyzed by the initial Fe(III)heme–H₂O₂ complex. Such a complex has been predicted computationally to be a powerful oxidant for thioether substrates. In the heme•DNAzyme, the DNA GQ enhances both the kinetics of formation of the active intermediate as well as the oxidation step of DBT by the active intermediate. We show, using both stopped flow spectrophotometry and EPR measurements, that a classic Compound I is not observable during the catalytic cycle for thioether sulfoxidation.     

Molecular ruler of tripeptidylpeptidase II: mechanistic principle of exopeptidase selectivity

The structure of tripeptidylpeptidase II (TPPII) has shown that it belongs to the group of exopeptidases which use a double-Glu motif to convey aminopeptidase activity. TPPII has been implicated in vital biological processes. At least one of these, antigen processing, requires the involvement of its endopeptidase activity. In order to understand the extent and molecular basis of this unusual functional promiscuity we have performed a systematic kinetic analysis of wild type Drosophila melanogaster TPPII and five point mutants of the double-Glu-motif (E312/E343) involving natural substrates. Unlike the known double-Glu motives of other exopeptidases, the double-Glu motif of TPPII is distinctly asymmetrical: E312 is the crucial determinant of the aminotripeptidolytic ruler mechanism. It both blocks the active-site cleft at substrate position P4 and forms a salt bridge with the N-terminus of the substrate. In contrast, E343 forms a much weaker salt bridge than E312 and it does not have a blocking role. An endopeptidase substrate can bind at relatively high affinity if the length of the substrate permits binding to several S′ sites. However, the lacking alignment of the substrate by the double-Glu motif causes the endopeptidolytic K_cat/K_M of TPPII to be very low.     

Optimized Concentration of Redox Mediator and Surface Protection of Li Metal for Maintenance of High Energy Efficiency in Li–O2 Batteries

Recently, various approaches for adding redox mediators to electrolytes and introducing protective layers onto Li metal have been suggested to overcome the low energy efficiency and poor cycle life of Li–O₂ batteries. However, the catalytic effect of the redox mediator for oxygen evolution gradually deteriorates during repeated cycling owing to its decomposition at the surfaces of both the oxygen electrode (cathode) and the Li metal electrode (anode). Here, optimized Li–O₂ batteries are designed with a continuously effective redox mediator and a stable protective layer for the Li metal electrode by optimizing the LiBr concentration and introducing a graphene–polydopamine composite layer, respectively. These synergistic modifications lead to a reduction of the charge potential to below 3.4 V and significantly improve the stability and cycle life of Li–O₂ batteries. Consequently, a high energy efficiency of above 80% is maintained over 150 cycles. Herein, it is confirmed that the relationships between all the battery materials should be understood in order to improve the performance of Li–O₂ batteries.     

Chemical Bases of Nonspecific Immunity

Our knowledge on the nature and quantity of reactive O₂forms generated in phagocytes, particularly in neutrophil leucocytes, and their role in nonspecific immunity is reviewed. In thermodynamical terms, oxygen is a very reactive molecule and, hence, can react with most chemical elements and many organic molecules. In kinetic terms, O₂is rather inert. Its reactivity can be increased either by reduction or excitation. After accepting four electrons, O₂is finally reduced to H₂O. Partial reduction resulting in highly reactive intermediates, namely, superoxide anion (O₂ ^·–), hydrogen peroxide (H₂O₂), and hydroxyl radical (^·OH), is possible. Singlet oxygen (¹O₂) is the product of O₂excitation. Phagocytes acting like agents of nonspecific immunity generate such reactive forms of O₂.     

Mutations of Trp275 and Trp397 altered the binding selectivity of Vibrio carchariae chitinase A

Point mutations of the active-site residues Trp168, Tyr171, Trp275, Trp397, Trp570 and Asp392 were introduced to Vibrio carchariae chitinase A. The modeled 3D structure of the enzyme illustrated that these residues fully occupied the substrate binding cleft and it was found that their mutation greatly reduced the hydrolyzing activity against pNP-[GlcNAc]₂ and colloidal chitin. Mutant W397F was the only exception, as it instead enhanced the hydrolysis of the pNP substrate to 142% and gave no activity loss towards colloidal chitin. The kinetic study with the pNP substrate demonstrated that the mutations caused impaired K_m and k_cat values of the enzyme. A chitin binding assay showed that mutations of the aromatic residues did not change the binding equilibrium. Product analysis by thin layer chromatography showed higher efficiency of W275G and W397F in G4–G6 hydrolysis over the wild type enzyme. Though the time course of colloidal chitin hydrolysis displayed no difference in the cleavage behavior of the chitinase variants, the time course of G6 hydrolysis exhibited distinct hydrolytic patterns between wild-type and mutants W275G and W397F. Wild type initially hydrolyzed G6 to G4 and G2, and finally G2 was formed as the major end product. W275G primarily created G2–G5 intermediates, and later G2 and G3 were formed as stable products. In contrast, W397F initially produced G1–G5, and then the high-M_r intermediates (G3–G5) were broken down to G1 and G2 end products. This modification of the cleavage patterns of chitooligomers suggested that residues Trp275 and Trp397 are involved in defining the binding selectivity of the enzyme to soluble substrates.     

DNA Ligases: Progress and Prospects

DNA ligases seal 5′-PO₄ and 3′-OH polynucleotide ends via three nucleotidyl transfer steps involving ligase-adenylate and DNA-adenylate intermediates. DNA ligases are essential guardians of genomic integrity, and ligase dysfunction underlies human genetic disease syndromes. Crystal structures of DNA ligases bound to nucleotide and nucleic acid substrates have illuminated how ligase reaction chemistry is catalyzed, how ligases recognize damaged DNA ends, and how protein domain movements and active-site remodeling are used to choreograph the end-joining pathway. Although a shared feature of DNA ligases is their envelopment of the nicked duplex as a C-shaped protein clamp, they accomplish this feat by using remarkably different accessory structural modules and domain topologies. As structural, biochemical, and phylogenetic insights coalesce, we can expect advances on several fronts, including (i) pharmacological targeting of ligases for antibacterial and anticancer therapies and (ii) the discovery and design of new strand-sealing enzymes with unique substrate specificities.     

荧光光谱法定量测定纤维素酶活性架构中单个氨基酸突变对底物结合力的影响

纤维素酶活性架构是酶分子中多个氨基酸残基构成的可结合并催化底物的功能区,其中色氨酸等芳香族残基在该区域中起着重要作用.本研究利用荧光光谱法,定量分析了纤维素酶Ch Cel5A活性架构中色氨酸与底物的结合动力学过程,通过色氨酸荧光猝灭的定量分析,确定了色氨酸特异性结合时的底物浓度范围,并且测定了Ch Cel5A活性架构中单个氨基酸突变导致的底物结合常数的变化,与催化动力学参数比较发现,荧光光谱法可准确表征纤维素酶与底物的结合力及其单个残基突变引起动力学参数的变化.此外,由于p NP中含有强的吸电子基团,因而以p NPC等为配体时会高估与色氨酸的结合常数约20~100倍.荧光光谱法可以测定纤维素酶结合糖分子底物的动力学参数,该方法具有灵敏和快速的特点,这为蛋白质与底物之间相互作用的定量分析提供了新的视角.     

Suicide-Peroxide inactivation of microperoxidase-11: A kinetic study

The kinetics of microperoxidase-11 (MP-11) in the oxidation reaction of guaiacol (AH) by hydrogen peroxide was studied, taking into account the inactivation of enzyme during reaction by its suicide substrate, H₂O₂. Concentrations of substrates were so selected that: 1) the reaction was first-order in relation to benign substrate, AH and 2) high ratio of suicide substrate to the benign substrate, [H₂O₂]>>[AH]. Validation and reliability of the obtained kinetic equations were evaluated in various nonlinear and linear forms. Fitting of experimental data into the obtained integrated equation showed a close match between the kinetic model and the experimental results. Indeed, a similar mechanism to horseradish peroxidase was found for the suicide-peroxide inactivation of MP-11. Kinetic parameters of inactivation including the intact activity of MP-11, α_i, and the apparent inactivation rate constant, k_i, were obtained as 0.282 ± 0.006 min^{? 1} and 0.497 ± 0.013 min^{? 1} at [H₂O₂] = 1.0 mM, 27°C, phosphate buffer 5.0 mM, pH = 7.0. Results showed that inactivation of microperoxidase as a peroxidase model enzyme can occur even at low concentrations of hydrogen peroxide (0.4 mM).     

Aromatic residues in the C-terminal region of glutathione transferase A1-1 influence rate-determining steps in the catalytic mechanism [Biochimica et Biophysica Acta 1597 (2002) 157-163]

Human glutathione transferase A1-1 (GST A1-1) has a flexible C-terminal segment that forms a helix (α9) closing the active site upon binding of glutathione and a small electrophilic substrate such as 1-chloro-2,4-dinitrobenzene (CDNB). In the absence of active-site ligands, the C-terminal segment is not fixed in one position and is not detectable in the crystal structure. A key residue in the α9-helix is Phe 220, which can interact with both the enzyme-bound glutathione and the second substrate, and possibly guide the reactants into the transition state. Mutation of Phe 220 into Ala and Thr was shown to reduce the catalytic efficiency of GST A1-1. The mutation of an additional residue, Phe 222, caused further decrease in activity. The presence of a viscosogen in the reaction medium decreased the kinetic parameters k_cat and k_cat/K_m for the conjugation of CDNB catalyzed by wild-type GST A1-1, in agreement with the view that product release is rate limiting for the substrate-saturated enzyme. The mutations cause a decrease of the viscosity dependence of both kinetic parameters, indicating that the motion of the α9-helix is linked to catalysis in wild-type GST A1-1. The isomerization reaction with the alternative substrate Δ⁵-androstene-3,17-dione (AD) is affected in a similar manner by the viscosogens. The transition state energy of the isomerization reaction, like that of the CDNB conjugation, is lowered by Phe 220 as indicated by the effects of the mutations on k_cat/K_m. The results demonstrate that Phe 220 and Phe 222, in the dynamic C-terminal segment, influence rate-determining steps in the catalytic mechanism of both the substitution and the isomerization reactions.     

Kinetic properties and substrate inhibition of α-galactosidase from Aspergillus niger

The recombinant AglB produced by Pichia pastoris exhibited substrate inhibition behavior for the hydrolysis of p-nitrophenyl α-galactoside, whereas it hydrolyzed the natural substrates, including galactomanno-oligosaccharides and raffinose family oligosaccharides, according to the Michaelian kinetics. These contrasting kinetic behaviors can be attributed to the difference in the dissociation constant of second substrate from the enzyme and/or to the ability of the leaving group of the substrates. The enzyme displays the grater k_cat/K_m values for hydrolysis of the branched α-galactoside in galactomanno-oligosaccharides than that of raffinose and stachyose. A sequence comparison suggested that AglB had a shallow active-site pocket, and it can allow to hydrolyze the branched α-galactosides, but not linear raffinose family oligosaccharides.