Mechanism of post-translational quinone formation in copper amine oxidases and its relationship to the catalytic turnover

Replacement of Tyrosines by Unnatural Amino Acid Aminophenylalanine Leads to Metal-Mediated Aniline Free Radical Formation in a Copper Amine Oxidase

Copper amine oxidases (CAOs) catalyze the oxidative deamination of primary amines to aldehyde, ammonia, and hydrogen peroxide as products and are widely distributed in bacteria, plants, and eukaryotes. These enzymes initiate the single turnover, post-translational conversion of an active site tyrosine to the redox cofactor 2,4,5-trihydroxyphenylalanine quinone (TPQ), subsequently employing TPQ to catalyze steady-state amine oxidation. The mechanisms of TPQ biogenesis and steady-state amine oxidation have been studied extensively, with consensus mechanisms proposed for both reactions. One unresolved issue has been whether the Cu2+ center must undergo formal reduction to Cu1+ in the course of the reaction. Herein, we investigate the properties of the active site of a yeast (Hansenula polymorpha) amine oxidase (HPAO) that has undergone site-specific insertion of a para-aminophenylalanine (pAF) into the position of either the precursor tyrosine to TPQ (Y405) or the two strictly conserved neighboring tyrosines (Y305 and Y407). While our original intention was to interrogate cofactor biogenesis using a precursor unnatural amino acid (UAA) of altered redox potential and pKa, we instead observe an unanticipated reaction assigned to an intramolecular electron transfer from pAF to the active site copper ion. We establish the generality of the observed active site chemistry using exogenously added, aniline-containing substrates under conditions that prevent side chain amine oxidation. The results support previous proposals that the activation of the TPQ precursor occurs in the absence of a formal valence change at the active site copper site. The described reaction of pAFs with the active site redox Cu2+ center of HPAO provides a prototype for either the engineering of the enzymatic oxidation of exogenous anilines or the insertion of site-specific free radical probes within proteins.

An intramolecular macrocyclase in plant ribosomal peptide biosynthesis

The biosynthetic dogma of ribosomally synthesized and posttranslationally modified peptides (RiPP) involves enzymatic intermolecular modification of core peptide motifs in precursor peptides. The plant-specific BURP-domain protein family, named after their four founding members, includes autocatalytic peptide cyclases involved in the biosynthesis of side-chain-macrocyclic plant RiPPs. Here we show that AhyBURP, a representative of the founding Unknown Seed Protein-type BURP-domain subfamily, catalyzes intramolecular macrocyclizations of its core peptide during the sequential biosynthesis of monocyclic lyciumin I via glycine-tryptophan crosslinking and bicyclic legumenin via glutamine-tyrosine crosslinking. X-ray crystallography of AhyBURP reveals the BURP-domain fold with two type II copper centers derived from a conserved stapled-disulfide and His motif. We show the macrocyclization of lyciumin-C(sp3)-N-bond formation followed by legumenin-C(sp3)-O-bond formation requires dioxygen and radical involvement based on enzyme assays in anoxic conditions and isotopic labeling. Our study expands enzymatic intramolecular modifications beyond catalytic moiety and chromophore biogenesis to RiPP biosynthesis.

Insight into the Spatial Arrangement of the Lysine Tyrosylquinone and Cu2+ in the Active Site of Lysyl Oxidase-like 2

Lysyl oxidase-2 (LOXL2) is a Cu²⁺ and lysine tyrosylquinone (LTQ)-dependent amine oxidase that catalyzes the oxidative deamination of peptidyl lysine and hydroxylysine residues to promote crosslinking of extracellular matrix proteins. LTQ is post-translationally derived from Lys653 and Tyr689, but its biogenesis mechanism remains still elusive. A 2.4 Å Zn²⁺-bound precursor structure lacking LTQ (PDB:5ZE3) has become available, where Lys653 and Tyr689 are 16.6 Å apart, thus a substantial conformational rearrangement is expected to take place for LTQ biogenesis. However, we have recently shown that the overall structures of the precursor (no LTQ) and the mature (LTQ-containing) LOXL2s are very similar and disulfide bonds are conserved. In this study, we aim to gain insights into the spatial arrangement of LTQ and the active site Cu²⁺ in the mature LOXL2 using a recombinant LOXL2 that is inhibited by 2-hydrazinopyridine (2HP). Comparative UV-vis and resonance Raman spectroscopic studies of the 2HP-inhibited LOXL2 and the corresponding model compounds and an EPR study of the latter support that 2HP-modified LTQ serves as a tridentate ligand to the active site Cu². We propose that LTQ resides within 2.9 Å of the active site of Cu²⁺ in the mature LOXL2, and both LTQ and Cu²⁺ are solvent-exposed.

Molecular cloning, expression, and functional analysis of copper amine oxidase gene from mulberry (Morus alba L.)

In this study, we investigated a key enzyme encoded by the gene copper amine oxidase (MaCAO), which is involved in the biosynthetic pathway of 1-deoxynojirimycin (DNJ)¹, an active ingredient in mulberry leaves. The 1680 bp long MaCAO was successfully cloned (GenBank accession no: MH205733). Subsequently, MaCAO was heterologously expressed using a recombinant plasmid, pET-22b (+)/MaCAO in Escherichia coli BL21 (DE3). A protein with a molecular mass of 62.9 kDa was obtained, whose function was validated through enzymatic reaction. Bioinformatics analysis identified that MaCAO contained the same conserved domain as that of copper amine oxidases ("NYDY"). Furthermore, the tertiary structure of the predicted protein using homology modeling revealed 46% similarity with that of copper amine oxidase (Protein Data Bank ID: 1W2Z). Gas chromatography-mass spectrometry analysis of the enzymatic reaction revealed that MaCAO could catalyze 1,5-pentanediamine to produce 5-aminopentanal. Additionally, levels of mulberry leaf DNJ content were significantly positively correlated with expression levels of MaCAO (P < 0.001). Our results conclude that MaCAO is the key enzyme involved in the biosynthetic pathway of DNJ. The function of MaCAO is validated, providing a foundation for the further analysis of biosynthetic pathways of DNJ in mulberry leaves using tools of synthetic biology.

Copper‐Catalyzed Monooxygenation of Phenols: Evidence for a Mononuclear Reaction Mechanism

The Cu^I salts [Cu(CH₃CN)₄]PF and [Cu(oDFB)₂]PF with the very weakly coordinating anion Al(OC(CF₃)₃)₄⁻ (PF) as well as [Cu(NEt₃)₂]PF comprising the unique, linear bis‐triethylamine complex [Cu(NEt₃)₂]⁺ were synthesized and examined as catalysts for the conversion of monophenols to o‐quinones. The activities of these Cu^I salts towards monooxygenation of 2,4‐di‐tert‐butylphenol (DTBP‐H) were compared to those of [Cu(CH₃CN)₄]X salts with “classic” anions (BF₄⁻, OTf⁻, PF₆⁻), revealing an anion effect on the activity of the catalyst and a ligand effect on the reaction rate. The reaction is drastically accelerated by employing Cu^II‐semiquinone complexes as catalysts, indicating that formation of a Cu^II complex precedes the actual catalytic cycle. This result and other experimental observations show that with these systems the oxygenation of monophenols does not follow a dinuclear, but a mononuclear pathway analogous to that of topaquinone cofactor biosynthesis in amine oxidase.

Plant Copper Metalloenzymes As Prospects for New Metabolism Involving Aromatic Compounds

Copper is an important transition metal cofactor in plant metabolism, which enables diverse biocatalysis in aerobic environments. Multiple classes of plant metalloenzymes evolved and underwent genetic expansions during the evolution of terrestrial plants and, to date, several representatives of these copper enzyme classes have characterized mechanisms. In this review, we give an updated overview of chemistry, structure, mechanism, function and phylogenetic distribution of plant copper metalloenzymes with an emphasis on biosynthesis of aromatic compounds such as phenylpropanoids (lignin, lignan, flavonoids) and cyclic peptides with macrocyclizations via aromatic amino acids. We also review a recent addition to plant copper enzymology in a copper-dependent peptide cyclase called the BURP domain. Given growing plant genetic resources, a large pool of copper biocatalysts remains to be characterized from plants as plant genomes contain on average more than 70 copper enzyme genes. A major challenge in characterization of copper biocatalysts from plant genomes is the identification of endogenous substrates and catalyzed reactions. We highlight some recent and future trends in filling these knowledge gaps in plant metabolism and the potential for genomic discovery of copper-based enzymology from plants.

Formation of Ni(II)-phenoxyl radical complexes by O2: a mechanistic insight into the reaction of Ni(II)-phenol complexes with O2

A reaction of Ni(ClO4)2·6H2O with a tripodal ligand having two di(tert-butyl)phenol moieties, H2tbuL, and 1 equivalent of triethylamine in CH2Cl2/CH3OH (1 : 1, v/v) under N2 gave a NiII-(phenol)(phenolate) complex, [Ni(HtbuL)(CH3OH)2]ClO4. The formation of the NiII-phenoxyl radical complex by O2 was observed in the reaction of this complex in the solid state. On the other hand, the NiII-phenoxyl radical complex [Ni(Me2NL)(CH3OH)2]ClO4 was obtained by the reaction of H2Me2NL having a p-(dimethylamino)phenol moiety with Ni(ClO4)2·6H2O in a similar procedure under O2, through the oxidation of the NiII-(phenol)(phenolate) complex. However, a direct redox reaction of the NiII ion could not be detected in the phenoxyl radical formation. The results of the reaction kinetics, XAS and X-ray structure analyses suggested that the O2 oxidation from the NiII-(phenol)(phenolate) complex to the NiII-phenoxyl radical complex occurs via the proton transfer-electron transfer (PT-ET) type mechanism of the phenol moiety weakly coordinated to the nickel ion.

Moving Through Barriers in Science and Life

This first serious attempt at an autobiographical accounting has forced me to sit still long enough to compile my thoughts about a long personal and scientific journey. I especially hope that my trajectory will be of interest and perhaps beneficial to much younger women who are just getting started in their careers. To paraphrase from Virginia Woolf's writings in A Room of One's Own at the beginning of the 20th century, "for most of history Anonymous was a Woman." However, Ms. Woolf is also quoted as saying "nothing has really happened until it has been described," a harbinger of the enormous historical changes that were about to be enacted and recorded by women in the sciences and other disciplines. The progress in my chosen field of study-the chemical basis of enzyme action-has also been remarkable, from the first description of an enzyme's 3D structure to a growing and deep understanding of the origins of enzyme catalysis.

Targeting the lysyl oxidases in tumour desmoplasia

The extracellular matrix (ECM) is a fundamental component of tissue microenvironments and its dysregulation has been implicated in a number of diseases, in particular cancer. Tumour desmoplasia (fibrosis) accompanies the progression of many solid cancers, and is also often induced as a result of many frontline chemotherapies. This has recently led to an increased interest in targeting the underlying processes. The major structural components of the ECM contributing to desmoplasia are the fibrillar collagens, whose key assembly mechanism is the enzymatic stabilisation of procollagen monomers by the lysyl oxidases. The lysyl oxidase family of copper-dependent amine oxidase enzymes are required for covalent cross-linking of collagen (as well as elastin) molecules into the mature ECM. This key step in the assembly of collagens is of particular interest in the cancer field since it is essential to the tumour desmoplastic response. LOX family members are dysregulated in many cancers and consequently the development of small molecule inhibitors targeting their enzymatic activity has been initiated by many groups. Development of specific small molecule inhibitors however has been hindered by the lack of crystal structures of the active sites, and therefore alternate indirect approaches to target LOX have also been explored. In this review, we introduce the importance of, and assembly steps of the ECM in the tumour desmoplastic response focussing on the role of the lysyl oxidases. We also discuss recent progress in targeting this family of enzymes as a potential therapeutic approach.

Characterization of the Preprocessed Copper Site Equilibrium in Amine Oxidase and Assignment of the Reactive Copper Site in Topaquinone Biogenesis

Copper-dependent amine oxidases produce their redox active cofactor, 2,4,5-trihydroxyphenylalanine quinone (TPQ), via the Cu^II-catalyzed oxygenation of an active site tyrosine. This study addresses possible mechanisms for this biogenesis process by presenting the geometric and electronic structure characterization of the Cu^II-bound, prebiogenesis (preprocessed) active site of the enzyme Arthrobacter globiformis amine oxidase (AGAO). Cu^II-loading into the preprocessed AGAO active site is slow ( k_obs = 0.13 h^-1), and is preceded by Cu^II binding in a separate kinetically favored site that is distinct from the active site. Preprocessed active site Cu^II is in a thermal equilibrium between two species, an entropically favored form with tyrosine protonated and unbound from the Cu^II site, and an enthalpically favored form with tyrosine bound deprotonated to the Cu^II active site. It is shown that the Cu^II-tyrosinate bound form is directly active in biogenesis. The electronic structure determined for the reactive form of the preprocessed Cu^II active site is inconsistent with a biogenesis pathway that proceeds through a Cu^I-tyrosyl radical intermediate, but consistent with a pathway that overcomes the spin forbidden reaction of ³O₂ with the bound singlet substrate via a three-electron concerted charge-transfer mechanism.

Activation of dioxygen by copper metalloproteins and insights from model complexes

Nature uses dioxygen as a key oxidant in the transformation of biomolecules. Among the enzymes that are utilized for these reactions are copper-containing metalloenzymes, which are responsible for important biological functions such as the regulation of neurotransmitters, dioxygen transport, and cellular respiration. Enzymatic and model system studies work in tandem in order to gain an understanding of the fundamental reductive activation of dioxygen by copper complexes. This review covers the most recent advancements in the structures, spectroscopy, and reaction mechanisms for dioxygen-activating copper proteins and relevant synthetic models thereof. An emphasis has also been placed on cofactor biogenesis, a fundamentally important process whereby biomolecules are post-translationally modified by the pro-enzyme active site to generate cofactors which are essential for the catalytic enzymatic reaction. Significant questions remaining in copper-ion-mediated O2-activation in copper proteins are addressed.

Aerobic catalytic systems inspired by copper amine oxidases: recent developments and synthetic applications

Recently, chemists have developed aerobic quinone-based catalytic systems in order to reproduce enzymatic activity and selectivity of copper amine oxidases but also to expand the scope of amine substrates.

Lysyl Oxidase Isoforms and Potential Therapeutic Opportunities for Fibrosis and Cancer

INTRODUCTION

The lysyl oxidase family of enzymes is classically known as being required for connective tissue maturation by oxidizing lysine residues in elastin and lysine and hydroxylysine residues in collagen precursors. The resulting aldehydes then participate in cross-link formation, which is required for normal connective tissue integrity. These enzymes have biological functions that extend beyond this fundamental biosynthetic role, with contributions to angiogenesis, cell proliferation, and cell differentiation. Dysregulation of lysyl oxidases occurs in multiple pathologies including fibrosis, primary and metastatic cancers, and complications of diabetes in a variety of tissues.

AREAS COVERED

This review summarizes the major findings of novel roles for lysyl oxidases in pathologies, and highlights some of the potential therapeutic approaches that are in development and which stem from these new findings.

EXPERT OPINION

Fundamental questions remain regarding the mechanisms of novel biological functions of this family of proteins, and regarding functions that are independent of their catalytic enzyme activity. However, progress is underway in the development of isoform-specific pharmacologic inhibitors, potential therapeutic antibodies and gaining an increased understanding of both tumor suppressor and metastasis promotion activities. Ultimately, this is likely to lead to novel therapeutic agents.

Enzymatic and non-enzymatic functions of the lysyl oxidase family in bone

Advances in the understanding of the biological roles of the lysyl oxidase family of enzyme proteins in bone structure and function are reviewed. This family of proteins is well-known as catalyzing the final reaction required for cross-linking of collagens and elastin. Novel emerging roles for these proteins in the phenotypic development of progenitor cells and in angiogenesis are highlighted and which point to enzymatic and non-enzymatic roles for this family in bone development and homeostasis and in disease. The explosion of interest in the lysyl oxidase family in the cancer field highlights the need to have a better understanding of the functions of this protein family in normal and abnormal connective tissue homeostasis at fundamental molecular and cellular levels including in mineralized tissues.

Bioinspired design of redox-active ligands for multielectron catalysis: effects of positioning pyrazine reservoirs on cobalt for electro- and photocatalytic generation of hydrogen from water

Mononuclear metalloenzymes in nature can function in cooperation with precisely positioned redox-active organic cofactors in order to carry out multielectron catalysis. Inspired by the finely tuned redox management of these bioinorganic systems, we present the design, synthesis, and experimental and theoretical characterization of a homologous series of cobalt complexes bearing redox-active pyrazines. These donor moieties are locked into key positions within a pentadentate ligand scaffold in order to evaluate the effects of positioning redox non-innocent ligands on hydrogen evolution catalysis. Both metal- and ligand-centered redox features are observed in organic as well as aqueous solutions over a range of pH values, and comparison with analogs bearing redox-inactive zinc(ii) allows for assignments of ligand-based redox events. Varying the geometric placement of redox non-innocent pyrazine donors on isostructural pentadentate ligand platforms results in marked effects on observed cobalt-catalyzed proton reduction activity. Electrocatalytic hydrogen evolution from weak acids in acetonitrile solution, under diffusion-limited conditions, reveals that the pyrazine donor of axial isomer 1-Co behaves as an unproductive electron sink, resulting in high overpotentials for proton reduction, whereas the equatorial pyrazine isomer complex 2-Co is significantly more active for hydrogen generation at lower voltages. Addition of a second equatorial pyrazine in complex 3-Co further minimizes overpotentials required for catalysis. The equatorial derivative 2-Co is also superior to its axial 1-Co congener for electrocatalytic and visible-light photocatalytic hydrogen generation in biologically relevant, neutral pH aqueous media. Density functional theory calculations (B3LYP-D2) indicate that the first reduction of catalyst isomers 1-Co, 2-Co, and 3-Co is largely metal-centered while the second reduction occurs at pyrazine. Taken together, the data establish that proper positioning of non-innocent pyrazine ligands on a single cobalt center is indeed critical for promoting efficient hydrogen catalysis in aqueous media, akin to optimally positioned redox-active cofactors in metalloenzymes. In a broader sense, these findings highlight the significance of electronic structure considerations in the design of effective electron-hole reservoirs for multielectron transformations.

Cu(II)-mediated phenol oxygenation: chemical evidence implicates a unique role of the enzyme active site in promoting the chemically difficult tyrosine monooxygenation in TPQ cofactor biogenesis of copper amine oxidases

Cu(II)-mediated autoxidations of 4-tert-butylphenol under various conditions was studied, the data confirmed imidazole is the best ligand to promote phenol oxygenation. The same reaction of 2,4-di-tert-butylphenol proceeded much more quickly to lead nearly exclusively to oxidative coupling rather than oxygenation under high pressure O2. These results suggested that Cu(II)-catalyzed phenol autoxidation by activating O2 and phenol in terms of a phenoxy radical (ArO)-Cu(II)-superoxide ternary complex, whereas selectivity between oxygenation and coupling depends mainly on the electronic structure of ArO. It is appeared that CuAOs could achieve stoichiometric tyrosine monooxygenation by modulating the redox potential of Cu(II) and stabilizing the ternary complex through protein conformational adjustment.

Human copper-dependent amine oxidases

Copper amine oxidases (CAOs) are a class of enzymes that contain Cu(2+) and a tyrosine-derived quinone cofactor, catalyze the conversion of a primary amine functional group to an aldehyde, and generate hydrogen peroxide and ammonia as byproducts. These enzymes can be classified into two non-homologous families: 2,4,5-trihydroxyphenylalanine quinone (TPQ)-dependent CAOs and the lysine tyrosylquinone (LTQ)-dependent lysyl oxidase (LOX) family of proteins. In this review, we will focus on recent developments in the field of research concerning human CAOs and the LOX family of proteins. The aberrant expression of these enzymes is linked to inflammation, fibrosis, tumor metastasis/invasion and other diseases. Consequently, there is a critical need to understand the functions of these proteins at the molecular level, so that strategies targeting these enzymes can be developed to combat human diseases.

Cofactor biosynthesis through protein post-translational modification

Post-translational modifications of amino acids can be used to generate novel cofactors capable of chemistries inaccessible to conventional amino acid side chains. The biosynthesis of these sites often requires one or more enzyme or protein accessory factors, the functions of which are quite diverse and often difficult to isolate in cases where multiple enzymes are involved. Herein is described the current knowledge of the biosynthesis of urease and nitrile hydratase metal centers, pyrroloquinoline quinone, hypusine, and tryptophan tryptophylquinone cofactors along with the most recent work elucidating the functions of individual accessory factors in these systems. These examples showcase the breadth and diversity of this continually expanding field.

Implication for functions of the ectopic adipocyte copper amine oxidase (AOC3) from purified enzyme and cell-based kinetic studies

AOC3 is highly expressed in adipocytes and smooth muscle cells, but its function in these cells is currently unknown. The in vivo substrate(s) of AOC3 is/are also unknown, but could provide an invaluable clue to the enzyme's function. Expression of untagged, soluble human AOC3 in insect cells provides a relatively simple means of obtaining pure enzyme. Characterization of enzyme indicates a 6% titer for the active site 2,4,5-trihydroxyphenylalanine quinone (TPQ) cofactor and corrected k(cat) values as high as 7 s(-1). Substrate kinetic profiling shows that the enzyme accepts a variety of primary amines with different chemical features, including nonphysiological branched-chain and aliphatic amines, with measured k(cat)/K(m) values between 10(2) and 10(4) M(-1) s(-1). K(m)(O(2)) approximates the partial pressure of oxygen found in the interstitial space. Comparison of the properties of purified murine to human enzyme indicates k(cat)/K(m) values that are within 3 to 4-fold, with the exception of methylamine and aminoacetone that are ca. 10-fold more active with human AOC3. With drug development efforts investigating AOC3 as an anti-inflammatory target, these studies suggest that caution is called for when screening the efficacy of inhibitors designed against human enzymes in non-transgenic mouse models. Differentiated murine 3T3-L1 adipocytes show a uniform distribution of AOC3 on the cell surface and whole cell K(m) values that are reasonably close to values measured using purified enzymes. The latter studies support a relevance of the kinetic parameters measured with isolated AOC3 variants to adipocyte function. From our studies, a number of possible substrates with relatively high k(cat)/K(m) have been discovered, including dopamine and cysteamine, which may implicate a role for adipocyte AOC3 in insulin-signaling and fatty acid metabolism, respectively. Finally, the demonstrated AOC3 turnover of primary amines that are non-native to human tissue suggests possible roles for the adipocyte enzyme in subcutaneous bacterial infiltration and obesity.

Characterization of a protein-generated O₂ binding pocket in PqqC, a cofactorless oxidase catalyzing the final step in PQQ production

PQQ is an exogenous, tricyclic, quino-cofactor for a number of bacterial dehydrogenases. The final step of PQQ formation is catalyzed by PqqC, a cofactorless oxidase. This study focuses on the activation of molecular oxygen in an enzyme active site without metal or cofactor and has identified a specific oxygen binding and activating pocket in PqqC. The active site variants H154N, Y175F,S, and R179S were studied with the goal of defining the site of O(2) binding and activation. Using apo-glucose dehydrogenase to assay for PQQ production, none of the mutants in this "O(2) core" are capable of PQQ/PQQH(2) formation. Spectrophotometric assays give insight into the incomplete reactions being catalyzed by these mutants. Active site variants Y175F, H154N, and R179S form a quinoid intermediate (Figure 1) anaerobically. Y175S is capable of proceeding further from quinoid to quinol, whereas Y175F, H154N, and R179S require O(2) to produce the quinol species. None of the mutations precludes substrate/product binding or oxygen binding. Assays for the oxidation of PQQH(2) to PQQ show that these O(2) core mutants are incapable of catalyzing a rate increase over the reaction in buffer, whereas H154N can catalyze the oxidation of PQQH(2) to PQQ in the presence of H(2)O(2) as an electron acceptor. Taken together, these data indicate that none of the targeted mutants can react fully to form quinone even in the presence of bound O(2). The data indicate a successful separation of oxidative chemistry from O(2) binding. The residues H154, Y175, and R179 are proposed to form a core O(2) binding structure that is essential for efficient O(2) activation.

The structures and physicochemical properties of organic cofactors in biocatalysis

Many crucial biochemical reactions in the cell require not only enzymes for catalysis but also organic cofactors or metal ions. Here, we analyse the physicochemical properties, chemical structures and functions of organic cofactors. Based on a thorough analysis of the literature complemented by our quantitative characterisation and classification, we found that most of these molecules are constructed from nucleotide and amino-acid-type building blocks, as well as some recurring cofactor-specific chemical scaffolds. We show that, as expected, organic cofactors are on average significantly more polar and slightly larger than other metabolites in the cell, yet they cover the full spectrum of physicochemical properties found in the metabolome. Furthermore, we have identified intrinsic groupings among the cofactors, based on their molecular properties, structures and functions, that represent a new way of considering cofactors. Although some classes of cofactors, as defined by their physicochemical properties, exhibit clear structural communalities, cofactors with similar structures can have diverse functional and physicochemical profiles. Finally, we show that the molecular functions of the cofactors not only may duplicate reactions performed by inorganic metal cofactors and amino acids, the cell's other catalytic tools, but also provide novel chemistries for catalysis.

pH-Potentiometric Investigation towards Chelating Tendencies of p-Hydroquinone and Phenol Iminodiacetate Copper(II) Complexes

Copper ions in the active sites of several proteins/enzymes interact with phenols and quinones, and this interaction is associated to the reactivity of the enzymes. In this study the speciation of the Cu²⁺ with iminodiacetic phenolate/hydroquinonate ligands has been examined by pH-potentiometry. The results reveal that the iminodiacetic phenol ligand forms mononuclear complexes with Cu²⁺ at acidic and alkaline pHs, and a binuclear O_phenolate-bridged complex at pH range from 7 to 8.5. The binucleating hydroquinone ligand forms only 2 : 1 metal to ligand complexes in solution. The pK values of the protonation of the phenolate oxygen of the two ligands are reduced about 2 units after complexation with the metal ion and are close to the pK values for the copper-interacting tyrosine phenol oxygen in copper enzymes.

Exploring the roles of the metal ions in Escherichia coli copper amine oxidase

To investigate the role of the active site copper in Escherichia coli copper amine oxidase (ECAO), we initiated a metal-substitution study. Copper reconstitution of ECAO (Cu-ECAO) restored only approximately 12% wild-type activity as measured by k(cat(amine)). Treatment with EDTA, to remove exogenous divalent metals, increased Cu-ECAO activity but reduced the activity of wild-type ECAO. Subsequent addition of calcium restored wild-type ECAO and further enhanced Cu-ECAO activities. Cobalt-reconstituted ECAO (Co-ECAO) showed lower but significant activity. These initial results are consistent with a direct electron transfer from TPQ to oxygen stabilized by the metal. If a Cu(I)-TPQ semiquinone mechanism operates, then an alternative outer-sphere electron transfer must also exist to account for the catalytic activity of Co-ECAO. The positive effect of calcium on ECAO activity led us to investigate the peripheral calcium binding sites of ECAO. Crystallographic analysis of wild-type ECAO structures, determined in the presence and absence of EDTA, confirmed that calcium is the normal ligand of these peripheral sites. The more solvent exposed calcium can be easily displaced by mono- and divalent cations with no effect on activity, whereas removal of the more buried calcium ion with EDTA resulted in a 60-90% reduction in ECAO activity and the presence of a lag phase, which could be overcome under oxygen saturation or by reoccupying the buried site with various divalent cations. Our studies indicate that binding of metal ions in the peripheral sites, while not essential, is important for maximal enzymatic activity in the mature enzyme.

Uncovering novel biochemistry in the mechanism of tryptophan tryptophylquinone cofactor biosynthesis

Catalytic quinone cofactors derived from post-translational modification of amino acid residues within the enzyme polypeptide have roles in a variety of biological processes ranging from metabolism in bacteria to inflammation and connective tissue maturation in humans. In recent years, studies of the biosynthesis of one of these cofactors, tryptophan tryptophylquinone (TTQ), have provided examples of novel chemistry that is required for the generation of these protein-derived cofactors. A novel c-type diheme enzyme, MauG, catalyzes a six-electron oxidation that completes TTQ biosynthesis in a 119-kDa protein substrate. The post-translational modification reactions proceed via an unprecedented Fe(V) equivalent catalytic intermediate comprising two hemes; one an Fe(IV)=O and the other a six-coordinate Fe(IV) with axial ligands provided by amino acid residues. This high-valent diheme species is an alternative to Compound I, an Fe(IV)=O heme with a porphyrin or amino acid cation radical, which is typically the reactive intermediate of heme-dependent oxygenases and peroxidases.

Spectroscopic and electronic structure studies of phenolate Cu(II) complexes: phenolate ring orientation and activation related to cofactor biogenesis

A combination of spectroscopies and DFT calculations have been used to define the electronic structures of two crystallographically defined Cu(II)-phenolate complexes. These complexes differ in the orientation of the phenolate ring which results in different bonding interactions of the phenolate donor orbitals with the Cu(II), which are reflected in the very different spectroscopic properties of the two complexes. These differences in electronic structures lead to significant differences in DFT calculated reactivities with oxygen. These calculations suggest that oxygen activation via a Cu(I) phenoxyl ligand-to-metal charge transfer complex is highly endergonic (>50 kcal/mol), hence an unlikely pathway. Rather, the two-electron oxidation of the phenolate forming a bridging Cu(II) peroxoquinone complex is more favorable (11.3 kcal/mol). The role of the oxidized metal in mediating this two-electron oxidation of the coordinated phenolate and its relevance to the biogenesis of the covalently bound topa quinone in amine oxidase are discussed.

Copper-Carbon Bonds in Mechanistic and Structural Probing of Proteins as well as in Situations where Copper is a Catalytic or Receptor Site

While copper-carbon bonds are well appreciated in organometallic synthetic chemistry, such occurrences are less known in biological settings. By far, the greatest incidence of copper-carbon moieties is in bioinorganic research aimed at probing copper protein active site structure and mechanism; for example, carbon monoxide (CO) binding as a surrogate for O2. Using infrared (IR) spectroscopy, CO coordination to cuprous sites has proven to be an extremely useful tool for determining active site copper ligation (e.g., donor atom number and type). The coupled (hemocyanin, tyrosinase, catechol oxidase) and non-coupled (peptidylglycine α-hydroxylating monooxygenase, dopamine β-monooxygenase) binuclear copper proteins as well as the heme-copper oxidases (HCOs) have been studied extensively via this method. In addition, environmental changes within the vicinity of the active site have been determined based on shifts in the CO stretching frequencies, such as for copper amine oxidases, nitrite reductases and again in the binuclear proteins and HCOs. In many situations, spectroscopic monitoring has provided kinetic and thermodynamic data on CuI-CO formation and CO dissociation from copper(I); recently, processes occurring on a femtosecond timescale have been reported. Copper-cyano moieties have also been useful for obtaining insights into the active site structure and mechanisms of copper-zinc superoxide dismutase, azurin, nitrous oxide reductase, and multi-copper oxidases. Cyanide is a good ligand for both copper(I) and copper(II), therefore multiple physical-spectroscopic techniques can be applied. A more obvious occurrence of a “Cu-C” moiety was recently described for a CO dehydrogenase which contains a novel molybdenum-copper catalytic site. A bacterial copper chaperone (CusF) was recently established to have a novel d-π interaction comprised of copper(I) with the arene containing side-chain of a tryptophan amino acid residue. Meanwhile, good evidence exists that a plant receptor site (ETR1) utilizes copper(I) to sense ethylene, a growth hormone. A copper olfactory receptor has also been suggested. All of the above mentioned occurrences or uses of carbon-containing substrates and/or probes are reviewed and discussed within the framework of copper proteins and other relevant systems.

Kinetics and spectroscopic evidence that the Cu(I)-semiquinone intermediate reduces molecular oxygen in the oxidative half-reaction of Arthrobacter globiformis amine oxidase

The role of copper during the reoxidation of substrate-reduced amine oxidases by O(2) has not yet been definitively established. Both outer-sphere and inner-sphere pathways for the reduction of O(2) to H(2)O(2) have been proposed. A key step in the inner-sphere mechanism is the reaction of O(2) directly with the Cu(I) center of a Cu(I)-semiquinone intermediate. To thoroughly examine this possibility, we have measured the spectral changes associated with single-turnover reoxidation by O(2) of substrate-reduced Arthrobacter globiformis amine oxidase (AGAO) under a wide range of conditions. We have previously demonstrated that the internal electron-transfer reaction [Cu(II)-TPQ(AMQ) --> Cu(I)-TPQ(SQ)] (where TPQ(AMQ) is the aminoquinol form of reduced TPQ and TPQ(SQ) is the semiquinone form) occurs at a rate that could permit the reaction of O(2) with both species to be observed on the stopped-flow time scale [Shepard, E. M., and Dooley, D. M. (2006) J. Biol. Inorg. Chem. 11, 1039-1048]. The transient absorption spectra observed for the reaction of O(2) with substrate-reduced AGAO provide compelling support for the reaction of the Cu(I)-TPQ(SQ) form. Further, global analysis of the kinetics and the transient absorption spectra are fully consistent with an inner-sphere reaction of the Cu(I)-semiquinone intermediate with O(2) and are inconsistent with an outer-sphere mechanism for the reaction of the reduced enzyme with O(2).

Discovery of a sensitive, selective, and tightly binding fluorogenic substrate of bovine plasma amine oxidase

We report a novel fluorogenic substrate of bovine plasma amine oxidase (BPAO), namely, (2-(6-(aminomethyl)naphthalen-2-yloxy)ethyl)trimethylammonium (ANETA), which displays extremely tight binding to BPAO (K(m) 183 +/- 14 nM) and yet is metabolized fairly quickly (k(cat) 0.690 +/- 0.010 s(-1)), with the aldehyde turnover product (2-(6-formylnaphthalen-2-yloxy)ethyl)trimethylammonium serving as a real time reporting fluorophore of the enzyme activity. This allowed for the development of a fluorometric noncoupled assay that is 2 orders of magnitude more sensitive than the spectrophotometric benzylamine assay. The discovery of ANETA involved elaboration of the lead compound 6-methoxy-2-naphthalenemethaneamine by structure-based design, which recognized the ancillary cation binding site of BPAO as the most significant structural features controlling binding affinity. Structure-based design further ensured a high level of selectivity: ANETA is a good substrate of BPAO but is not a substrate of either porcine kidney diamine oxidase (pkDAO) or rat liver monoamine oxidase (MAO-B). ANETA represents the first highly sensitive, selective, and tight binding fluorogenic substrate of a copper amine oxidase that is able to respond directly to the enzyme activity in real time.

Mechanistic study of asymmetric oxidative biaryl coupling: evidence for self-processing of the copper catalyst to achieve control of oxidase vs oxygenase activity

Copper(I) and copper(II) 1,5-diaza-cis-decalin complexes [(N2)Cu] are effective precatalysts for aerobic oxidative coupling of naphthol substrates. Mechanistic studies, however, reveal that these complexes are not the reactive form of the catalyst under steady-state conditions. Rather, the active catalyst forms in a presteady-state self-processing step that involves oxygenation of the naphthol substrate. The oxygenated substrate, NapHOX, serves as a cofactor that combines with the (N2)Cu complexes to achieve highly selective, steady-state oxidase reactivity (aerobic oxidative biaryl coupling).

Trapping of a dopaquinone intermediate in the TPQ cofactor biogenesis in a copper-containing amine oxidase from Arthrobacter globiformis

The biogenesis of the topaquinone (TPQ) cofactor of copper amine oxidase (CAO) is self-catalyzed and requires copper and molecular oxygen. A dopaquinone intermediate has been proposed to undergo 1,4-addition of a copper-associated water molecule to form the reduced form of TPQ (TPQ(red)), followed by facile oxidation by O(2) to yield the mature TPQ (TPQ(ox)). In this study, we have incorporated a lysine residue in the active site of Arthrobacter globiformis CAO (AGAO) by site-directed mutagenesis to produce D298K-AGAO. The X-ray crystal structure of D298K-AGAO at 1.7-A resolution revealed that a covalent linkage formed between the epsilon-amino side chain of Lys298 and the C2 position of a dopaquinone derived from Tyr382, a precursor to TPQ(ox). We assigned the species as an iminoquinone tautomer (LTI) of lysine tyrosylquinone (LTQ), the organic cofactor of lysyl oxidase (LOX). The time course of the formation of LTI at pH 6.8 was followed by UV/vis and resonance Raman spectroscopies. In the early phase of the reaction, an LTQ-like intermediate was observed. This intermediate then slowly converted to LTI in an isosbestic manner. Not only is the presence of a dopaquinone intermediate in the TPQ biogenesis confirmed, but it also provides strong support for the proposed intermediacy of a dopaquinone in the biogenesis of LTQ in LOX. Further, this study indicates that the dopaquinone intermediate in AGAO is mobile and can swing from the copper site into the active-site wedge to react with Lys298.

Model Studies of 6,7-Indolequinone Cofactors of Quinoprotein Amine Dehydrogenases

The electronic effects of the C-4 substituent on the physicochemical properties and reactivity of the 6,7-inodolequinone cofactors (CTQ and TTQ) have extensively been investigated with use of a series of C-4 substituted 6,7-inodolequinone derivatives (1-4). The one-electron reduction potentials of the 6,7-inodolequinone derivatives decrease with increasing the electron donating ability of the C-4 substituent (with the following order of E degrees': 4>1>2>3). The reaction of indolequinones 1-3 with benzylamine proceeds stepwise through the iminoquinone and the product-imine intermediates to give aminophenol as the final product as the case of TTQ model compound 4. The rate constants of each step have been determined by the detailed kinetic analysis, and the kinetic deuterium isotope effects have also been examined to confirm the rate-determining step. The reactivity of CTQ model compound 1 toward the amines is by one order of magnitude lower than that of TTQ model compound 4. The reactivity of indolequinones 2 and 3 is further decreased due to their stronger electron-donating substituents at C-4. A more important difference between CTQ model compound 1 and TTQ model compound 4 is the reactivity of the iminoquinone intermediate: the reaction of the CTQ model compound with amines stops at the iminoquinone formation stage at room temperature, whereas the reaction of the TTQ model compound with amines proceeds up to the aminophenol formation. Thus, the energy barrier for the rearrangement of the iminoquinone to the product-imine is higher in the CTQ model system than in the TTQ model system.

Intramolecular electron transfer rate between active-site copper and TPQ in Arthrobacter globiformis amine oxidase

Copper amine oxidases catalyze the oxidative deamination of primary amines operating through a ping-pong bi bi mechanism, divided into reductive and oxidative half-reactions. Considerable debate still exists regarding the role of copper in the oxidative half-reaction, where O2 is reduced to H2O2. Substrate-reduced amine oxidases display an equilibrium between a Cu(II) aminoquinol and a Cu(I) semiquinone, with the magnitude of the equilibrium constant being dependent upon the enzyme source. The initial electron transfer to dioxygen has been proposed to occur from either the reduced Cu(I) center or the reduced aminoquinol cofactor. In order for Cu(I) to be involved, it must be shown that the rate of electron transfer (kET) between the aminoquinol and Cu(II) is sufficiently rapid to place the Cu(I) semiquinone moiety on the mechanistic pathway. To further explore this issue, we measured the intramolecular electron transfer rate for the Cu(II) aminoquinol left arrow over right arrow Cu(I) semiquinone equilibrium in Arthrobacter globiformis amine oxidase (AGAO) by temperature-jump relaxation techniques. The results presented herein establish that kET is greater than the rate of catalysis (kcat) for the preferred amine substrate beta-phenylethylamine at three pH values, thereby permitting the Cu(I) semiquinone to be a viable catalytic intermediate during enzymatic reoxidation in this enzyme. The data show that kET is approximately equivalent at pH 6.2 and 7.2, being 2.5 times kcat for these pH values. At pH 8.2, however, kET decreases, becoming comparable to kcat. Potential reasons for the decreased kET at basic pH are presented. The implications of these results in light of a previously published study measuring reoxidation rates of substrate-reduced AGAO are also addressed.

Reduction of plastocyanin by tyrosine-containing oligopeptides

Oxidized plastocyanin (PC) was reduced with TyrTyrTyr and LysLysLysLysTyrTyrTyr (KKKKYYY) oligopeptides at neutral pH. The TyrTyrTyr site of the peptides provided an electron to the copper active site of PC, whereas the tetralysine site of KKKKYYY functioned as the recognition site for the negative patch of PC. The reciprocal initial rate constant (1/k(int)) increased linearly with the reciprocal TyrTyrTyr concentration and proton concentration, although the electron transfer rate decreased gradually with time. The results showed that PC was reduced by the deprotonated species of TyrTyrTyr. A linear increase of log k(int) with increase in the ionic strength was observed due to decrease in the electrostatic repulsion between negatively charged PC and deprotonated (TyrTyrTyr)(-). PC was reduced faster by an addition of KKKKYYY to the PC-TyrTyrTyr solution, although KKKKYYY could not reduce PC without TyrTyrTyr. The ESI-LCMS spectrum of the products from the reaction between PC and TyrTyrTyr showed molecular ion peaks at m/z 1015.7 and 1037.7, which suggested formation of a dimerized peptide that may be produced from the reaction of a tyrosyl radical. The results indicate that PC and the tyrosine-containing oligopeptides form an equilibrium, PC(ox)/(oligopeptide)(-)-->/<--PC(red)/(oligopeptide)(*). The equilibrium is usually shifted to the left, but could shift to the right when the produced oligopeptide radical reacts with unreacted peptides. For the reaction of PC with KKKKYYY in the absence of TyrTyrTyr, the produced KKKK(YYY)(*) radical peptide could not react with other KKKKYYY peptides, since they were positively charged. In the presence of both KKKKYYY and TyrTyrTyr, PC may interact effectively with KKKKYYY through its tetralysine site and receive an electron from its TyrTyrTyr site, where the produced KKKK(YYY)(*) may interact with TyrTyrTyr peptides.

Investigation of Cu(I)-dependent 2,4,5-trihydroxyphenylalanine quinone biogenesis in Hansenula polymorpha amine oxidase

Copper, a mediator of redox chemistries in biology, is often found in enzymes that bind and reduce dioxygen. Among these, the copper amine oxidases catalyze the oxidative deamination of primary amines utilizing a type(II) copper center and 2,4,5-trihydroxyphenylalanine quinone (TPQ), a covalent cofactor derived from the post-translational modification of an active site tyrosine. Previous studies established the dependence of TPQ biogenesis on Cu(II); however, the dependence of cofactor formation on the biologically relevant Cu(I) ion has remained untested. In this study, we demonstrate that the apoform of the Hansenula polymorpha amine oxidase readily binds Cu(I) under anaerobic conditions and produces the quinone cofactor at a rate of 0.28 h(-1) upon subsequent aeration to yield a mature enzyme with kinetic properties identical to the protein product of the Cu(II)-dependent reaction. Because of the change in magnetic properties associated with the oxidation of copper, electron paramagnetic resonance spectroscopy was employed to investigate the nature of the rate-limiting step of Cu(I)-dependent cofactor biogenesis. Upon aeration of the unprocessed enzyme prebound with Cu(I), an axial Cu(II) electron paramagnetic resonance signal was found to appear at a rate equivalent to that for the cofactor. These data provide strong evidence for a rate-limiting release of superoxide from a Cu(II)(O(2)(.)) complex as a prerequisite for the activation of the precursor tyrosine and its transformation for TPQ. As copper is trafficked to intracellular protein targets in the reduced, Cu(I) state, these studies offer possible clues as to the physiological significance of the acquisition of Cu(I) by nascent H. polymorpha amine oxidase.

Photoactivated H/D Exchange in Tyrosine: Involvement of a Radical Anion Intermediate

The aromatic hydrogen nuclei of tyrosine are photochemically labile and exchange with deuterons in neutral D(2)O solution. The site meta to the ring hydroxyl substituent is preferentially deuterated, exhibiting a meta/ortho deuteration rate of approximately 4:1. In contrast with acid-catalyzed H/D exchange and with nearly all of the reported photoactivated H/D exchange studies, the UV-induced H/D exchange of tyrosine is optimal at pH 9 and is effectively quenched at acid pH. Photochemical H/D exchange is strongly stimulated by the alpha-amino group (the aromatic hydrogens of p-cresol are far less subject to exchange) and by imidazole or phosphate buffers. On the basis of the results obtained here and on the previously identified cyclohexadienyl radical (Bussandri, A.; van Willigen, H. J. Phys. Chem. A 2002, 106, 1524-1532), we conclude that the exchange reaction involves a radical intermediate and results from two distinct roles of tyrosine: (1) as a phototransducer of light energy into solvated electrons (e(aq)(-)), and (2) as an acceptor of an electron to create a radical anion intermediate which is rapidly protonated, yielding a neutral cyclohexadienyl radical. Regeneration of the tyrosine can occur via a bimolecular redox reaction of the cyclohexadienyl and phenoxyl radicals to yield a carbocation/phenoxide pair, followed by deprotonation of the carbocation. The oxidation step is pH dependent, requiring the deprotonated form of the cyclohexadienyl radical. The H/D exchange thus results from a cyclic one-electron (Birch) reduction/protonation/reoxidation (by phenoxyl radical)/deprotonation cycle. Consistent with these mechanistic conclusions, the aromatic hydrogens of tyrosine O-methyl ether are photochemically inert, but become labile in the presence of tyrosine at high pH. The deuteration rate of O-methyl tyrosine is lower than that of tyrosine and shows a preference for the ortho positions. This difference is proposed to result from a variation in the oxidation step, characterized by a preferential oxidation of a cyclohexadienyl resonance structure with the unpaired electron localized on the oxygen substituent.