Copper Binding Sites in the Manganese-Oxidizing Mnx Protein Complex Investigated by Electron Paramagnetic Resonance Spectroscopy

Catalase-peroxidase StKatG2 from Salinicola tamaricis: a versatile Mn(II) oxidase that decolorizes malachite green

Manganese (Mn) oxidation processes have garnered significant attention recently due to their potential for degrading organic pollutants. These processes are primarily catalyzed by Mn(II) oxidases. Salinicola tamaricis F01, an endophytic bacterium derived from wetland plants, has demonstrated Mn(II)-oxidizing capacity. In this study, a catalase-peroxidase, StKatG2, was cloned and overexpressed in Escherichia coli from the strain F01. The purified recombinant StKatG2 exhibited Mn(II)-oxidizing activity with K m and K cat values of 2.529 mmol/L and 2.82 min-1, respectively. Optimal catalytic conditions for StKatG2 were observed at pH 7.5 and 55°C, with 45.1% activity retention after an 8-h exposure to 80°C. The biogenic manganese oxides produced by StKatG2 exhibited mixed-valence states with Mn(II), including Mn(III), Mn(IV), and Mn(VII). Furthermore, StKatG2 demonstrated superior decolorization efficiency for malachite green (MG), achieving decolorization rates of 73.38% for 20 mg/L MG and 60.08% for 50 mg/L MG, while degrading MG into 4-(dimethylamino)benzophenone. Therefore, the catalase-peroxidase StKatG2 exhibits multifunctionality in Mn(II)-oxidizing activity and has the potential to serve as an environmentally friendly enzyme for MG removal.

Cryo-EM Structure of the Mnx Protein Complex Reveals a Tunnel Framework for the Mechanism of Manganese Biomineralization

The global manganese cycle relies on microbes to oxidize soluble Mn(II) to insoluble Mn(IV) oxides. Some microbes require peroxide or superoxide as oxidants, but others can use O2 directly, via multicopper oxidase (MCO) enzymes. One of these, MnxG from Bacillus sp. strain PL-12, was isolated in tight association with small accessory proteins, MnxE and MnxF. The protein complex, called Mnx, has eluded crystallization efforts, but we now report the 3D structure of a point mutant using cryo-EM single particle analysis, cross-linking mass spectrometry, and AlphaFold Multimer prediction. The β-sheet-rich complex features MnxG enzyme, capped by a heterohexameric ring of alternating MnxE and MnxF subunits, and a tunnel that runs through MnxG and its MnxE3F3 cap. The tunnel dimensions and charges can accommodate the mechanistically inferred binuclear manganese intermediates. Comparison with the Fe(II)-oxidizing MCO, ceruloplasmin, identifies likely coordinating groups for the Mn(II) substrate, at the entrance to the tunnel. Thus, the 3D structure provides a rationale for the established manganese oxidase mechanism, and a platform for further experiments to elucidate mechanistic details of manganese biomineralization.

Interpretation of EPR and optical spectra of Ni(II) ions in crystalline lattices at ambient temperature

Many biologically important paramagnetic metal ions are characterized by electron paramagnetic resonance (EPR) spectroscopy to use as spin probes to investigate the structure and function of biomolecules. Though nickel(II) ions are an essential trace element and part of many biomolecules, the EPR properties are least understood. Herein, the EPR and optical absorption spectra measured at 300 K for Ni(II) ions diluted in two different diamagnetic hosts are investigated and reported. The EPR spectrum of a polycrystalline Ni/Mg(3-methylpyrazole)₆ (ClO₄ )₂ [Ni/MMPC] shows two transitions at X-band frequency (~9.5 GHz), suggesting the zero-field splitting parameter (D) is larger than the resonance field of the free electron (H_o ). This incomplete and complex spectrum is successfully analyzed to obtain EPR parameters. The EPR spectrum of the polycrystalline Ni/Zn(pyrazole)₆ (NO₃ )₂ [Ni/ZPN] shows a triplet spectrum indicating D < H_o . A detailed analysis of single-crystal EPR data yielded the spin Hamiltonian parameters. The optical absorption spectra are deconvoluted to understand the symmetry of the coordination environment in the complex.

Metallo-inhibition of Mnx, a bacterial manganese multicopper oxidase complex

The manganese oxidase complex, Mnx, from Bacillus sp. PL-12 contains a multicopper oxidase (MCO) and oxidizes dissolved Mn(II) to form insoluble manganese oxide (MnO₂) mineral. Previous kinetic and spectroscopic analyses have shown that the enzyme's mechanism proceeds through an activation step that facilitates formation of a series of binuclear Mn complexes in the oxidation states II, III, and IV on the path to MnO₂ formation. We now demonstrate that the enzyme is inhibited by first-row transition metals in the order of the Irving-Williams series. Zn(II) strongly (K_i ~ 1.5 μM) inhibits both activation and turnover steps, as well as the rate of Mn(II) binding. The combined Zn(II) and Mn(II) concentration dependence establishes that the inhibition is non-competitive. This result is supported by electron paramagnetic resonance (EPR) spectroscopy, which reveals unaltered Mnx-bound Mn(II) EPR signals, both mono- and binuclear, in the presence of Zn(II). We infer that inhibitory metals bind at a site separate from the substrate sites and block the conformation change required to activate the enzyme, a case of allosteric inhibition. The likely biological role of this inhibitory site is discussed in the context of Bacillus spore physiology. While Cu(II) inhibits Mnx strongly, in accord with the Irving-Williams series, it increases Mnx activation at low concentrations, suggesting that weakly bound Cu, in addition to the four canonical MCO-Cu, may support enzyme activity, perhaps as an electron transfer agent.

A merged copper(I/II) cluster isolated from Glaser coupling

Ubiquitous copper-oxygen species are pivotal in enabling multifarious oxidation reactions in biological and chemical transformations. We herein construct a macrocycle-protected mixed-valence cluster [(^tBuC≡CCu^I₃)-(μ₂-OH)-Cu^II] by merging a copper acetylide cluster with a copper-oxygen moiety formed in Glaser coupling. This merged Cu(I/II) cluster shows remarkably strong oxidation capacity, whose reduction potential is among the most positive for Cu(II) and even comparable with some Cu(III) species. Consequently, the cluster exhibits high hydrogen atom transfer (HAT) reactivity with inert hydrocarbons. In contrast, the degraded [Cu^II-(μ₂-OH)-Cu^II] embedded in a small macrocyclic homologue shows no HAT reactivity. Theoretical calculations indicate that the strong oxidation ability of Cu(II) in [(^tBuC≡CCu^I₃)-(μ₂-OH)-Cu^II] is mainly ascribed to the uneven charge distribution of Cu(I) ions in the ^tBuC≡CCu^I₃ unit because of significant [d_Cu(I) → π*_(C≡C)] back donation. The present study on in situ formed metal clusters opens a broad prospect for mechanistic studies of Cu-based catalytic reactions.

Copper-oxygen species in organometallic complexes and enzymes are involved in many oxidation reactions. Here, the authors synthesize a macrocycle-protected mixed valence Cu(I/II) cluster with an unusually strong oxidation capacity and apply it to hydrogen atom transfer reactions with inert hydrocarbons.

Stability of Cu(ii) complexes with FomA protein fragments containing two His residues in the peptide chain

The coordination process of Cu(ii) ions with FomA protein fragments ofFusobacterium nucleatumcontaining two histydyl residues was determined.

MopA, the Mn Oxidizing Protein From Erythrobacter sp. SD-21, Requires Heme and NAD+ for Mn(II) Oxidation

Bacterial manganese (Mn) oxidation is catalyzed by a diverse group of microbes and can affect the fate of other elements in the environment. Yet, we understand little about the enzymes that catalyze this reaction. The Mn oxidizing protein MopA, from Erythrobacter sp. strain SD-21, is a heme peroxidase capable of Mn(II) oxidation. Unlike Mn oxidizing multicopper oxidase enzymes, an understanding of MopA is very limited. Sequence analysis indicates that MopA contains an N-terminal heme peroxidase domain and a C-terminal calcium binding domain. Heterologous expression and nickel affinity chromatography purification of the N-terminal peroxidase domain (MopA-hp) from Erythrobacter sp. strain SD-21 led to partial purification. MopA-hp is a heme binding protein that requires heme, NAD⁺, and calcium (Ca²⁺) for activity. Mn oxidation is also stimulated by the presence of pyrroloquinoline quinone. MopA-hp has a K_M for Mn(II) of 154 ± 46 μM and k_cat = 1.6 min⁻¹. Although oxygen requiring MopA-hp is homologous to peroxidases based on sequence, addition of hydrogen peroxide and hydrogen peroxide scavengers had little effect on Mn oxidation, suggesting this is not the oxidizing agent. These studies provide insight into the mechanism by which MopA oxidizes Mn.

Mn(III) species formed by the multi-copper oxidase MnxG investigated by electron paramagnetic resonance spectroscopy

The multi-copper oxidase (MCO) MnxG from marine Bacillus bacteria plays an essential role in geochemical cycling of manganese by oxidizing Mn²⁺(aq) to form manganese oxide minerals at rates that are three to five orders of magnitude faster than abiotic rates. The MCO MnxG protein is isolated as part of a multi-protein complex, denoted as Mnx, which includes one MnxG unit and a hexamer of MnxE₃F₃ subunit. During the oxidation of Mn²⁺(aq) catalyzed by the Mnx protein complex, an enzyme-bound Mn(III) species was trapped recently in the presence of pyrophosphate (PP) and analyzed using parallel-mode electron paramagnetic resonance (EPR) spectroscopy. Herein, we provide a full analysis of this enzyme-bound Mn(III) intermediate via temperature dependence studies and spectral simulations. This Mnx-bound Mn(III) species is characterized by a hyperfine-coupling value of A(⁵⁵Mn) = 4.2 mT (corresponding to 120 MHz) and a negative zero-field splitting (ZFS) value of D = - 2.0 cm^-1. These magnetic properties suggest that the Mnx-bound Mn(III) species could be either six-coordinate with a ⁵B_1g ground state or square-pyramidal five-coordinate with a ⁵B₁ ground state. In addition, as a control, Mn(III)PP is also analyzed by parallel-mode EPR spectroscopy. It exhibits distinctly different magnetic properties with a hyperfine-coupling value of A(⁵⁵Mn) = 4.8 mT (corresponding to 140 MHz) and a negative ZFS value of D = - 2.5 cm^-1. The different ZFS values suggest differences in ligand environment of Mnx-bound Mn(III) and aqueous Mn(III)PP species. These studies provide further insights into the mechanism of biological Mn²⁺(aq) oxidation.

Surface Induced Dissociation Coupled with High Resolution Mass Spectrometry Unveils Heterogeneity of a 211 kDa Multicopper Oxidase Protein Complex

Manganese oxidation is an important biogeochemical process that is largely regulated by bacteria through enzymatic reactions. However, the detailed mechanism is poorly understood due to challenges in isolating and characterizing these unknown enzymes. A manganese oxidase, Mnx, from Bacillus sp. PL-12 has been successfully overexpressed in active form as a protein complex with a molecular mass of 211 kDa. We have recently used surface induced dissociation (SID) and ion mobility-mass spectrometry (IM-MS) to release and detect folded subcomplexes for determining subunit connectivity and quaternary structure. The data from the native mass spectrometry experiments led to a plausible structural model of this multicopper oxidase, which has been difficult to study by conventional structural biology methods. It was also revealed that each Mnx subunit binds a variable number of copper ions. Becasue of the heterogeneity of the protein and limited mass resolution, ambiguities in assigning some of the observed peaks remained as a barrier to fully understanding the role of metals and potential unknown ligands in Mnx. In this study, we performed SID in a modified Fourier transform-ion cyclotron resonance (FTICR) mass spectrometer. The high mass accuracy and resolution offered by FTICR unveiled unexpected artificial modifications on the protein that had been previously thought to be iron bound species based on lower resolution spectra. Additionally, isotopically resolved spectra of the released subcomplexes revealed the metal binding stoichiometry at different structural levels. This method holds great potential for in-depth characterization of metalloproteins and protein-ligand complexes. Graphical Abstract ᅟ.

Mn(II) Oxidation by the Multicopper Oxidase Complex Mnx: A Coordinated Two-Stage Mn(II)/(III) and Mn(III)/(IV) Mechanism

The bacterial manganese oxidase MnxG of the Mnx protein complex is unique among multicopper oxidases (MCOs) in carrying out a two-electron metal oxidation, converting Mn(II) to MnO₂ nanoparticles. The reaction occurs in two stages: Mn(II) → Mn(III) and Mn(III) → MnO₂. In a companion study , we show that the electron transfer from Mn(II) to the low-potential type 1 Cu of MnxG requires an activation step, likely forming a hydroxide bridge at a dinuclear Mn(II) site. Here we study the second oxidation step, using pyrophosphate (PP) as a Mn(III) trap. PP chelates Mn(III) produced by the enzyme and subsequently allows it to become a substrate for the second stage of the reaction. EPR spectroscopy confirms the presence of Mn(III) bound to the enzyme. The Mn(III) oxidation step does not involve direct electron transfer to the enzyme from Mn(III), which is shown by kinetic measurements to be excluded from the Mn(II) binding site. Instead, Mn(III) is proposed to disproportionate at an adjacent polynuclear site, thereby allowing indirect oxidation to Mn(IV) and recycling of Mn(II). PP plays a multifaceted role, slowing the reaction by complexing both Mn(II) and Mn(III) in solution, and also inhibiting catalysis, likely through binding at or near the active site. An overall mechanism for Mnx-catalyzed MnO₂ production from Mn(II) is presented.

Mn(II) Oxidation by the Multicopper Oxidase Complex Mnx: A Binuclear Activation Mechanism

The bacterial protein complex Mnx contains a multicopper oxidase (MCO) MnxG that, unusually, catalyzes the two-electron oxidation of Mn(II) to MnO₂ biomineral, via a Mn(III) intermediate. Although Mn(III)/Mn(II) and Mn(IV)/Mn(III) reduction potentials are expected to be high, we find a low reduction potential, 0.38 V (vs Normal Hydrogen Electrode, pH 7.8), for the MnxG type 1 Cu²⁺, the electron acceptor. Indeed the type 1 Cu²⁺ is not reduced by Mn(II) in the absence of molecular oxygen, indicating that substrate oxidation requires an activation step. We have investigated the enzyme mechanism via electronic absorption spectroscopy, using chemometric analysis to separate enzyme-catalyzed MnO₂ formation from MnO₂ nanoparticle aging. The nanoparticle aging time course is characteristic of nucleation and particle growth; rates for these processes followed expected dependencies on Mn(II) concentration and temperature, but exhibited different pH optima. The enzymatic time course is sigmoidal, signaling an activation step, prior to turnover. The Mn(II) concentration and pH dependence of a preceding lag phase indicates weak Mn(II) binding. The activation step is enabled by a pK_a > 8.6 deprotonation, which is assigned to Mn(II)-bound H₂O; it induces a conformation change (consistent with a high activation energy, 106 kJ/mol) that increases Mn(II) affinity. Mnx activation is proposed to decrease the Mn(III/II) reduction potential below that of type 1 Cu(II/I) by formation of a hydroxide-bridged binuclear complex, Mn(II)(μ-OH)Mn(II), at the substrate site. Turnover is found to depend cooperatively on two Mn(II) and is enabled by a pK_a 7.6 double deprotonation. It is proposed that turnover produces a Mn(III)(μ-OH)₂Mn(III) intermediate that proceeds to the enzyme product, likely Mn(IV)(μ-O)₂Mn(IV) or an oligomer, which subsequently nucleates MnO₂ nanoparticles. We conclude that Mnx exploits manganese polynuclear chemistry in order to facilitate an otherwise difficult oxidation reaction, as well as biomineralization. The mechanism of the Mn(III/IV) conversion step is elucidated in an accompanying paper .