Crystal structure of manganese catalase from Lactobacillus plantarum

An active dimanganese(III)-tyrosyl radical cofactor in Escherichia coli class Ib ribonucleotide reductase

Escherichia coli class Ib ribonucleotide reductase (RNR) converts nucleoside 5'-diphosphates to deoxynucleoside 5'-diphosphates and is expressed under iron-limited and oxidative stress conditions. This RNR is composed of two homodimeric subunits: alpha2 (NrdE), where nucleotide reduction occurs, and beta2 (NrdF), which contains an unidentified metallocofactor that initiates nucleotide reduction. nrdE and nrdF are found in an operon with nrdI, which encodes an unusual flavodoxin proposed to be involved in metallocofactor biosynthesis and/or maintenance. Ni affinity chromatography of a mixture of E. coli (His)(6)-NrdI and NrdF demonstrated tight association between these proteins. To explore the function of NrdI and identify the metallocofactor, apoNrdF was loaded with Mn(II) and incubated with fully reduced NrdI (NrdI(hq)) and O(2). Active RNR was rapidly produced with 0.25 +/- 0.03 tyrosyl radical (Y*) per beta2 and a specific activity of 600 units/mg. EPR and biochemical studies of the reconstituted cofactor suggest it is Mn(III)(2)-Y*, which we propose is generated by Mn(II)(2)-NrdF reacting with two equivalents of HO(2)(-), produced by reduction of O(2) by NrdF-bound NrdI(hq). In the absence of NrdI(hq), with a variety of oxidants, no active RNR was generated. By contrast, a similar experiment with apoNrdF loaded with Fe(II) and incubated with O(2) in the presence or absence of NrdI(hq) gave 0.2 and 0.7 Y*/beta2 with specific activities of 80 and 300 units/mg, respectively. Thus NrdI(hq) hinders Fe(III)(2)-Y* cofactor assembly in vitro. We propose that NrdI is an essential player in E. coli class Ib RNR cluster assembly and that the Mn(III)(2)-Y* cofactor, not the diferric-Y* one, is the active metallocofactor in vivo.

Validation of broken-symmetry density functional methods for the calculation of electron paramagnetic resonance parameters of dinuclear mixed-valence MnIVMnIII complexes

. The EPR parameters of a series of dinuclear manganese(III,IV) complexes with mono(μ-oxo), bis(μ-oxo), (μ-oxo)(μ-carboxylato), bis(μ-oxo)(μ-carboxylato), and (μ-oxo)bis(μ-carboxylato) bridges were studied by broken-symmetry density functional (DFT) methods. The influence of the exchange-correlation functional on the agreement with experiment has been evaluated systematically for g tensors; 55Mn, 14N, and 1H hyperfine coupling tensors; and Heisenberg exchange couplings. 14N and 1H hyperfine couplings, 55Mn hyperfine anisotropies, g tensors, and exchange couplings are well described by hybrid functionals with moderate exact-exchange admixtures such as B3LYP. The isotropic 55Mn hyperfine couplings require larger exact-exchange admixtures. However, the errors of the B3LYP calculations are systematic and may be corrected by a constant scaling factor, providing good predictive power for a wide range of EPR parameters with broken-symmetry DFT and standard functionals. The influence of terminal and bridging ligands on structure, spin-density distributions, and EPR parameters are evaluated systematically. Computed hyperfine and g tensors are not covariant to each other. This may have consequences for spectra simulations. The nature of the broken-symmetry state and the origin of its spin contamination were analyzed by an expansion into restricted determinants, based on paired orbitals.

Bis{μ-4,4′-dimethoxy-2,2′-[propane-1,2-diylbis(nitrilomethylidyne)]diphenolato}bis({4,4′-dimethoxy-2,2′-[propane-1,2-diylbis(nitrilomethylidyne)]diphenol}manganese(III)) bis(hexafluoridophosphate)

In the title complex, [Mn₂(C₁₉H₂₀N₂O₄)₂(C₁₉H₂₂N₂O₄)₂](PF₆)₂, the Mn^III ion is coordinated by two O [Mn—O = 1.855 (2) and 1.887 (2) Å] and two N [Mn—N = 1.982 (3) and 1.977 (3) Å] atoms from the tetra­dentate Schiff base ligand and a coordinated axial ligand [Mn—O = 2.129 (2) Å]. The centrosymmetric dimer contains two Jahn–Teller-distorted Mn^III ions, each in a nearly octa­hedral geometry, connected through two phenolate bridges from two ligands. There are two stereogenic centers. The methyl group and the H atom attached to the middle propane C atom are disordered over two positions with occupancy factors in the ratio 0.58:0.42. The crystal is therefore a mixture of two diasteroisomers, viz. RS/SR and RR/SS. In the axial ligand, the two benzene rings form a dihedral angle of 56.97 (5)° and the dihedral angle between the two MnNC₃O chelate rings is 2.98 (12)°

Manganese import is a key element of the OxyR response to hydrogen peroxide in Escherichia coli

Very little manganese is imported into Escherichia coli under routine growth conditions: the import system is weakly expressed, the manganese content is low, and a manganese-dependent enzyme is not correctly metallated. Mutants that lack MntH, the importer, grow at wild-type rates, indicating that manganese plays no critical role. However, MntH supports the growth of iron-deficient cells, suggesting that manganese can substitute for iron in activating at least some metalloenzymes. MntH is also strongly induced when cells are stressed by hydrogen peroxide. This adaptation is essential, as E. coli cannot tolerate peroxide stress if mntH is deleted. Other workers have observed that manganese improves the ability of a variety of microbes to tolerate oxidative stress, and the prevailing hypothesis is that manganese does so by chemically scavenging hydrogen peroxide and/or superoxide. We found that manganese does not protect peroxide-stressed cells by scavenging peroxide. Instead, the beneficial effects of manganese correlate with its ability to metallate mononuclear enzymes. Because iron-loaded enzymes are vulnerable to the Fenton reaction, the substitution of manganese may prevent protein damage. Accordingly, during H2O2 stress, mutants that cannot import manganese and/or are unable to sequester iron suffer high rates of protein oxidation.

A possible evolutionary origin for the Mn4 cluster in photosystem II: from manganese superoxide dismutase to oxygen evolving complex

The recently published X-ray absorption fine structure of photosystem II provides a more detailed architecture of the oxygen-evolving complex (OEC) and the surrounding amino acids. In this paper, a comparison between manganese superoxide dismutase, dinuclear manganese catalase enzymes and the oxygen evolving complex in photosystem II is reported. The author suggests that the development of oxygenic photosynthesis occurred in steps, the first of which involved only one manganese ion (Mn(II)) that oxidized two water molecules to hydrogen peroxide and then oxygen.

Interaction of Cyanide with Enzymes Containing Vanadium, Manganese, Non-Heme Iron, and Zinc

Since the early discovery of Prussian Blue, cyano transition metal complexes have played a fundamental role in coordination chemistry. They represent important compounds with fascinating chemical and physical properties which turn them into valuable tools for both chemists and biologists. HCN as a precursor in prebiotic chemistry has gained interest in view of its polymers being involved in the formation of amino acids, purines, and orotic acid, a biosynthetic precursor of uracil. Clearly, the rapid formation of adenine by aqueous polymerization of HCN is one of the key discoveries in these experiments. The cyanide anion is usually toxic for most aerobic organisms because of its inhibitory effects on respiratory enzymes, but as a substrate it is an important source of carbon and nitrogen for microorganisms, fungi and plants. Most interestingly, the cyanide anion is a ligand of important metal-dependent biomolecules, such as the hydrogenases and the cobalt site in vitamin B12.

Occurrence, phylogeny, structure, and function of catalases and peroxidases in cyanobacteria

Cyanobacteria have evolved approximately 3x10(9) years ago from ancient phototrophic microorganisms that already lived on our planet Earth. By opening the era of an aerobic, oxygen-containing biosphere, they are the true pacemakers of geological and biological evolution. Cyanobacteria must have been among the first organisms to elaborate mechanisms for the detoxification of partially reduced oxygen species including (hydrogen) peroxide. Since there is still an suprising lack of knowledge on the type, role, and mechanism(s) of peroxide-degrading enzymes in these bacteria, all 44 fully or partially sequenced genomes for haem and non-haem catalases and peroxidases have been critically analysed based on well known structure-function relationships of the corresponding oxidoreductases. It is demonstrated that H(2)O(2)-dismutating enzymes are mainly represented by bifunctional (haem) catalase-peroxidases and (binuclear) manganese catalases, with the latter being almost exclusively found in diazotrophic species. Several strains even lack a gene that encodes an enzyme with catalase activity. Two groups of peroxidases are found. Genes encoding putative (primordial) haem peroxidases (with homology to corresponding mammalian enzymes) and vanadium-containing iodoperoxidases are found only in a few species, whereas genes encoding peroxiredoxins (1-Cys, 2-Cys, type II, and Q-type) are ubiquitous in cyanobacteria. In addition, approximately 70% contain NADPH-dependent glutathione peroxidase-like proteins. The occurrence and phylogeny of these enzymes is discussed, as well as the present knowledge of their physiological role(s).

Evolution of catalases from bacteria to humans

Excessive hydrogen peroxide is harmful for almost all cell components, so its rapid and efficient removal is of essential importance for aerobically living organisms. Conversely, hydrogen peroxide acts as a second messenger in signal-transduction pathways. H(2)O(2) is degraded by peroxidases and catalases, the latter being able both to reduce H(2)O(2) to water and to oxidize it to molecular oxygen. Nature has evolved three protein families that are able to catalyze this dismutation at reasonable rates. Two of the protein families are heme enzymes: typical catalases and catalase-peroxidases. Typical catalases comprise the most abundant group found in Eubacteria, Archaeabacteria, Protista, Fungi, Plantae, and Animalia, whereas catalase-peroxidases are not found in plants and animals and exhibit both catalatic and peroxidatic activities. The third group is a minor bacterial protein family with a dimanganese active site called manganese catalases. Although catalyzing the same reaction (2 H(2)O(2)--> 2 H(2)O+ O(2)), the three groups differ significantly in their overall and active-site architecture and the mechanism of reaction. Here, we present an overview of the distribution, phylogeny, structure, and function of these enzymes. Additionally, we report about their physiologic role, response to oxidative stress, and about diseases related to catalase deficiency in humans.

Multifrequency pulsed electron paramagnetic resonance study of the S2 state of the photosystem II manganese cluster

Multifrequency electron spin-echo envelope modulation (ESEEM) spectroscopy is employed to measure the strength of the hyperfine coupling of magnetic nuclei to the paramagnetic (S = 1/2) S2 form of photosystem II (PSII). Previous X-band-frequency ESEEM studies indicated that one or more histidine nitrogens are electronically coupled to the tetranuclear manganese cluster in the S2 state of PSII. However, the spectral resolution was relatively poor at the approximately 9 GHz excitation frequency, precluding any in-depth analysis of the corresponding bonding interaction between the detected histidine and the manganese cluster. Here we report ESEEM experiments using higher X-, P-, and Ka-band microwave frequencies to target PSII membranes isolated from spinach. The X- to P-band ESEEM spectra suffer from the same poor resolution as that observed in previous experiments, while the Ka-band spectra show remarkably well-resolved features that allow for the direct determination of the nuclear quadrupolar couplings for a single I = 1(14)N nucleus. The Ka-band results demonstrate that at an applied field of 1.1 T we are much closer to the exact cancellation limit (alpha iso = 2nu(14)N) that optimizes ESEEM spectra. These results reveal hyperfine (alpha iso = 7.3 +/- 0.20 MHz and alpha dip = 0.50 +/- 0.10 MHz) and nuclear quadrupolar (e(2)qQ = 1.98 +/- 0.05 MHz and eta = 0.84 +/- 0.06) couplings for a single (14)N nucleus magnetically coupled to the manganese cluster in the S 2 state of PSII. These values are compared to the histidine imidazole nitrogen hyperfine and nuclear quadrupolar couplings found in superoxidized manganese catalase as well as (14)N couplings in relevant manganese model complexes.

Protein Ligation of the Photosynthetic Oxygen-Evolving Center

Photosynthetic water oxidation is catalyzed by a unique Mn(4)Ca cluster in Photosystem II. The ligation environment of the Mn(4)Ca cluster optimizes the cluster's reactivity at each step in the catalytic cycle and minimizes the release of toxic, partly oxidized intermediates. However, our understanding of the cluster's ligation environment remains incomplete. Although the recent X-ray crystallographic structural models have provided great insight and are consistent with most conclusions of earlier site-directed mutagenesis studies, the ligation environments of the Mn(4)Ca cluster in the two available structural models differ in important respects. Furthermore, while these structural models and the earlier mutagenesis studies agree on the identity of most of the Mn(4)Ca cluster's amino acid ligands, they disagree on the identity of others. This review describes mutant characterizations that have been undertaken to probe the ligation environment of the Mn(4)Ca cluster, some of which have been inspired by the recent X-ray crystallographic structural models. Many of these characterizations have involved Fourier Transform Infrared (FTIR) difference spectroscopy because of the extreme sensitivity of this form of spectroscopy to the dynamic structural changes that occur during an enzyme's catalytic cycle.

Bis{μ-2,2'-[1,1'-(ethane-1,2-diyldinitrilo)diethyl-idyne]diphenolato}bis-[(benzoato-κO)manganese(III)] dihydrate

The title compound, [Mn(2)(C(18)H(18)N(2)O(2))(2)(C(7)H(5)O(2))(2)]·2H(2)O, was synthesized by the reaction between manganese(II) benzoate and the Schiff base generated in situ by the condensation of ethane-1,2-diamine and o-hydroxy-aceto-phen-one. The Jahn-Teller-distorted manganese(III) ions of the centrosymmetric dimer are connected through phen-oxy bridges. Hydrogen-bonding inter-actions between the uncoord-in-ated C=O of the benzoate and uncoordinated water mol-ecules link the dimers into a chain running parallel to the c axis.

A systematic density functional study of the zero-field splitting in Mn(II) coordination compounds

This work presents a detailed evaluation of the performance of density functional theory (DFT) for the prediction of zero-field splittings (ZFSs) in Mn(II) coordination complexes. Eighteen experimentally well characterized four-, five-, and six-coordinate complexes of the general formula [Mn(L)nL'2] with L' = Cl, Br, I, NCS, or N3 (L = an oligodentate ligand) are considered. Several DFT-based approaches for the prediction of the ZFSs are compared. For the estimation of the spin-orbit coupling (SOC) part of the ZFS, it was found that the Pederson-Khanna (PK) approach is more successful than the previously proposed quasi-restricted orbitals (QRO)-based method. In either case, accounting for the spin-spin (SS) interaction either with or without the inclusion of the spin-polarization effects improves the results. This argues for the physical necessity of accounting for this important contribution to the ZFS. On average, the SS contribution represents approximately 30% of the axial D parameters. In addition to the SS part, the SOC contributions of d-d spin flip (alphabeta) and ligand-to-metal charge transfer excited states (betabeta) were found to dominate the SOC part of the D parameter; the observed near cancellation between the alphaalpha and betaalpha parts is discussed in the framework of the PK model. The calculations systematically (correlation coefficient approximately 0.99) overestimate the experimental D values by approximately 60%. Comparison of the signs of calculated and measured D values shows that the signs of the calculated axial ZFS parameters are unreliable once E/D > 0.2. Finally, we find that the calculated D and E/D values are highly sensitive to small structural changes. It is observed that the use of theoretically optimized geometries leads to a significant deterioration of the theoretical predictions relative to the experimental geometries derived from X-ray diffraction. The standard deviation of the theoretical predictions for the D values almost doubles from approximately 0.1 to approximately 0.2 cm-1 upon using quantum chemically optimized structures. We do not find any noticeable improvement in considering basis sets larger than standard double- (SVP) or triple-zeta (TZVP) basis sets or using functionals other than the BP functional.

Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon

Since convergent evolution of enzyme active sites was first identified in serine proteases, other individual instances of this phenomenon have been documented. However, a systematic analysis assessing the frequency of this phenomenon across enzyme space is still lacking. This work uses the Query3d structural comparison algorithm to integrate for the first time detailed knowledge about catalytic residues, available through the Catalytic Site Atlas (CSA), with the evolutionary information provided by the Structural Classification of Proteins (SCOP) database. This study considers two modes of convergent evolution: (i) mechanistic analogues which are enzymes that use the same mechanism to perform related, but possibly different, reactions (considered here as sharing the first three digits of the EC number); and (ii) transformational analogues which catalyse exactly the same reaction (identical EC numbers), but may use different mechanisms. Mechanistic analogues were identified in 15% (26 out of 169) of the three-digit EC groups considered, showing that this phenomenon is not rare. Furthermore 11 of these groups also contain transformational analogues. The catalytic triad is the most widespread active site; the results of the structural comparison show that this mechanism, or variations thereof, is present in 23 superfamilies. Transformational analogues were identified for 45 of the 951 four-digit EC numbers present within the CSA and about half of these were also mechanistic analogues exhibiting convergence of their active sites. This analysis has also been extended to the whole Protein Data Bank to provide a complete and manually curated list of the all the transformational analogues whose structure is classified in SCOP. The results of this work show that the phenomenon of convergent evolution is not rare, especially when considering large enzymatic families.