Bioinorganic insights of the PQQ-dependent alcohol dehydrogenases.

Among the several alcohol dehydrogenases, PQQ-dependent enzymes are mainly found in the α, ß, and γ-proteobacteria. These proteins are classified into three main groups. Type I ADHs are localized in the periplasm and contain one Ca2+-PQQ moiety, being the methanol dehydrogenase (MDH) the most representative. In recent years, several lanthanide-dependent MDHs have been discovered exploding the understanding of the natural role of lanthanide ions. Type II ADHs are localized in the periplasm and possess one Ca2+-PQQ moiety and one heme c group. Finally, type III ADHs are complexes of two or three subunits localized in the cytoplasmic membrane and possess one Ca2+-PQQ moiety and four heme c groups, and in one of these proteins, an additional [2Fe-2S] cluster has been discovered recently. From the bioinorganic point of view, PQQ-dependent alcohol dehydrogenases have been revived recently mainly due to the discovery of the lanthanide-dependent enzymes. Here, we review the three types of PQQ-dependent ADHs with special focus on their structural features and electron transfer processes. The PQQ-Alcohol dehydrogenases are classified into three main groups. Type I and type II ADHs are located in the periplasm, while type III ADHs are in the cytoplasmic membrane. ADH-I have a Ca-PQQ or a Ln-PQQ, ADH-II a Ca-PQQ and one heme-c and ADH-III a Ca-PQQ and four hemes-c. This review focuses on their structural features and electron transfer processes.

The structure of a novel membrane-associated 6-phosphogluconate dehydrogenase from Gluconacetobacter diazotrophicus (Gd6PGD) reveals a subfamily of short-chain 6PGDs.

The enzyme 6-phosphogluconate dehydrogenase catalyzes the conversion of 6-phosphogluconate to ribulose-5-phosphate. It represents an important reaction in the oxidative pentose phosphate pathway, producing a ribose precursor essential for nucleotide and nucleic acid synthesis. We succeeded, for the first time, to determine the three-dimensional structure of this enzyme from an acetic acid bacterium, Gluconacetobacter diazotrophicus (Gd6PGD). Active Gd6PGD, a homodimer (70 kDa), was present in both the soluble and the membrane fractions of the nitrogen-fixing microorganism. The Gd6PGD belongs to the newly described subfamily of short-chain (333 AA) 6PGDs, compared to the long-chain subfamily (480 AA; e.g., Ovis aries, Homo sapiens). The shorter amino acid sequence in Gd6PGD induces the exposition of hydrophobic residues in the C-terminal domain. This distinct structural feature is key for the protein to associate with the membrane. Furthermore, in terms of function, the short-chain 6PGD seems to prefer NAD+ over NADP+ , delivering NADH to the membrane-bound NADH dehydrogenase of the microorganisms required by the terminal oxidases to reduce dioxygen to water for energy conservation. ENZYME: ECnonbreakingspace1.1.1.343. DATABASE: Structural data are available in PDB database under the accession number 6VPB.

Introduction: Transition Metals and Sulfur.

The number of transition metal ions which are essential to life - also often called trace elements - increased steadily over the years. In parallel, the list of biological functions in which transition metals are involved, has grown, and is still growing tremendously. Significant progress has been made in understanding the chemistry operating at the biological sites where metal ions have been discovered. Early on, based on the application of physical, chemical, and biological techniques, it became likely that numerous of these metal centers carry sulfur ligands in their coordination sphere, such as sulfide (S2-), cysteine (RS-), or methionine (RSCH3). Notably, the structure and the reactivity of the metal active sites turned out to be quite different from anything previously observed in simple coordination complexes. Consequently, the prediction of active-site structures, based on known properties of transition metal ion complexes, turned out to be difficult and incorrect in many cases. Yet, biomimetic inorganic chemistry, via synthesis and detailed structural and electronic characterization of synthetic analogues, became an important factor and helped to understand the properties of the metal active sites. Striking advances came from molecular biology techniques and protein crystallography, as documented by the publication of the first high-resolution structures of iron-sulfur proteins and the blue copper protein plastocyanin approximately five decades ago. In this volume of METAL IONS IN LIFE SCIENCES the focus will be on some of the most intriguing, in our view, transition metal-sulfur sites discovered in living organisms. These include the type 1 Cu mononuclear center, the purple mixed-valent [Cu1.5+-(Cys)2-Cu1.5+] CuA, the tetranuclear copper-sulfide catalytic center of nitrous oxide reductase, the heme-thiolate site in cytochrome P450, the iron-sulfur proteins with bound inorganic (S2-) and organic (Cys-) sulfur, the pterin dithiolene cofactor (Moco) coordinated to either molybdenum or tungsten, the [8Fe-7S] P-cluster and the [Mo-7Fe-9S-C]-homocitrate catalytic site of nitrogenase, the siroheme-[4Fe-4S] center involved in the reduction of sulfite (SO32-) to hydrogen sulfide (H2S), the NiFeS sites of hydrogenases and CO dehydrogenase, and the zinc finger domains. We apologize to all researchers and their associates who have made tremendous contributions to our current knowledge of the steadily increasing transition metal sulfur sites in proteins and enzymes but are not mentioned here. These omissions are by no means intentional but merely the consequence of time and space. We are fully aware of the excellent books and authoritative reviews on various aspects of the subject, however, it is our motivation to cover in one single volume this exciting domain of bioinorganic chemistry.

Sulfur, the Versatile Non-metal.

The non-metallic chemical element sulfur, 3216S , referred to in Genesis as brimstone and identified as element by Lavoisier, is the tenth most abundant element in the universe and the fifth most common element on Earth. Important inorganic forms of sulfur in the biosphere are elemental sulfur (S8), sulfate (SO2-4), and sulfide (S2-), sulfite (SO2-3), thiosulfate, (S2O23), and polythionates (S3O62-; S4O62-). Because of its wide range of stable oxidation states, from +6to -2, sulfur plays important roles in central biochemistry as a structural and redoxactive element and is intimately related to life on Earth. Unusual reaction pathways involving sulfur compounds become possible by the specific properties of this element. Sulfur occurs in all the major classes of biomolecules, including enzymes, proteins, sugars, nucleic acids, vitamin cofactors, and metabolites. The flexibility of these biomolecules follows from its versatile chemistry. The best known sulfur mineral is perhaps pyrite (Fool's gold), with the chemical formula, FeS2. Sulfur radical anions, such as [S3].-, are responsible for the intense blue color of lapis lazuli, one of the most desired and expensive artists' materials. In the microbial world, inorganic sulfur compounds, e.g., elemental sulfur and sulfate, belong to the most important electron acceptors. Studies on microbial sulfur metabolism revealed many novel enzymes and pathways and advanced the understanding on metabolic processes used for energy conservation, not only of the microbes, but of biology in general. Transition metal sulfur complexes display intriguing catalytic activities, they provide surfaces and complex cavities in metalloenzymes that activate inert molecules such as H2, CO, N2 or N2O, and they catalyze the transformations of numerous organic molecules. Both thiamine diphosphate- (ThDP) and S-adenosyl- L-methionine- (SAM) dependent enzymes belong to Nature's most powerful catalysts with a remarkable spectrum of catalytic activities. In conclusion, given sulfur's diverse properties, evolution made an excellent choice in selecting sulfur as one the basic elements of life.

Cytochrome P450. The Dioxygen-Activating Heme Thiolate.

Cytochromes P450 (CYPs) are heme b-binding enzymes and belong to Nature's most versatile catalysts. They participate in countless essential life processes, and exist in all domains of life, Bacteria, Archaea, and Eukarya, and in viruses. CYPs attract the interest of researchers active in fields as diverse as biochemistry, chemistry, biophysics, molecular biology, pharmacology, and toxicology. CYPs fight chemicals such as drugs, poisonous compounds in plants, carcinogens formed during cooking, and environmental pollutants. They represent the first line of defense to detoxify and solubilize poisonous substances by modifying them with dioxygen. The heme iron is proximally coordinated by a thiolate residue, and this ligation state represents the active form of the enzyme. The Fe(III) center displays characteristic UV/Vis and EPR spectra (Soret maximum at 418 nm; g-values at 2.41, 2.26, 1.91). The Fe(II) state binds the inhibitor carbon monoxide (CO) to produce a Fe(II)-CO complex, with the major absorption maximum at 450 nm, hence, its name P450. CYPs are flexible proteins in order to allow a vast range of substrates to enter and products to leave. Two extreme forms exist: substrate-bound (closed) and substrate-free (open). CYPs share a sophisticated catalytic cycle that involves a series of consecutive transformations of the heme thiolate active site, with the strong oxidants compound I and II as key intermediates. Each of these high-valent Fe(IV) species has its characteristic features and chemical properties, crucial for the activation of dioxygen and cleavage of strong C-H bonds.

The magic of dioxygen.

Oxygen has to be considered one of the most important elements on Earth. Earlier, some dispute arose as to which of the three scientists, Carl Wilhelm Scheele (Sweden), Joseph Priestley (United Kingdom) or Antoine Lavoisier (France), should get credit for the air of life.Today it is agreed that the Swede discovered it first, the fire air in 1772. The British chemist published it first, the dephlogisticated air in 1775, and the Frenchman understood it first, the oxygen in 1775-1778. Surely, there is credit enough for all three to split the "Nobel Prize" awarded by Carl Djerassi and Roald Hoffmann in their play Oxygen. Molecular oxygen means life. So-called aerobes - these include humans, animals, and plants - need O2 to conserve the energy they have to gain from their environment. Eliminate O2 and these organisms cannot support an active lifestyle. What makes dioxygen that special? It is a non-metal and oxidizing agent that readily reacts with most elements to form compounds, notably oxides. From a biological point of view, the most important compound of course is water, H2O, which provides an excellent solvent for biomolecules. It influences the climate of the Earth, and it is the source of almost all of the molecular oxygen in the atmosphere.

Interference of ruthenium red analogues at photosystem II of spinach thylakoids.

The effect of ruthenium red analogues on several thylakoid photosynthetic activities has been investigated. RR, RV, RRPh1, RRPh2 and Ph inhibit ATP synthesis and electron flow from water to MV (basal, phosphorylating and uncoupled) as their concentration increases, thus, they act as a Hill reaction inhibitor. They inhibit uncoupled electron transport through PSII from water to DCPIP and partially from DPC to DCPIP. However, these compounds do not affect uncoupled PSI electron transport from DCPIP to MV. Therefore, the target of interaction is at the level of OEC and the span P(680) to Q(A) for RR, RRPh1 and RRPh2. Chlorophyll a fluorescence studies corroborate the already found interference sites and may affect the disconnection between chlorophyll molecules within the LHCII and/or between antennae and RCs, or decreases the exciton to reach the RC and inhibition of PSII occurs. RRPh2 is six times more active than RR. Finally, Ph inhibits electron flow interacting at the level of Q(B).

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 B(12).

Magnetic and high-frequency EPR studies of an octahedral Fe(III) compound with unusual zero-field splitting parameters.

Temperature-dependent magnetic susceptibility and multi-frequency EPR (9.4, 34.5, 94 and 188 GHz) spectroscopic measurements have been carried out together with an X-ray study at 100 K to study [Fe(DMSO)(6)](NO(3))(3). The iron(III) ion remains high-spin (S = 5/2) in the temperature range studied, therefore, the EPR data were interpreted using the conventional S = 5/2 spin Hamiltonian. A full analysis of EPR spectra at 95 GHz of a powdered sample at 290 K revealed that they are extremely sensitive to D and E values. The zfs parameters were precisely determined: D = + 0.1730 cm(-1), E = 0.00 cm(-1) and lambda = |E/D| = 0.00. A sequence of the spectra neatly shows that the compound has a clear magnetic dependence on temperature. The study at 5 K, showed that the zfs parameters increase: D = + 0.1970 cm(-1), E = 0.017 cm(-1) and lambda = |E/D| = 0.086. These data indicate that as the temperature decreases the D tensor increases slightly showing an increase in the rhombicity. These results confirm that |2D| is congruent to h nu at X-band in this case. Additionally, it has been shown by X-ray crystal analysis of [Fe(DMSO)(6)](NO(3))(3) at 100 K that this is involved in a hydrogen bonding network, consisting of C-H...O interactions between the nitrate anions and the methyl groups of the coordinated DMSO molecules, thus suggesting that the differences found in the spectroscopic parameters D and E at different temperatures must be due to these supramolecular interactions.

High-field EPR study and crystal and molecular structure of trans-RSSR-[CrCl2(cyclam)]nX (X=ZnCl4 2-, Cl- and Cl-.4H2O.0.5HCl).

For the first time, HF-EPR (94.5 GHz) spectroscopy has been used to determine crystal field parameters in chromium(III) coordination compounds. The large zero-field splitting parameters of the dark-green photochromic trans-RSSR-[CrCl(2)(cyclam)](2)ZnCl(4), 1, the red-purple trans-RSSR-[CrCl(2)(cyclam)]Cl, 2, and the red-purple trans-RSSR-[CrCl(2)(cyclam)]Cl.4H(2)O.0.5HCl, 3, where cyclam = 1,4,8,11-tetraazacyclotetradecane, have been obtained. A full analysis of EPR spectra at 94.5 GHz of diluted complexes 1, 2 and 3 at 300 K revealed that they are extremely sensitive to D and E values. The rhombic distortion was precisely determined for each compound. For 1, g= 2.01, D=-0.305 cm(-1), E= 0.041 cm(-1) and lambda=|E/D|= 0.1396; for 2, g= 2.01; D=-0.348 cm(-1), E= 0.042 cm(-1) and lambda=|E/D|= 0.1206 and for 3, g= 1.99, D=-0.320 cm(-1), E= 0.041 cm(-1) and ambda=|E/D|= 0.1281. The EPR study at 94.5 GHz at 10 K allowed us to confirm the sign of the D value for all compounds. These data indicate that at room temperature the crystal field is mainly rhombic and as the temperature decreases, the rhombicity of the D tensor increases slightly. These found differences between 1, 2 and 3 allowed us to establish the importance of the intermolecular interactions in the solid state due to different hydrogen bonding networks in their crystalline arrangement.