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Paracoccus pantotrophus pseudoazurin is an electron donor to cytochrome c peroxidase, Pauleta, S. R., Guerlesquin F., Goodhew C. F., Devreese B., Van Beeumen J., Pereira A. S., Moura I., and Pettigrew G. W. , Biochemistry, Sep 7, Volume 43, Number 35, p.11214-11225, (2004) AbstractWebsite

The gene for pseudoazurin was isolated from Paracoccus pantotrophus LMD 52.44 and expressed in a heterologous system with a yield of 54.3 mg of pure protein per liter of culture. The gene and protein were shown to be identical to those from P. pantotrophus LMD 82.5. The extinction coefficient of the protein was re-evaluated and was found to be 3.00 mM(-1) cm(-1) at 590 nm. It was confirmed that the oxidized protein is in a weak monomer/dimer equilibrium that is ionic- strength-dependent. The pseudoazurin was shown to be a highly active electron donor to cytochrome c peroxidase, and activity showed an ionic strength dependence consistent with an electrostatic interaction. The pseudoazurin has a very large dipole moment, the vector of which is positioned at the putative electron-transfer site, His81, and is conserved in this position across a wide range of blue copper proteins. Binding of the peroxidase to pseudoazurin causes perturbation of a set of NMR resonances associated with residues on the His81 face, including a ring of lysine residues. These lysines are associated with acidic residues just back from the rim, the resonances of which are also affected by binding to the peroxidase. We propose that these acidic residues moderate the electrostatic influence of the lysines and so ensure that specific charge interactions do not form across the interface with the peroxidase.

Partial purification and characterization of the first hydrogenase isolated from a thermophilic sulfate-reducing bacterium, Fauque, G., Czechowski M., Berlier Y. M., Lespinat P. A., Legall J., and Moura J. J. , Biochem Biophys Res Commun, May 15, Volume 184, Number 3, p.1256-60, (1992) AbstractWebsite

A soluble [NiFe] hydrogenase has been partially purified from the obligate thermophilic sulfate-reducing bacterium Thermodesulfobacterium mobile. A 17% purification yield was obtained after four chromatographic steps and the hydrogenase presents a purity index (A398 nm/A277 nm) equal to 0.21. This protein appears to be 75% pure on SDS-gel electrophoresis showing two major bands of molecular mass around 55 and 15 kDa. This hydrogenase contains 0.6-0.7 nickel atom and 7-8 iron atoms per mole of enzyme and has a specific activity of 783 in the hydrogen uptake reaction, of 231 in the hydrogen production assay and of 84 in the deuterium-proton exchange reaction. The H2/HD ratio is lower than one in the D2-H+ exchange reaction. The enzyme is very sensitive to NO, relatively little inhibited by CO but unaffected by NO2-. The EPR spectrum of the native hydrogenase shows the presence of a [3Fe-4S] oxidized cluster and of a Ni(III) species.

Periplasmic nitrate reductase and formate dehydrogenase: similar molecular architectures with very different enzymatic activities, Cerqueira, N., Gonzalez P. J., Fernandes P. A., Moura J. J. G., and Ramos M. J. , Acc Chem Res, Volume 48, p.2875−2884, (2015)
Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum, Najmudin, S., Gonzalez P. J., Trincao J., Coelho C., Mukhopadhyay A., Cerqueira N. M., Romao C. C., Moura I., Moura J. J., Brondino C. D., and Romao M. J. , J Biol Inorg Chem, Jun, Volume 13, Number 5, p.737-53, (2008) AbstractWebsite

Nitrate reductase from Desulfovibrio desulfuricans ATCC 27774 (DdNapA) is a monomeric protein of 80 kDa harboring a bis(molybdopterin guanine dinucleotide) active site and a [4Fe-4S] cluster. Previous electron paramagnetic resonance (EPR) studies in both catalytic and inhibiting conditions showed that the molybdenum center has high coordination flexibility when reacted with reducing agents, substrates or inhibitors. As-prepared DdNapA samples, as well as those reacted with substrates and inhibitors, were crystallized and the corresponding structures were solved at resolutions ranging from 1.99 to 2.45 A. The good quality of the diffraction data allowed us to perform a detailed structural study of the active site and, on that basis, the sixth molybdenum ligand, originally proposed to be an OH/OH(2) ligand, was assigned as a sulfur atom after refinement and analysis of the B factors of all the structures. This unexpected result was confirmed by a single-wavelength anomalous diffraction experiment below the iron edge (lambda = 1.77 A) of the as-purified enzyme. Furthermore, for six of the seven datasets, the S-S distance between the sulfur ligand and the Sgamma atom of the molybdenum ligand Cys(A140) was substantially shorter than the van der Waals contact distance and varies between 2.2 and 2.85 A, indicating a partial disulfide bond. Preliminary EPR studies under catalytic conditions showed an EPR signal designated as a turnover signal (g values 1.999, 1.990, 1.982) showing hyperfine structure originating from a nucleus of unknown nature. Spectropotentiometric studies show that reduced methyl viologen, the electron donor used in the catalytic reaction, does not interact directly with the redox cofactors. The turnover signal can be obtained only in the presence of the reaction substrates. With use of the optimized conditions determined by spectropotentiometric titration, the turnover signal was developed with (15)N-labeled nitrate and in D(2)O-exchanged DdNapA samples. These studies indicate that this signal is not associated with a Mo(V)-nitrate adduct and that the hyperfine structure originates from two equivalent solvent-exchangeable protons. The new coordination sphere of molybdenum proposed on the basis of our studies led us to revise the currently accepted reaction mechanism for periplasmic nitrate reductases. Proposals for a new mechanism are discussed taking into account a molybdenum and ligand-based redox chemistry, rather than the currently accepted redox chemistry based solely on the molybdenum atom.

Periplasmic nitrate reductases and formate dehydrogenases: Biological control of the chemical properties of Mo and W for fine tuning of reactivity, substrate specificity and metabolic role, Gonzalez, P. J., Rivas M. G., Mota C. S., Brondino C. D., Moura I., and Moura J. J. G. , Coord Chem Rev, Volume 257, p.315-331, (2013)
Peroxidase-like activity of cytochrome b5 is triggered upon hemichrome formation in alkaline pH, Samhan-Arias, A., Maia L. B., Cordas C. M., Moura I., Gutierrez-Merino C., and Moura J. J. G. , BBA - Proteins and Proteomics, Volume 1866, p.373-378, (2018)
Perturbation of membrane dynamics in nerve cells as an early event during bilirubin-induced apoptosis, Rodrigues, C. M., Sola S., Castro R. E., Laires P. A., Brites D., and Moura J. J. , J Lipid Res, Jun, Volume 43, Number 6, p.885-94, (2002) AbstractWebsite

Increased levels of unconjugated bilirubin, the end product of heme catabolism, impair crucial aspects of nerve cell function. In previous studies, we demonstrated that bilirubin toxicity may be due to cell death by apoptosis. To characterize the sequence of events leading to neurotoxicity, we exposed developing rat brain astrocytes and neurons to unconjugated bilirubin and investigated whether changes in membrane dynamic properties can mediate apoptosis. Bilirubin induced a rapid, dose-dependent increase in apoptosis, which was nevertheless preceded by impaired mitochondrial metabolism. Using spin labels and electron paramagnetic resonance spectroscopy analysis of whole cell and isolated mitochondrial membranes exposed to bilirubin, we detected major membrane perturbation. By physically interacting with cell membranes, bilirubin induced an almost immediate increase in lipid polarity sensed at a superficial level. The enhanced membrane permeability coincided with an increase in lipid fluidity and protein mobility and was associated with significant oxidative injury to membrane lipids. In conclusion, apoptosis of nerve cells induced by bilirubin is mediated by its primary effect at physically perturbing the cell membrane. Bilirubin directly interacts with membranes influencing lipid polarity and fluidity, protein order, and redox status. These data suggest that nerve cell membranes are primary targets of bilirubin toxicity.

The photochemical reaction between uranyl nitrate and azulene, Burrows, Hugh D., Cardoso Augusto C., Formosinho Sebastião J., Gil Ana M. P. C., da Miguel Maria Graça M., Barata Belamino, and J.G. Moura José , Journal of Photochemistry and Photobiology A: Chemistry, Volume 68, Number 3, p.279-287, (1992) AbstractWebsite
The photochemical reaction between uranyl-nitrate and azulene, Burrows, H. D., Cardoso A. C., Formosinho S. J., Gil Ampc, Miguel M. D., Barata B., and Moura J. J. G. , Journal of Photochemistry and Photobiology a-Chemistry, Sep 30, Volume 68, Number 3, p.279-287, (1992) AbstractWebsite

On photolysis of solutions of azulene and uranyl nitrate in alcohols, a dark, amorphous precipitate is formed. Various analytical techniques show that this is a mixture of a uranium salt and an organic component, suggested to be polyazulene. The effects of various parameters on the yield of the product have been studied and it is found that oxygen facilitates the reaction. Electron spin resonance studies show that the product is paramagnetic, in agreement with the established ease of oxidation of polyazulene, and suggest that it is formed via electron transfer from azulene to excited uranyl ion, followed by successive dimerizations and deprotonations of radical cation intermediates.

Physico-chemical and Spectroscopic Properties of the Monohemic Cytochrome C552 from Pseudomonas nautica 617, Saraiva, Lígia M., Fauque Guy, Besson Stéphane, and Moura Isabel , European Journal of Biochemistry, Volume 224, Number 3, p.1011-1017, (1994) AbstractWebsite

A c-type monohemic ferricytochrome c552 (11 kDa) was isolated from the soluble extract of a marine denitrifier, Pseudomonas nautica strain 617, grown under anaerobic conditions with nitrate as final electron acceptor. The NH2-terminal sequence and the amino acid composition of the cytochrome were determined. The heme iron of the cytochrome c552 has histidine-methionine as axial ligands, and a pH-dependent mid-point redox potential, equal to 250 mV at pH 7.6. The presence of methionine was demonstrated by visible, EPR and NMR spectroscopies. The assignment of most of the hemic protons was performed applying two-dimensional NOE spectroscopy (NOESY), and the aromatic region was assigned through two-dimensional correlated spectroscopy (COSY) experiments. The EPR spectrum of the oxidised form of the cytochrome c552 is typical of a low-spin ferric heme.

Potential therapeutic approaches for a sleeping pathogen: tuberculosis a case for bioinorganic chemistry, Sousa, E. H. S., Diógenes I. C. N., Lopes L. G. F., and Moura J. J. G. , J Biol Inorg Chem, Volume 25, p.685, (2020)
Predicting Protein-Protein Interactions Using BiGGER: Case Studies, Almeida, R. M., Dell'Acqua S., Krippahl L., Moura J. J. G., and Pauleta S. R. , Molecules, Volume 21, p.1037, (2016) Website
Prediction of Signal Peptides and Signal Anchors of Cytocrome c Nitrite Reductase from Desulfovibrio desulfuricans ATCC 27774 Using Bioinformatic Tools, Gonçalves, L. L., Almeida M. G., Lampreia J., Moura J. J. G., and Moura I. , Essays in Bioinformatics, Volume Vol. 368, p.203-208, (2005) Abstract


Preliminary crystallographic analysis and further characterization of a dodecaheme cytochrome c from Desulfovibrio desulfuricans ATCC 27774, Coelho, A. V., Matias P. M., Sieker L. C., Morais J., Carrondo M. A., Lampreia J., Costa C., Moura J. J., Moura I., and Legall J. , Acta Crystallogr D Biol Crystallogr, Nov 1, Volume 52, Number Pt 6, p.1202-8, (1996) AbstractWebsite

Dodecaheme cytochrome c has been purified from Desulfovibrio (D.) desulfuricans ATCC 27774 cells grown under both nitrate and sulfate-respiring conditions. Therefore, it is likely to play a role in the electron-transfer system of both respiratory chains. Its molecular mass (37768 kDa) was determined by electrospray mass spectrometry. Its first 39 amino acids were sequenced and a motif was found between amino acids 32 and 37 that seems to exist in all the cytochromes of the c(3) type from sulfate-reducing bacteria sequenced at present. The midpoint redox potentials of this cytochrome were estimated to be -68, -120, -248 and -310 mV. Electron paramagnetic resonance spectroscopy of the oxidized cytochrome shows several low-spin components with a g(max) spreading from 3.254 to 2.983. Two crystalline forms were obtained by vapour diffusion from a solution containing 2% PEG 6000 and 0.25-0.75 M acetate buffer pH = 5.5. Both crystals belong to monoclinic space groups: one is P2(1), with a = 61.00, b = 106.19, c = 82.05 A, beta = 103.61 degrees, and the other is C2 with a = 152.17, b = 98.45, c = 89.24 A, beta = 119.18 degrees. Density measurements of the P2(1) crystals suggest that there are two independent molecules in the asymmetric unit. Self-rotation function calculations indicate, in both crystal forms, the presence of a non-crystallographic axis perpendicular to the crystallographic twofold axis. This result and the calculated values for the volume per unit molecular weight of the C2 crystals suggest the presence of two or four molecules in the asymmetric unit.

Preliminary crystallographic analysis of the oxidized form of a two mono-nuclear iron centres protein from Desulfovibrio desulfuricans ATCC 27774, Coelho, A. V., Matias P. M., Carrondo M. A., Tavares P., Moura J. J., Moura I., Fulop V., Hajdu J., and Legall J. , Protein Sci, Jun, Volume 5, Number 6, p.1189-91, (1996) AbstractWebsite

Crystals of the fully oxidized form of desulfoferrodoxin were obtained by vapor diffusion from a solution containing 20% PEG 4000, 0.1 M HEPES buffer, pH 7.5, and 0.2 M CaCl2. Trigonal and/or rectangular prisms could be obtained, depending on the temperature used for the crystal growth. Trigonal prisms belong to the rhombohedral space group R32, with a = 112.5 A and c = 63.2 A; rectangular prisms belong to the monoclinic space group C2, with a = 77.7 A, b = 80.9 A, c = 53.9 A, and beta = 98.1 degrees. The crystallographic asymmetric unit of the rhombohedral crystal form contains one molecule. There are two molecules in the asymmetric unit of the monoclinic form, in agreement with the self-rotation function.

The presence of redox-sensitive nickel in the periplasmic hydrogenase from Desulfovibrio gigas, Legall, J., Ljungdahl P. O., Moura I., Peck, H. D. Jr., Xavier A. V., Moura J. J., Teixera M., Huynh B. H., and Dervartanian D. V. , Biochem Biophys Res Commun, May 31, Volume 106, Number 2, p.610-6, (1982) AbstractWebsite
Primary sequence, oxidation-reduction potentials and tertiary-structure prediction of Desulfovibrio desulfuricans ATCC 27774 flavodoxin, Caldeira, J., Palma P. N., Regalla M., Lampreia J., Calvete J., Schafer W., Legall J., Moura I., and Moura J. J. , Eur J Biochem, Mar 15, Volume 220, Number 3, p.987-95, (1994) AbstractWebsite

Flavodoxin was isolated and purified from Desulfovibrio desulfuricans ATCC 27774, a sulfate-reducing organism that can also utilize nitrate as an alternative electron acceptor. Mid-point oxidation-reduction potentials of this flavodoxin were determined by ultraviolet/visible and EPR methods coupled to potentiometric measurements and their pH dependence studied in detail. The redox potential E2, for the couple oxidized/semiquinone forms at pH 6.7 and 25 degrees C is -40 mV, while the value for the semiquinone/hydroquinone forms (E1), at the same pH, -387 mV. E2 varies linearly with pH, while E1 is independent of pH at high values. However, at low pH (< 7.0), this value is less negative, compatible with a redox-linked protonation of the flavodoxin hydroquinone. A comparative study is presented for Desulfovibrio salexigens NCIB 8403 flavodoxin [Moura, I., Moura, J.J.G., Bruschi, M. & LeGall, J. (1980) Biochim. Biophys. Acta 591, 1-8]. The complete primary amino acid sequence was obtained by automated Edman degradation from peptides obtained by chemical and enzymic procedures. The amino acid sequence was confirmed by FAB/MS. Using the previously determined tridimensional structure of Desulfovibrio vulgaris flavodoxin as a model [similarity, 48.6%; Watenpaugh, K.D., Sieker, L.C., Jensen, L.H., LeGall, J. & Dubourdieu M. (1972) Proc. Natl Acad. Sci. USA 69, 3185-3188], the tridimensional structure of D. desulfuricans ATCC 27774 flavodoxin was predicted using AMBER force-field calculations.

Primary structure of desulfoferrodoxin from Desulfovibrio desulfuricans ATCC 27774, a new class of non-heme iron proteins, Devreese, B., Tavares P., Lampreia J., Van Damme N., Legall J., Moura J. J., Van Beeumen J., and Moura I. , FEBS Lett, May 6, Volume 385, Number 3, p.138-42, (1996) AbstractWebsite

The primary structure of desulfoferrodoxin from Desulfovibrio desulfuricans ATCC 27774, a redox protein with two mononuclear iron sites, was determined by automatic Edman degradation and mass spectrometry of the composing peptides. It contains 125 amino acid residues of which five are cysteines. The first four, Cys-9, Cys-12, Cys-28 and Cys-29, are responsible for the binding of Center I which has a distorted tetrahedral sulfur coordination similar to that found in desulforedoxin from D. gigas. The remaining Cys-115 is proposed to be involved in the coordination of Center II, which is probably octahedrally coordinated with predominantly nitrogen/oxygen containing ligands as previously suggested by Mossbauer and Raman spectroscopy.

The primary structure of the beta subunit of Desulfovibrio desulfuricans (ATCC 27774) NiFe hydrogenase, Franco, R., Calvete J. J., Thole H. H., Raida M., Moura I., and Moura J. J. G. , Protein and Peptide Letters, Apr, Volume 4, Number 2, p.131-138, (1997) AbstractWebsite

The periplasmic [NiFe] hydrogenase isolated from Desulfovibrio (D.) desulfuricans (ATCC 27774) is a heterodimer of a 28 kDa (beta) and a 60 kDa (alpha) subunit. Here we report the complete amino acid sequence of the small (beta) polypeptide chain determined by Edman degradation of proteolytic fragments. Electrospray-ionization mass spectrometry of the native protein confirmed the sequencing results. The sequence is compared with that of D. gigas [NiFe] hydrogenase whose three-dimensional structure has been recently published.

The primary structure of the split-Soret cytochrome c from Desulfovibrio desulfuricans ATCC 27774 reveals an unusual type of diheme cytochrome c, Devreese, B., Costa C., Demol H., Papaefthymiou V., Moura I., Moura J. J., and Van Beeumen J. , Eur J Biochem, Sep 1, Volume 248, Number 2, p.445-51, (1997) AbstractWebsite

The complete amino acid sequence of the unusual diheme split-Soret cytochrome c from the sulphate-reducing Desulfovibrio desulfuricans strain ATCC 27774 has been determined using classical chemical sequencing techniques and mass spectrometry. The 247-residue sequence shows almost no similarity with any other known diheme cytochrome c, but the heme-binding site of the protein is similar to that of the cytochromes c3 from the sulphate reducers. The cytochrome-c-like domain of the protein covers only the C-terminal part of the molecule, and there is evidence for at least one more domain containing four cysteine residues, which might bind another cofactor, possibly a non-heme iron-containing cluster. This domain is similar to a sequence fragment of the genome of Archaeoglobus fulgidus, which confirms the high conservation of the genes involved in sulfate reduction.

Protein effects on the electronic structure of the [Fe4S4]2+ cluster in ferredoxin and HiPIP, Glaser, T., Bertini I., Moura J. J., Hedman B., Hodgson K. O., and Solomon E. I. , J Am Chem Soc, May 23, Volume 123, Number 20, p.4859-60, (2001) AbstractWebsite
Proteins containing the factor F430 from methanosarcina barkeri and methanobacterium thermoautotrophicum: Isolation and properties, Moura, Isabel, Moura José J. G., Santos Helena, Xavier Antonio V., Burch Gary, Peck Jr Harry D., and Legall Jean , Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Volume 742, Number 1, p.84-90, (1983) AbstractWebsite
Proteins dominate in the surface layers formed on materials exposed to extracellular polymeric substances from bacterial cultures, Yang, Y., Wikieł A. J., Dall'agnol L. T., Eloy P., Genet M. J., Moura J. J. G., Sand W., Dupont-Gillain C. C., and Rouxhet P. G. , Biofouling, Volume 32, p.95-108, (2016)
Proteómica: a Interface entre a Biologia Molecular e a Biochemistry de Proteínas, Almeida, G., Rodrigues C., and Lampreia J. , Bol. Soc. Port. Química, Volume 82, p.49-56, (2001) Abstract