Isabel Moura

Crystal structure of the xanthine oxidase-related aldehyde oxido-reductase from D. gigas

The crystal structure of the aldehyde oxido-reductase (Mop) from the sulfate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas has been determined at 2.25 Å resolution by multiple isomorphous replacement and refined. The protein, a homodimer of 907 amino acid residues subunits, is a member of the xanthine oxidase family. The protein contains a molybdopterin cofactor (Mo-co) and two different [2Fe-2S] centers. It is folded into four domains of which the first two bind the iron sulfur centers and the last two are involved in Mo-co binding. Mo-co is a molybdenum molybdopterin cytosine dinucleotide. Molybdopterin forms a tricyclic system with the pterin bicycle annealed to a pyran ring. The molybdopterin dinucleotide is deeply buried in the protein. The cis-dithiolene group of the pyran ring binds the molybdenum, which is coordinated by three more (oxygen) ligands.

Crystal structure of the first dissimilatory nitrate reductase at 1.9 Å solved by MAD methods

BACKGROUND The periplasmic nitrate reductase (NAP) from the sulphate reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is induced by growth on nitrate and catalyses the reduction of nitrate to nitrite for respiration. NAP is a molybdenum-containing enzyme with one bis-molybdopterin guanine dinucleotide (MGD) cofactor and one [4Fe-4S] cluster in a single polypeptide chain of 723 amino acid residues. To date, there is no crystal structure of a nitrate reductase. RESULTS The first crystal structure of a dissimilatory (respiratory) nitrate reductase was determined at 1.9 A resolution by multiwavelength anomalous diffraction (MAD) methods. The structure is folded into four domains with an alpha/beta-type topology and all four domains are involved in cofactor binding. The [4Fe-4S] centre is located near the periphery of the molecule, whereas the MGD cofactor extends across the interior of the molecule interacting with residues from all four domains. The molybdenum atom is located at the bottom of a 15 A deep crevice, and is positioned 12 A from the [4Fe-4S] cluster. The structure of NAP reveals the details of the catalytic molybdenum site, which is coordinated to two MGD cofactors, Cys140, and a water/hydroxo ligand. A facile electron-transfer pathway through bonds connects the molybdenum and the [4Fe-4S] cluster. CONCLUSIONS The polypeptide fold of NAP and the arrangement of the cofactors is related to that of Escherichia coli formate dehydrogenase (FDH) and distantly resembles dimethylsulphoxide reductase. The close structural homology of NAP and FDH shows how small changes in the vicinity of the molybdenum catalytic site are sufficient for the substrate specificity.

A novel type of catalytic copper cluster in nitrous oxide reductase

Nitrous oxide (N2O) is a greenhouse gas, the third most significant contributor to global warming. As a key process for N2O elimination from the biosphere, N2O reductases catalyze the two-electron reduction of N2O to N2. These 2 × 65 kDa copper enzymes are thought to contain a CuA electron entry site, similar to that of cytochrome c oxidase, and a CuZ catalytic center. The copper anomalous signal was used to solve the crystal structure of N2O reductase from Pseudomonas nautica by multiwavelength anomalous dispersion, to a resolution of 2.4 Å. The structure reveals that the CuZ center belongs to a new type of metal cluster, in which four copper ions are liganded by seven histidine residues. N2O binds to this center via a single copper ion. The remaining copper ions might act as an electron reservoir, assuring a fast electron transfer and avoiding the formation of dead-end products.

Gene Sequence and the 1.8 A Crystal Structure of the Tungsten-Containing Formate Dehydrogenase from Desulfovibrio Gigas

Desulfovibrio gigas formate dehydrogenase is the first representative of a tungsten-containing enzyme from a mesophile that has been structurally characterized. It is a heterodimer of 110 and 24 kDa subunits. The large subunit, homologous to E. coli FDH-H and to D. desulfuricans nitrate reductase, harbors the W site and one [4Fe-4S] center. No small subunit ortholog containing three [4Fe-4S] clusters has been reported. The structural homology with E. coli FDH-H shows that the essential residues (SeCys158, His159, and Arg407) at the active site are conserved. The active site is accessible via a positively charged tunnel, while product release may be facilitated, for H(+) by buried waters and protonable amino acids and for CO(2) through a hydrophobic channel.

Revisiting the catalytic CuZ cluster of nitrous oxide (N2O) reductase. Evidence of a bridging inorganic sulfur.

Nitrous-oxide reductases (N2OR) catalyze the two-electron reduction of N2O to N2. The crystal structure of N2ORs from Pseudomonas nautica(Pn) and Paracoccus denitrificans (Pd) were solved at resolutions of 2.4 and 1.6 Å, respectively. The Pn N2OR structure revealed that the catalytic CuZ center belongs to a new type of metal cluster in which four copper ions are liganded by seven histidine residues. A bridging oxygen moiety and two other hydroxide ligands were proposed to complete the ligation scheme (Brown, K., Tegoni, M., Prudencio, M., Pereira, A. S., Besson, S., Moura, J. J. G., Moura, I., and Cambillau, C. (2000) Nat. Struct. Biol.7, 191–195). However, in the CuZ cluster, inorganic sulfur chemical determination and the high resolution structure of Pd N2OR identified a bridging inorganic sulfur instead of an oxygen. This result reconciles the novel CuZ cluster with the hitherto puzzling spectroscopic data.

The presence of redox-sensitive nickel in the periplasmic hydrogenase from Desulfovibriogigas

Abstract A new and improved method for the purification of the periplasmic hydrogenase from Desulfovibrio gigas is described. This preparation of hydrogenase was found to contain 0.64 g atom of nickel per mole of protein. In the oxidized state, the hydrogenase exhibited an isotropic signal at g = 2.02 and a characteristic Ni(III) signal with g-values at 2.31, 2.20 and ∼2.0. The EPR spectrum of the reduced enzyme consisted of multiple species. One set of g-values are determined as 2.17, 2.08 and 2.04. The other minor species exhibited a resonance at g = 2.28. On partial reoxidation of the hydrogenase, the initial Ni(III) signals reappeared along with additional signals attributed to multiple Ni(III) species. It is proposed that Ni is an important functional unit in this hydrogenase.

Unambiguous identification of the nickel EPR signal in 61Ni-enriched Desulfovibrio gigas hydrogenase

Summary A highly active hydrogenase from Desulfovibrio gigas (sp. act. 440 μmoles H 2 evolved/min. mg) was purified from cells grown in 61 Ni enriched medium. The nuclear spin (I = 3/2) of 61 Ni induces hyperfine structure in the EPR spectra of purified hydrogenase, unequivocally identifying the previously observed signal as a Ni(III) species (LeGall, J., Ljungdahl, P., Moura, I., Peck, H.D. Jr., Xavier, A.V., Moura, J.J.G., Teixeira, M., Huynh, B.H. and DerVartanian, D.V., (1982) Biochem. Biophys. Res. Commun. 106 , 610–616). Samples reduced under hydrogen also show hyperfine structure suggesting the presence of a transient Ni(III) species in the reduced active state of the enzyme.

Regulation of the hexaheme nitrite/nitric oxide reductase of Desulfovibrio desulfuricans, Wolinella succinogenes and Escherichia coli: A mass spectrometric study

Dissimilatory nitrite reduction, carried out by hexaheme proteins, gives ammonia as the final product. Representatives of this enzyme group from 3 bacterial species can also reduce NO to either ammonia or N2O. The redox regulation of the nitrite/nitric oxide activities is discussed in the context of the denitrifying pathway.

Using Cytochrome c{sub 3} to Make Selenium Nanowires

We report on a new method to make nanostructures, in this case selenium nanowires, in aqueous solution at room temperature. We used the protein cytochrome c{sub 3} to reduce selenate (SeO{sub 4}{sup 2{minus}}) to selenium (Se{sup 0}). Cytochrome c{sub 3} is known for its ability to catalyze reduction of metals including U{sup VI} {yields} U{sup IV}, Cr{sup VI} {yields} Cr{sup III}, Mo{sup VI} {yields} Mo{sup IV}, Cu{sup II} {yields} Cu{sup 0}, Pb{sup II} {yields} Pb{sup 0}, Hg{sup II} {yields} Hg{sup 0}. Nanoparticles of Se{sup 0} precipitated from an aqueous solution at room temperature, followed by spontaneous self-assembling into nanowires. Cytochrome c{sub 3} was extracted from the sulfate-reducing bacteria Desulfovibrio vulgaris (strain Holdenborough) and isolated by the procedure of DerVartanian and Legall.

Isolation and characterization of desulforedoxin, a new type of non-heme iron protein from Desulfovibrio gigas

Abstract Desulfovibrio gigas desulforedoxin is a new type of non-heme iron protein of molecular weight 7,900. It contains two iron atoms, no labile sulfide and eight cysteine residues per molecule. The optical spectrum of the oxidized form presents important differences from that of the rubredoxin type proteins. Upon reduction with dithionite there is no contribution to the visible region. The oxidation-reduction process is reversible but the protein is sensitive to repeated redox cycles. The protein contains 73 amino-acid residues. Like rubredoxin it does not contain histidine and arginine but it also lacks proline, isoleucine, phenylalanine, and tryptophan. The N-terminal sequence has been determined up to 35 residues and no evident homology was found with other non-heme iron proteins.