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The surface-charge asymmetry and dimerisation of cytochrome c550 from Paracoccus denitrificans--implications for the interaction with cytochrome c peroxidase, Pettigrew, G. W., Gilmour R., Goodhew C. F., Hunter D. J., Devreese B., Van Beeumen J., Costa C., Prazeres S., Krippahl L., Palma P. N., Moura I., and Moura J. J. , Eur J Biochem, Dec 1, Volume 258, Number 2, p.559-66, (1998) AbstractWebsite

The implications of the dimeric state of cytochrome c550 for its binding to Paracoccus cytochrome c peroxidase and its delivery of the two electrons required to restore the active enzyme during catalysis have been investigated. The amino acid sequence of cytochrome c550 of Paracoccus denitrificans strain LMD 52.44 was determined and showed 21 differences from that of strain LMD 22.21. Based on the X-ray structure of the latter, a structure for the cytochrome c550 monomer from strain 52.44 is proposed and a dipole moment of 945 debye was calculated with an orientation close to the exposed haem edge. The behaviour of the cytochrome on molecular-exclusion chromatography is indicative of an ionic strength-dependent monomer (15 kDa)/dimer (30 kDa) equilibrium that can also be detected by 1H-NMR spectroscopy. The apparent mass of 50 kDa observed at very low ionic strength was consistent with the presence of a strongly asymmetric dimer. This was confirmed by cross-linking studies, which showed that a cross-linked species of mass 30 kDa on SDS behaved with an apparent mass of 50 kDa on molecular-exclusion chromatography. A programme which carried out and evaluated molecular docking of two monomers to give a dimer generated a most probable dimer in which the monomer dipoles lay almost antiparallel to each other. The resultant dipole moment of the dimer is therefore small. Although this finding calls into question the possibility of preorientation of a strongly asymmetrically charged cytochrome as it collides with a redox partner, the stoichiometry of complex formation with cytochrome c peroxidase as studied by 1H-NMR spectroscopy shows that it is the monomer that binds.

Electrochemical study on cytochrome c peroxidase from Paracoccus denitrificans: a shifting pattern of structural and thermodynamic properties as the enzyme is activated, Lopes, H., Pettigrew G. W., Moura I., and Moura J. J. G. , Journal of Biological Inorganic Chemistry, Dec, Volume 3, Number 6, p.632-642, (1998) AbstractWebsite

The di-haem cytochrome c peroxidase of Paracoccus denitrificans is a calcium binding dimer of 37.5 kDa subunits. It is responsible for reduction of H(2)O(2) to H(2)O with oxidation of cytochrome c(550) and is isolated in a fully oxidised state (inactive) in which one haem (centre I) is in a high-spin/low-spin equilibrium and high potential and the other (centre II) is low-spin and low potential. The enzyme undergoes direct electron transfer (without the need for mediators) with a 4,4'-dithiodipyridine-modified gold electrode and the response of both haem groups can be observed. By combination of the cyclic and pulse voltammetric data with the established spectroscopic information, it was demonstrated that entry of one electron to the high potential haem leads (in a mechanism involving strong haem-haem interactions) to a complex change of spin states and redox potentials of both haems in order to attain a "ready state" for binding, reduction and cleavage of the hydrogen peroxide. In the absence of endogenous calcium, haem communication can be completely disconnected and is recovered only when Ca(2+) is added, an essential step for the formation of the peroxidatic site. The intricate electrochemical behaviour of this enzyme was interpreted as a mechanism involving, both reduction and oxidation of the high potential haem, an interfacial electron transfer coupled to a homogenous chemical reaction (EC mechanism). We discuss two different models for the sequence of events leading to the appearance of the active pentacoordinated peroxidatic haem.

Metal binding to the tetrathiolate motif of desulforedoxin and related polypeptides, Kennedy, M., Yu L., Lima M. J., Ascenso C. S., Czaja C., Moura I., Moura J. J. G., and Rusnak F. , Journal of Biological Inorganic Chemistry, Dec, Volume 3, Number 6, p.643-649, (1998) AbstractWebsite

Desulforedoxin and the N-terminus of desulfoferrodoxin share a 36 amino acid domain containing a (Cys-S)(4) metal binding site. Recombinant forms of desulforedoxin, an N-terminal fragment of desulfoferrodoxin, and two desulforedoxin mutant proteins were reconstituted with Fe3+ Cd2+, and Zn2+ and relative metal ion affinities assessed by proton titrations. Protons compete with metal for protein ligands, a process that can be followed by monitoring the optical spectrum of the metal-protein complex as a function of pH. For all polypeptides, Fe3+ bound with the highest affinity, whereas the affinity of Zn2+ was greater than Cd2+ in desulforedoxin and the N-terminal fragment of desulfoferrodoxin, but this order was reversed in desulforedoxin mutant proteins. Metal binding in both mutants was significantly impaired. Furthermore, the Fe3+ complex of both mutants underwent a time-dependent bleaching process which coincided with increased reactivity of cysteine residues to Ellman's reagent and concomitant metal dissociation. It is hypothesized that this results from an autoredox reaction in which Fe3+ is reduced to Fe2+ with attendant oxidation of ligand thiols.

Isolation and characterisation of a novel sulphate-reducing bacterium of the Desulfovibrio genus, Feio, M. J., Beech I. B., Carepo M., Lopes J. M., Cheung C. W., Franco R., Guezennec J., Smith J. R., Mitchell J. I., Moura J. J., and Lino A. R. , Anaerobe, Apr, Volume 4, Number 2, p.117-30, (1998) AbstractWebsite

A novel sulphate-reducing bacterium (Ind 1) was isolated from a biofilm removed from a severely corroded carbon steel structure in a marine environment. Light microscopy observations revealed that cells were Gram-negative, rod shaped and very motile. Partial 16S rRNA gene sequencing and analysis of the fatty acid profile demonstrated a strong similarity between the new species and members from the Desulfovibrio genus. This was confirmed by the results obtained following purification and characterisation of the key proteins involved in the sulphate-reduction pathway. Several metal-containing proteins, such as two periplasmic proteins: hydrogenase and cytochrome c3, and two cytoplasmic proteins: ferredoxin and sulphite reductase, were isolated and purified. The latter proved to be of the desulfoviridin type which is typical of the Desulfovibrio genus. The study of the remaining proteins revealed a high degree of similarity with the homologous proteins isolated from Desulfovibrio gigas. However, the position of the strain within the phylogenetic tree clearly indicates that the bacterium is closely related to Desulfovibrio gabonensis, and these three strains form a separate cluster in the delta subdivision of the Proteobacteria. On the basis of the results obtained, it is suggested that Ind 1 belongs to a new species of the genus Desulfovibrio, and the name Desulfovibrio indonensis is proposed.

NMR determination of the global structure of the 113Cd derivative of desulforedoxin: investigation of the hydrogen bonding pattern at the metal center, Goodfellow, B. J., Rusnak F., Moura I., Domke T., and Moura J. J. , Protein Sci, Apr, Volume 7, Number 4, p.928-37, (1998) AbstractWebsite

Desulforedoxin (Dx) is a simple homodimeric protein isolated from Desulfovibrio gigas (Dg) containing a distorted rubredoxin-like center with one iron coordinated by four cysteinyl residues (7.9 kDa with 36 amino acids per monomer). In order to probe the geometry and the H-bonding at the active site of Dx, the protein was reconstituted with 113Cd and the solution structure determined using 2D NMR methods. The structure of this derivative was initially compared with the NMR solution structure of the Zn form (Goodfellow BJ et al., 1996, J Biol Inorg Chem 1:341-353). Backbone amide protons for G4, D5, G13, L11 NH, and the Q14 NH side-chain protons, H-bonded in the X-ray structure, were readily exchanged with solvent. Chemical shift differences observed for amide protons near the metal center confirm the H-bonding pattern seen in the X-ray model (Archer M et al., 1995, J Mol Biol 251:690-702) and also suggest that H-bond lengths may vary between the Fe, Zn, and 113Cd forms. The H-bonding pattern was further probed using a heteronuclear spin echo difference (HSED) experiment; the results confirm the presence of NH-S H-bonds inferred from D2O exchange data and observed in the NMR family of structures. The presence of "H-bond mediated" coupling in Dx indicates that the NH-S H-bonds at the metal center have significant covalent character. The HSED experiment also identified an intermonomer "through space" coupling for one of the L26 methyl groups, indicating its proximity to the 113Cd center in the opposing monomer. This is the first example of an intermonomer "through space" coupling. Initial structure calculations produced subsets of NMR families with the S of C28 pointing away from or toward the L26 methyl: only the subset with the C28 sulfur pointing toward the L26 methyl could result in a "through space" coupling. The HSED result was therefore included in the structure calculations. Comparison of the Fe, Zn, and 113Cd forms of Dx suggests that the geometry of the metal center and the global fold of the protein does not vary to any great extent, although the H-bond network varies slightly when Cd is introduced. The similarity between the H-bonding pattern seen at the metal center in Dx, Rd (including H-bonded and through space-mediated coupling), and many zinc-finger proteins suggests that these H-bonds are structurally vital for stabilization of the metal centers in these proteins.

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.

Enzymatic properties and effect of ionic strength on periplasmic nitrate reductase (NAP) from Desulfovibrio desulfuricans ATCC 27774, Bursakov, S. A., Carneiro C., Almendra M. J., Duarte R. O., Caldeira J., Moura I., and Moura J. J. , Biochem Biophys Res Commun, Oct 29, Volume 239, Number 3, p.816-22, (1997) AbstractWebsite

Some sulfate reducing bacteria can induce nitrate reductase when grown on nitrate containing media being involved in dissimilatory reduction of nitrate, an important step of the nitrogen cycle. Previously, it was reported the purification of the first soluble nitrate reductase from a sulfate-reducing bacteria Desulfovibrio desulfuricans ATCC 27774 (S.A. Bursakov, M.-Y. Liu, W.J. Payne, J. LeGall, I. Moura, and J.J.G. Moura (1995) Anaerobe 1, 55-60). The present work provides further information about this monomeric periplasmic nitrate reductase (Dd NAP). It has a molecular mass of 74 kDa, 18.6 U specific activity, KM (nitrate) = 32 microM and a pHopt in the range 8-9.5. Dd NAP has peculiar properties relatively to ionic strength and cation/anion activity responses. It is shown that monovalent cations (potassium and sodium) stimulate NAP activity and divalent (magnesium and calcium) inhibited it. Sulfate anion also acts as an activator in KPB buffer. NAP native form is protected by phosphate anion from cyanide inactivation. In the presence of phosphate, cyanide even stimulates NAP activity (up to 15 mM). This effect was used in the purification procedure to differentiate between nitrate and nitrite reductase activities, since the later is effectively blocked by cyanide. Ferricyanide has an inhibitory effect at concentrations higher than 1 mM. The N-terminal amino acid sequence has a cysteine motive C-X2-C-X3-C that is most probably involved in the coordination of the [4Fe-4S] center detected by EPR spectroscopy. The active site of the enzyme consists in a molybdopterin, which is capable for the activation of apo-nit-1 nitrate reductase of Neurospora crassa. The oxidized product of the pterin cofactor obtained by acidic hidrolysis of native NAP with sulfuric acid was identified by HPLC chromatography and characterized as a molybdopterin guanine dinucleotide (MGD).

Fe-57 Q-band pulsed ENDOR of the hetero-dinuclear site of nickel hydrogenase: Comparison of the NiA, NiB, and NiC states, Huyett, J. E., Carepo M., Pamplona A., Franco R., Moura I., Moura J. J. G., and Hoffman B. M. , Journal of the American Chemical Society, Oct 1, Volume 119, Number 39, p.9291-9292, (1997) AbstractWebsite
Nitrate and nitrite utilization in sulfate-reducing bacteria, Moura, I., Bursakov S., Costa C., and Moura J. J. , Anaerobe, Oct, Volume 3, Number 5, p.279-90, (1997) AbstractWebsite
Encapsulation of flavodoxin in reverse micelles, Andrade, S., Kamenskaya E. O., Levashov A. V., and Moura J. J. , Biochem Biophys Res Commun, May 29, Volume 234, Number 3, p.651-4, (1997) AbstractWebsite

The regulation of the properties of Desulfovibrio gigas flavodoxin in AOT/water/iso-octane micellar system was studied. UV-visible spectroscopic studies have shown that photoreduction of flavodoxin in the presence of EDTA leads to hydroquinone formation through the intermediate semiquinone. The [free FMN] - [bound to flavodoxin FMN] equilibrium (and hence, the amount of apoprotein) depends on redox state of FMN and on hydration degree which controls the micellar size. Thus, a new method of reversible cofactor removing under mild conditions (at low hydration degree of micelles) is suggested, accompained by isolation of apo-form of the protein.

The formate dehydrogenase isolated from the aerobe Methylobacterium sp. RXM is a molybdenum-containing protein, Duarte, R. O., Reis A. R., Girio F., Moura I., Moura J. J., and Collaco T. A. , Biochem Biophys Res Commun, Jan 3, Volume 230, Number 1, p.30-4, (1997) AbstractWebsite

The formate dehydrogenase (FDH) isolated from cells of Methylobacterium sp. RXM grown on molybdenum-containing mineral medium using methanol as carbon source, was partially purified (at least 90% pure as revealed by SDS-PAGE). The enzyme is unstable under oxygen and all the purification steps were conducted under strict anaerobic conditions. The molecular mass is 75 kDa (gel exclusion 300 kDa). The enzyme was characterized in terms of the kinetic parameters towards different substrates and electron acceptors, pH and temperature dependence and the effect of a wide range of compounds in the enzymatic activity. The EPR spectra of the dithionite reduced sample show, at low temperature (below 20 K), two rhombic EPR signals due to two distinct [Fe-S] centres (centre I at g-values 2.023, 1.951 and 1.933, and centre II at g-values 2.054 and 1.913). At high temperature (around 100 K) another rhombic EPR signal is optimally observed at g-values 2.002, 1.987 and 1.959 and attributed to the molybdenum site. The EPR signals assigned to the iron-sulfur centres show a strong analogy with the aldehyde oxido-reductase from Desulfovibrio gigas known to contain a Mo-pterin and two [2Fe-2S] centres and whose crystallographic structure was recently resolved.

Conversion of desulforedoxin into a rubredoxin center, Yu, L., Kennedy M., Czaja C., Tavares P., Moura J. J., Moura I., and Rusnak F. , Biochem Biophys Res Commun, Feb 24, Volume 231, Number 3, p.679-82, (1997) AbstractWebsite

Rubredoxin and desulforedoxin both contain an Fe(S-Cys)4 center. However, the spectroscopic properties of the center in desulforedoxin differ from rubredoxin. These differences arise from a distortion of the metal site hypothesized to result from adjacent cysteine residues in the primary sequence of desulforedoxin. Two desulforedoxin mutants were generated in which either a G or P-V were inserted between adjacent cysteines. Both mutants exhibited optical spectra with maxima at 278, 345, 380, 480, and 560 nm while the low temperature X-band EPR spectra indicated highspin Fe3+ ions with large rhombic distortions (E/D = 0.21-0.23). These spectroscopic properties are distinct from wild type desulforedoxin and virtually identical to rubredoxin.

Formate dehydrogenase from Desulfovibrio desulfuricans ATCC 27774: Isolation and spectroscopic characterization of the active sites (heme, iron-sulfur centers and molybdenum), Costa, C., Teixeira M., Legall J., Moura J. J. G., and Moura I. , Journal of Biological Inorganic Chemistry, Apr, Volume 2, Number 2, p.198-208, (1997) AbstractWebsite

An air-stable formate dehydrogenase, an enzyme that catalyzes the oxidation of formate to CO2, was purified from a sulfate-reducing organism, Desulfovibrio desulfuricans ATCC 27774. The enzyme has a molecular mass of approximately 150 kDa (three different subunits: 88, 29 and 16 kDa) and contains three types of redox-active centers: four c-type hemes, nonheme iron arranged as two [4Fe-4S](2+/1+) centers and a molybdenum-pterin site. Selenium was also chemically detected. The enzyme specific activity is 78 units per mg of protein. Mo(V) EPR signals were observed in the native, reduced and formate-reacted states. EPR signals related to the presence of multiple low-spin hemes were also observed in the oxidized state. Upon reduction, an examination of the EPR data under appropriate conditions distinguishes two types of iron-sulfur centers, an [Fe-S] center I (g(max)=2.050, g(med)=1.947, g(min)=1.896) and an [Fe-S] center II (g(max)=2.071, g(med)=1.926, g(min)=1.865). Mossbauer spectroscopy confirmed the presence of four hemes in the low-spin state. The presence of two [4Fe-4S](2+/1+) centers was confirmed, one of these displaying very small hyperfine coupling constants in the +1 oxidation state. The midpoint redox potentials of the enzyme metal centers were also estimated.

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.

Structure and function of molybdopterin containing enzymes, Romao, M. J., Knablein J., Huber R., and Moura J. J. , Prog Biophys Mol Biol, Volume 68, Number 2-3, p.121-44, (1997) AbstractWebsite

Molybdopterin containing enzymes are present in a wide range of living systems and have been known for several decades. However, only in the past two years have the first crystal structures been reported for this type of enzyme. This has represented a major breakthrough in this field. The enzymes share common structural features, but reveal different polypeptide folding topologies. In this review we give an account of the related spectroscopic information and the crystallographic results, with emphasis on structure-function studies.

Conversion of adrenaline to indolic derivatives by the human erythrocyte plasma membrane, Marques, F., Duarte R. O., Moura J. J., and Bicho M. P. , Biol Signals, Sep-Oct, Volume 5, Number 5, p.275-82, (1996) AbstractWebsite

The conversion of adrenaline to aminochromes by the human erythrocyte plasma membranes at pH 9.5 was shown to be a complex reaction that proceeded at least by two distinct phases. The first one, corresponding to the formation of adrenochrome, is catalyzed in the presence of the membranes, suggesting the involvement of an enzyme-mediated process. Active oxygen species were identified as intermediates during this phase. Oxygen radical scavengers (catalase and superoxide dismutase) suggested H2O2 and O2- involvement. Adrenochrome formation was stimulated by NADH indicating the participation of another enzyme (NADH dehydrogenase) which is known to be present in the human erythrocyte plasma membrane. The second phase, corresponding to the disappearance of adrenochrome, is also stimulated by NADH and inhibited in the presence of the membranes. In this reaction, adrenochrome is converted to aminochromes via adrenochrome semiquinone. The formation of radical species is demonstrated by EPR spectroscopy. The results led to the proposal of a mechanism for the formation of adrenochrome and other oxidation products from adrenaline.

Redox properties of cytochrome c nitrite reductase from Desulfovibrio desulfuricans ATCC 27774, Costa, C., Moura J. J., Moura I., Wang Y., and Huynh B. H. , J Biol Chem, Sep 20, Volume 271, Number 38, p.23191-6, (1996) AbstractWebsite

The dissimilatory nitrite reductase from Desulfovibrio desulfuricans ATCC 27774 catalyzes the reduction of nitrite to ammonia. Previous spectroscopic investigation revealed that it is a hexaheme cytochrome containing one high spin ferric heme and five low spin ferric hemes in the oxidized enzyme. The current study uses the high resolution of Mossbauer spectroscopy to obtain redox properties of the six heme groups. Correlating the Mossbauer findings with the EPR data reveals the pairwise spin-spin coupling among four of the heme groups. The other two hemes are found to be magnetically isolated. Reduction with dithionite and reaction with CO further indicate that only the high spin heme is capable of binding small exogenous ligands. These results confirm our previous finding that Desulfovibrio desulfuricans nitrite reductase contains six heme groups and that the high spin ferric heme is the substrate and inhibitor binding site.

Functional necessity and physicochemical characteristics of the 2Fe-2S cluster in mammalian ferrochelatase, Lloyd, S. G., Franco R., Moura J. J. G., Moura I., Ferreira G. C., and Huynh B. H. , Journal of the American Chemical Society, Oct 16, Volume 118, Number 41, p.9892-9900, (1996) AbstractWebsite

The recently discovered [2Fe-2S] cluster in mouse liver ferrochelatase has been characterized using UV-vis, EPR, and Mossbauer spectroscopic techniques. Studies are reported here for the recombinant protein purified from an overproducing transformed Escherichia coli strain. A positive correlation is observed between the presence of the [2Fe-2S] cluster and the enzymatic specific activity and demonstrates the necessity of this cofactor. Chemical analysis revealed that the preparations contained up to 1.3 Fe/molecule and indicated a 1:1 stoichiometry between Fe and acid-labile sulfide. The [2Fe-2S] cluster in the as-isolated ferrochelatase exhibits a UV-vis spectrum indicative of a [2Fe-2S](2+) cluster and is EPR-silent. The 8 T Mossbauer spectrum of the Fe-57-enriched as-isolated protein is well simulated by parameters Delta E(Q) = 0.69 +/- 0.03 mm/s and delta = 0.28 +/- 0.02 mm/s and confirms the presence of a diamagnetic ground state. Upon reduction with sodium dithionite, ferrochelatase shows a near-axial EPR spectrum with g-values of 2.00, 1.93, and 1.91, consistent with a S = 1/2 mixed valent Fe3+-Fe2+ cluster. The Orbach temperature dependence of the EPR line widths was used to provide an estimate of the exchange coupling J, which was determined to be on the order of 500-650 cm(-1) (+JS(1) . S-2 model). Redox titrations monitored by UV-vis and EPR spectroscopy revealed midpoint potentials of -390 +/- 10 and -405 +/- 10 mV, respectively. Mossbauer spectra of the sodium dithionite-reduced Fe-57-enriched ferrochelatase collected at 4.2 K in the presence of magnetic fields of 60 mT and 8 T strengths were analyzed in the mixed-valent S = 1/2 ground state. Parameters for the ferric site are Delta E(Q) = 1.2 +/- 0.2 mm/s and delta = 0.28 +/- 0.03 mm/s, with somewhat anisotropic hyperfine splittings; for the ferrous site, Delta E(Q) = 3.3 +/- 0.1 mm/s and delta = 0.67 +/- 0.04 mm/s with anisotropic hyperfine splittings characteristic of high-spin ferrous ion. The similarities and differences with other characterized [2Fe-2S](+) cluster-containing proteins are discussed.

Structure of the Ni sites in hydrogenases by X-ray absorption spectroscopy. Species variation and the effects of redox poise, Gu, Z. J., Dong J., Allan C. B., Choudhury S. B., Franco R., Moura J. J. G., Legall J., Przybyla A. E., Roseboom W., Albracht S. P. J., Axley M. J., Scott R. A., and Maroney M. J. , Journal of the American Chemical Society, Nov 13, Volume 118, Number 45, p.11155-11165, (1996) AbstractWebsite

Structural information obtained from the analysis of nickel K-edge X-ray absorption spectroscopic data of [NiFe]hydrogenases from Desulfovibrio gigas, Thiocapsa roseopersicina, Desulfovibrio desulfuricans (ATCC 27774), Escherichia coli (hydrogenase-1), Chromatium vinosum, and Alcaligenes eutrophus H16 (NAD(+)-reducing, soluble hydrogenase), poised in different redox states, is reported. The data allow the active-site structures of enzymes from several species to be compared, and allow the effects of redox poise on the structure of the nickel sites to be examined. In addition, the structure of the nickel site obtained from recent crystallographic studies of the D. gigas enzyme (Volbeda, A.; Charon, M.-H.; Piras, C.; Hatchikian, E. C.; Frey, M.; Fontecilla-Camps, J. C. Nature 1995, 373, 580-587) is compared with the structural features obtained from the analysis of XAS data from the same enzyme. The nickel sites of all but the oxidized (as isolated) sample of A. eutrophus hydrogenase are quite similar. The nickel K-edge energies shift 0.9-1.5 eV to lower energy upon reduction from oxidized (forms A and B) to fully reduced forms. This value is comparable with no more than a one-electron metal-centered oxidation state change. With the exception of T. roseopersicina hydrogenase, most of the edge energy shift (-0.8 eV) occurs upon reduction of the oxidized enzymes to the EPR-silent intermediate redox level (SI). Analysis of the XANES features assigned to 1s-->3d electronic transitions indicates that the shift in energy that occurs for reduction of the enzymes to the SI level may be attributed at least in part to an increase in the coordination number from five to six. The smallest edge energy shift is observed for the T. roseopersicina enzyme, where the XANES data indicate that the nickel center is always six-coordinate. With the exception of the oxidized sample of A. eutrophus hydrogenase, the EXAFS data are dominated by scattering from S-donor ligands at similar to 2.2 Angstrom. The enzyme obtained from T. roseopersicina also shows evidence for the presence of O,N-donor ligands. The data from A. eutrophus hydrogenase are unique in that they indicate that a significant structural change occurs upon reduction of the enzyme. EXAFS data obtained from the oxidized (as isolated) A. eutrophus enzyme indicate that the EXAFS is dominated by scattering from 3-4 N,O-donor atoms at 2.06(2) Angstrom, with contributions from 2-3 S-donor ligands at 2.35(2) Angstrom. This changes upon reduction to a more typical nickel site composed of similar to 4 S-donor ligands at a Ni-S distance of 2.19(2) Angstrom. Evidence for the presence of atoms in the 2.4-2.9 Angstrom distance range is found in most samples, particularly the reduced enzymes (SI, form C, and R). The analysis of these data is complicated by the fact that it is difficult to distinguish between S and Fe scattering atoms at this distance, and by the potential presence of both S and another metal atom at similar distances. The results of EXAFS analysis are shown to be in general agreement with the published crystal structure of the D. gigas enzyme.

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.

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.

A single histidine is required for activity of cytochrome c peroxidase from Paracoccus denitrificans, McGinnity, D. F., Devreese B., Prazeres S., Van Beeumen J., Moura I., Moura J. J., and Pettigrew G. W. , J Biol Chem, May 10, Volume 271, Number 19, p.11126-33, (1996) AbstractWebsite

The diheme cytochrome c peroxidase from Paracoccus denitrificans was modified with the histidine-specific reagent diethyl pyrocarbonate. At low excess of reagent, 1 mol of histidine was modified in the oxidized enzyme, and modification was associated with loss of the ability to form the active state. With time, the modification reversed, and the ability to form the active state was recovered. The agreement between the spectrophotometric measurement of histidine modification and radioactive incorporation using a radiolabeled reagent indicated little modification of other amino acids. However, the reversal of histidine modification observed spectrophotometrically was not matched by loss of radioactivity, and we propose a slow transfer of the ethoxyformyl group to an unidentified amino acid. The presence of CN- bound to the active peroxidatic site of the enzyme led to complete protection of the essential histidine from modification. Limited subtilisin treatment of the native enzyme followed by tryptic digest of the C-terminal fragment (residues 251-338) showed that radioactivity was located in a peptide containing a single histidine at position 275. We propose that this conserved residue, in a highly conserved region, is central to the function of the active mixed-valence state.

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.

Crystal structure of flavodoxin from Desulfovibrio desulfuricans ATCC 27774 in two oxidation states, Romero, A., Caldeira J., Legall J., Moura I., Moura J. J., and Romao M. J. , Eur J Biochem, Jul 1, Volume 239, Number 1, p.190-6, (1996) AbstractWebsite

The crystal structures of the flavodoxin from Desulfovibrio desulfuricans ATCC 27774 have been determined and refined for both oxidized and semi-reduced forms to final crystallographic R-factors of 17.9% (0.8-0.205-nm resolution) and 19.4% (0.8-0.215-nm resolution) respectively. Native flavodoxin crystals were grown from ammonium sulfate with cell constants a = b = 9.59 nm, c=3.37nm (oxidized crystals) and they belong to space group P3(2)21. Semireduced crystals showed some changes in cell dimensions: a = b = 9.51 nm, c=3.35 nm. The three-dimensional structures are similar to other known flavodoxins and deviations are found essentially in the isoalloxazine ring environment. Conformational changes are observed between both redox states and a flip of the Gly61-Met62 peptide bond occurs upon one-electron reduction of the FMN group. These changes influence the redox potential of the oxidized/semiquinone couple. Modulation of the redox potentials is known to be related to the association constant of the FMN group to the protein. The flavodoxin from D. desulfuricans now studied has a large span between E2 (oxidized --> semiquinone) and E1 (semiquinone --> hydroquinone) redox potentials, both these values being substantially more positive within known flavodoxins. A comparison of their FMN environment was made in both oxidation states in order to correlate functional and structural differences.

Characterization of a 7Fe ferredoxin isolated from the marine denitrifier Pseudomonas nautica strain 617: spectroscopic and electrochemical studies, Macedo, A. L., Besson S., Moreno C., Fauque G., Moura J. J., and Moura I. , Biochem Biophys Res Commun, Dec 13, Volume 229, Number 2, p.524-30, (1996) AbstractWebsite

A 7Fe ferredoxin, isolated from the marine denitrifier Pseudomonas nautica strain 617, was characterized. The NH2-terminal sequence analysis, performed until residue number 56, shows a high similarity with the 7Fe ferredoxins isolated from Azotobacter vinelandii, Pseudomonas putida, and Pseudomonas stutzeri. EPR and NMR spectroscopies identify the presence of both [3Fe-4S] and [4Fe-4S] clusters, with cysteinyl coordination. The electrochemical studies on [Fe-S] clusters show that a fast diffusion-dominated electron transfer, promoted by Mg(II), takes place between the ferredoxin and the glassy carbon electrode. Square wave voltammetry studies gave access to the electrosynthesis of a 4Fe center formed within the [3Fe-4S] core. The [3Fe-4S] cluster exhibited two reduction potentials at -175 and -680 +/- 10 mV and the [4Fe-4S] cluster was characterized by an unusually low reduction potential of -715 +/- 10 mV, at pH 7.6