Crystal structure of the oxidised and reduced acidic cytochrome c3 from Desulfovibrio africanus

Nørager, S.; Legrand, Pierre; Pieulle, Lætitia; Hatchikian, Claude E.; Roth, M.

doi:10.1006/jmbi.1999.2917

Cited by 66 publications

(94 citation statements)

References 67 publications

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“…The reduced protein, containing three iron(II) hemes, undergoes stepwise oxidation after the addition of CrO 4 2Ϫ . The hemes are labeled I, III, and IV in analogy to the labeling of the four-heme Cyt c 3 , which is more characterized (26)(27)(28)(29)(30). The heme II is missing in the present protein, Cyt c 7 .…”

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confidence: 99%

The metal reductase activity of some multiheme cytochromes c : NMR structural characterization of the reduction of chromium(VI) to chromium(III) by cytochrome c ₇

Assfalg

Bertini

Bruschi

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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The redox reaction between CrO 4 2Ϫ and the fully reduced threeheme cytochrome c 7 from Desulfuromonas acetoxidans to give chromium(III) and the fully oxidized protein has been followed by NMR spectroscopy. The hyperfine coupling between the oxidized protein protons and chromium(III), which remains bound to the protein, gives rise to line-broadening effects on the NMR resonances that can be transformed into proton-metal distance restraints. Structure calculations based on these unconventional constraints allowed us to demonstrate that chromium(III) binds at a unique site and to locate it on the protein surface. The metal ion is located 7.9 ؎ 0. S ulfur-and sulfate-reducing bacteria constitute a group of anaerobic organisms, the common feature of which is the use of sulfur and its oxidized forms as electron acceptors. Thiosulfate, sulfur, sulfite, or sulfate ''respiration'' produces sulfide. The end product of the reaction, hydrogen sulfide, can react with heavy metal ions to form less toxic insoluble metal sulfides (1). These bacteria are also able to enzymatically reduce and precipitate heavy metals (2-8). They therefore are important for the geochemical cycle of metals and become particularly relevant for possible applications in the decontamination of environments polluted by toxic heavy metals through bioreduction coupled with precipitation as insoluble sulfides. Among the metals that can be reduced by these bacteria, chromium(VI) is particularly relevant from the technological and environmental point of view, because it represents one of the most common polluting metals and is highly soluble and toxic. § The three heme-containing cytochrome c 7 from the sulfurreducing bacterium Desulfuromonas acetoxidans (Cyt c 7 hereafter) has been proposed to have a role as electron-transfer protein in the sulfur metabolism of this bacterium, acting as a terminal reductase in the metabolic pathway by directly reducing elemental sulfur to sulfide (9); it has been suggested also that it could be involved in the reduction of iron(III) and manganese(IV) (10). The solution structures of the fully oxidized and fully reduced species are available, followed by the x-ray structure of the oxidized species (11)(12)(13)(14). The availability of the assigned NMR spectra and the nuclear Overhauser effects (NOEs; refs. 11 and 15) prompted us to study by NMR the reaction between CrO 4 2Ϫ and fully reduced Cyt c 7 . The products of the reaction are chromium(III) and the oxidized protein with three iron(III) hemes. Because chromium(III) is kinetically inert with respect to ligand exchange, it remains bound to protein residues through which electron transfer occurs. The hyperfine coupling between the unpaired electrons of chromium(III) and the proton nuclei of the protein gives rise to particular features in the NMR spectra (16) that could be used to obtain structural information about the chromium(III) binding site. The redox-inert MoO 4 2Ϫ was used to map the binding site of the anion. NMR has allowed us to obtain a clear picture of the...

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confidence: 99%

The metal reductase activity of some multiheme cytochromes c : NMR structural characterization of the reduction of chromium(VI) to chromium(III) by cytochrome c ₇

Assfalg

Bertini

Bruschi

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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“…The heme group arrangement of nitrite reductase showed similarities to the one of hydroxylamine oxidoreductase (7), although sequence homologies were negligible, and structural homologies were limited to few regions of the protein (5). The conservation of the heme group arrangements in multiheme c cytochromes has been observed and discussed (8,9), but the significance of such highly conserved motifs is not yet understood.…”

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confidence: 99%

Cytochrome c Nitrite Reductase from Wolinella succinogenes

Einsle¹,

Stach²,

Messerschmidt³

et al. 2000

Journal of Biological Chemistry

186

116

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Cytochrome c nitrite reductase catalyzes the 6-electron reduction of nitrite to ammonia. This second part of the respiratory pathway of nitrate ammonification is a key step in the biological nitrogen cycle. The x-ray structure of the enzyme from the ⑀-proteobacterium Wolinella succinogenes has been solved to a resolution of 1.6 Å. It is a pentaheme c-type cytochrome whose heme groups are packed in characteristic motifs that also occur in other multiheme cytochromes. Structures of W. succinogenes nitrite reductase have been obtained with water bound to the active site heme iron as well as complexes with two inhibitors, sulfate and azide, whose binding modes and inhibitory functions differ significantly. Cytochrome c nitrite reductase is part of a highly optimized respiratory system found in a wide range of Gram-negative bacteria. It reduces both anionic and neutral substrates at the distal side of a lysine-coordinated high-spin heme group, which is accessible through two different channels, allowing for a guided flow of reaction educt and product. Based on sequence comparison and secondary structure prediction, we have demonstrated that cytochrome c nitrite reductases constitute a protein family of high structural similarity.The biogeochemical nitrogen cycle represents a network of reactions catalyzed by enzymes with different metal cofactors, which allows for redox transitions of nitrogen between its oxidation state (ϩ5), as in nitrate, and (Ϫ3), as in ammonia and its most abundant form dinitrogen. The one respiratory pathway that covers the whole range between nitrate and ammonia is the dissimilatory nitrate reduction to ammonia (1). Hereby, nitrate is first reduced to nitrite in a 2-electron step by a nitrate reductase, and subsequently the product nitrite is converted to ammonia in a 6-electron step catalyzed by a cytochrome c nitrite reductase (NiR), 1 the subject of this study. Cytochrome c nitrite reductases are pentaheme enzymes with a molecular mass of 55-65 kDa, encoded by a single gene termed nrfA (2). They have been found so far in proteobacteria belonging to the subdivisions ␥ (Escherichia coli (3) and Haemophilus influenzae Rd (4)) and ⑀ (Sulfurospirillum deleyianum (5) and Wolinella succinogenes (6)). The x-ray structure of NiR from S. deleyianum was solved recently to a resolution of 1.9 Å (5) and showed the enzyme to be a compact homodimer. The active site was localized at heme 1, and a Ca 2ϩ ion was observed in close proximity. The heme group arrangement of nitrite reductase showed similarities to the one of hydroxylamine oxidoreductase (7), although sequence homologies were negligible, and structural homologies were limited to few regions of the protein (5). The conservation of the heme group arrangements in multiheme c cytochromes has been observed and discussed (8, 9), but the significance of such highly conserved motifs is not yet understood.Here we report on the purification, crystallization, and structural analysis of cytochrome c nitrite reductase from the ⑀-proteobacterium W. succinogene...

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“…The distinction between these cytochromes c 3 is based on structural, functional, and genetic features (18). In structural terms, TpII-c 3 can be distinguished by several local differences relative to the overall fold of TpI-c 3 , with the most relevant points being an exposed heme 1 surrounded by a negative surface charge, and the heme 4 lacking the characteristic surface lysine patch proposed to be the site of interaction and electron exchange of TpI-c 3 with a negatively charged region of hydrogenase (18,49). This suggests that TpII-c 3 interacts with its physiological partner via heme 1 rather than heme 4, and that its role is not to receive electrons directly from hydrogenase as is the case for TpI-c 3 .…”

Section: Resultsmentioning

confidence: 99%

“…Using coordinates retrieved from the Protein Data Bank (44), a more detailed comparison is included below between the different domains of HmcA, and the TpI-c 3 and TpII-c 3 folds, as well as the integral 9HcA fold, represented by the 9HcA from Dd27k (PDB 19HC) (16). The TpI-c 3 structure chosen as a model for comparisons was that of DvH (PDB 2CTH) (52), and the TpII-c 3 structure is that of Da (PDB 3CAO) (49). A comparison of the three-heme domain with the triheme cytochrome c 3 (cyt.c 7 ) from Dac (PDB 1HH5) (53) is also included.…”

Section: Resultsmentioning

confidence: 99%

“…4) shows that this molecule is less negatively charged overall than 9HcA (15) and the Da TpII-c 3 (18,49). In addition, and in agreement with the poor reactivity of HmcA toward hydrogenase (26), the regions near the exposed parts of hemes 3 and 16 in HmcA (which correspond to cyt.c 3 heme 4 and are at each extremity of the molecule) lack the characteristic positive surface patch around heme 4 of TpI-c 3 .…”

Section: Resultsmentioning

confidence: 99%

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Sulfate Respiration in Desulfovibrio vulgaris Hildenborough

Matías

Coelho

Valente

et al. 2002

Journal of Biological Chemistry

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The crystal structure of the high molecular mass cytochrome c HmcA from Desulfovibrio vulgaris Hildenborough is described. HmcA contains the unprecedented number of sixteen hemes c attached to a single polypeptide chain, is associated with a membranebound redox complex, and is involved in electron transfer from the periplasmic oxidation of hydrogen to the cytoplasmic reduction of sulfate. The structure of HmcA is organized into four tetraheme cytochrome c 3 -like domains, of which the first is incomplete and contains only three hemes, and the final two show great similarity to the nine-heme cytochrome c from Desulfovibrio desulfuricans. An isoleucine residue fills the vacant coordination space above the iron atom in the five-coordinated high-spin Heme 15. The characteristics of each of the tetraheme domains of HmcA, as well as its surface charge distribution, indicate this cytochrome has several similarities with the nine-heme cytochrome c and the Type II cytochrome c 3 molecules, in agreement with their similar genetic organization and mode of reactivity and further support an analogous physiological function for the three cytochromes. Based on the present structure, the possible electron transfer sites between HmcA and its redox partners (namely Type I cytochrome c 3 and other proteins of the Hmc complex), as well as its physiological role, are discussed.

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Crystal structure of the oxidised and reduced acidic cytochrome c3 from Desulfovibrio africanus

Cited by 66 publications

References 67 publications

The metal reductase activity of some multiheme cytochromes c : NMR structural characterization of the reduction of chromium(VI) to chromium(III) by cytochrome c ₇

The metal reductase activity of some multiheme cytochromes c : NMR structural characterization of the reduction of chromium(VI) to chromium(III) by cytochrome c ₇

Cytochrome c Nitrite Reductase from Wolinella succinogenes

Sulfate Respiration in Desulfovibrio vulgaris Hildenborough

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Crystal structure of the oxidised and reduced acidic cytochrome c3 from Desulfovibrio africanus

Cited by 66 publications

References 67 publications

The metal reductase activity of some multiheme cytochromes c : NMR structural characterization of the reduction of chromium(VI) to chromium(III) by cytochrome c 7

The metal reductase activity of some multiheme cytochromes c : NMR structural characterization of the reduction of chromium(VI) to chromium(III) by cytochrome c 7

Cytochrome c Nitrite Reductase from Wolinella succinogenes

Sulfate Respiration in Desulfovibrio vulgaris Hildenborough

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The metal reductase activity of some multiheme cytochromes c : NMR structural characterization of the reduction of chromium(VI) to chromium(III) by cytochrome c ₇

The metal reductase activity of some multiheme cytochromes c : NMR structural characterization of the reduction of chromium(VI) to chromium(III) by cytochrome c ₇