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Preparation and properties of immobilized rubredoxin.

Rubredoxin, one of the three protein components of the epoxidation/hydroxylation system of Pseudomonas oleovorans was immobilized by attachment to CNBr-activated agarose (Sepharose 4B). Since this represents the first reported example of the preparation of a water-insoluble derivative of an enzyme of this type, the electron transfer and physical properties of the conjugate were examined in order to allow comparison with those of the soluble enzyme. Immobilized rubredoxin exhibits all of the major spectral properties of the soluble enzyme above 300 nm, but some distortion in the 280 nm abosrbance band was observed. The immobilized enzyme accepts electrons from dithionite or form NADPH in the presence of spinach ferredoxin-NADP reductase, and upon reduction the visible absorbance is bleached. Immobilized rubredoxin mediates the reduction of cytochrome c in the presence of NADPH and spinach reductase, although it is less efficient in this role than soluble rubredoxin. The oxidation-reduction potential of immobilized rubredoxin was determined and found to be similar to that of the soluble enzyme. In the presence of 2.5 m guanidine HCL, the immobilized enzyme is considerably more stable than soluble rubredoxin toward denaturation. After anaerobic reduction, iron was readily removed from immobilized rubredoxin by washing in 0.5 m Tris base, PH 9.5 containing 0.07 M mercaptoethanol, and the resulting immobilized apoenzyme could then be reconstituted to give back a conjugate with the original iron content, as judged from its absorbance at 497 NM. Reptition of the entire reduction-dissociation-reconstitution cycle gave the same results as were obtained after the initial reconstitution.

Anaerobiosis

Isolation and characterization of a rubredoxin and an (8Fe-8S) ferredoxin from Desulfuromonas acetoxidans.

A two cluster (4Fe-4S) ferredoxin and a rubredoxin have been isolated from the sulfur-reducing bacterium Desulfuromonas acetoxidans. Their amino acid compositions are reported and compared to those of other iron-sulfur proteins. The ferredoxin contains 8 cysteine residues, 8 atoms of iron and 8 atoms of labile sulfur per molecule; its minimum molecular weight is 6163. The protein exhibits an abosrbance ratio of A385/A283 = 0.74. Storage results in a bleaching of the chromophore; the denatured ferredoxin is reconstitutable with iron and sulfide. The instability temperature is 52 degrees C. The rubredoxin does not differ markedly from rubredoxins from other anaerobic bacteria.

Amino Acids

Isolation and characterization of a rubredoxin and two ferredoxins from Desulfovibrio africanus.

Rubredoxin and two distinct ferredoxins have been purified from Desulfovibrio africanus. The rubredoxin has a molecular weight of 6000 while the ferredoxins appear to be dimers of identical subunits of approximately 6000 to 7000 molecular weight. Rubredoxin contains one iron atom, no acid-labile sulfide and four cysteine residues per molecule. Its absorbance ratio A278/A490 is 2.23 and its amino acid composition is characterized by the absence of leucine and a preponderance of acidic amino acids. The two ferredoxins, designated I and II, are readily separated on DEAE-cellulose. The amino acid compositions of ferredoxins I and II show them to be different protein species; the greater number of acidic amino acid residues in ferredoxin I than in ferredoxin II appears to account for separation based on electronic charge. Both ferredoxins contain four iron atoms, four acid-labile residues per molecule. Spectra of the two ferredoxins differ from those of ferredoxins of other Desulfovibrio species by exhibiting a pronounced absorption peak at 283 nm consistent with an unusual high content of aromatic residues. The A385/A283 absorbance ratio of ferredoxins I and II are 0.56 and 0.62, respectively. The N-terminal sequencing data of the two ferredoxins clearly indicate that ferredoxins I and II are different protein species. However, the two proteins exhibit a high degree of homology.

Amino Acid Sequence

Non-heme iron proteins. The amino acid sequence of rubredoxin from Desulfovibrio vulgaris.

A non-heme iron protein, rubredoxin has been isolated from the sulfate-reducing bacterium, Desulfovibrio vulgaris, strain Hildenborough. The complete amino acid sequence has been established. The 52 amino acid residues of the protein were aligned with the aid of tryptic and chymotryptic peptides and of a fragment produced by cleavage of the Asn-Gly bond (22-23) by hydroxylamine. The sequence of the first 30 residues of the molecule was determined using an automatic sequenator, after removal of the N-terminal methionine by CNBr. In comparing this sequence with those of Micrococcus aerogenes, Clostridium pasteurianum and Peptostreptococcus elsdenii rubredoxins, a high degree of mutation was observed between these homologous proteins. It has been shown that 20 amino acid residues occurred in identical positions. The locations of the four cysteine residues were found to be invariable. A crystallographic study of the Desulfovibrio vulgaris rubredoxin is in progress.

Amino Acid Sequence

Phylogenetic studies of two rubredoxins from sulfate reducing bacteria.

The sequences of two rubredoxins isolated from the sulfate reducing bacteria: Desulfovibrio vulgaris and Desulfovibrio gigas have been elucidated. They have similar sequences but many more differences occur than would be expected from two bacteria of the same genus. Of the 52 sites, only 37 are occupied by identical residues. The primary structures are compared with those of the anaerobic bacteria rubredoxins of Clostridium pasteurianum, Micrococcus aerogenes, Pseudomonas oleovorans and Peptostreptococcus elsdenii: only 12 identities are found, mostly in the two clusters that contain two iron-bound cysteines each. A phylogenetic tree based on the primary structures is presented and possible relations with plant and bacterial ferredoxins are discussed. A secondary and tertiary structure stereochemically compatible with the sequence data, is proposed.

Amino Acid Sequence

Isoelectric focusing of ferredoxins, flavordoxins and a rubredoxin.

Isoelectric points of ferredoxins, flavodoxins and a rubredoxin from a range of sources were measured by electrofocusing over the pH range between 2.5 and 5.0 on thin layers of polyacrylamide gel. The pH gradient along the gel was measured directly by a surface electrode. The isoelectric points of the plant-type ferredoxins were between approx. 3.15 and 3.35, and those of the flavodoxins close to 3.5. Ferredoxin, rubredoxin and flavodoxin from Clostridium pasteurianum had isolectric points of the of 2.75, 2.9, and 3.1, respectively. The values for the isoelectric points ferredoxins are significantly lower than previous results in the literature suggest.

Bacteria

The iron-sulfur environment in rubredoxin.

The atomic environment around the iron site in the nonheme iron sulfur protein rubredoxin was studied by the extended X-ray absorption fine structure (EXAFS) technique. Within experimental error, the Fe-S bonds in oxidized Clostridium pasteurianum rubredoxin are the same as in the analogue anion [Fe(S2-o-xyl)2]-synthesized by Holm. The average Fe-S bond length is 2.267 +/- 0.003A and the root mean square deviation about this average due to structural disorder is 0.032 + 0.013 - 0.032.

Absorption

Purification and characterization of cytochrome c3, ferredoxin, and rubredoxin isolated from Desulfovibrio desulfuricans Norway.

Different electron carriers of the non-desulfoviridin-containing, sulfate-reducing bacterium Desulfovibrio desulfuricans (Norway strain) have been studied. Two nonheme iron proteins, ferredoxin and rubredoxin, have been purified. This ferredoxin contains four atoms of non-heme iron and acid-labile sulfur and six residues of cysteine per molecule. Its amino acid composition suggests that it is homologous with the other Desulfovibrio ferredoxins. The rubredoxin is also an acidic protein of 6,000 molecular weight and contains one atom of iron and four cysteine residues per molecule. The amino acid composition and molecular weight of the cytochrome c3 from D. desulfuricans (strain Norway 4) are reported. Its spectral properties are very similar to those of the other cytochromes c3 (molecular weight, 13,000) of Desulfovibrio and show that it contains four hemes per molecule. This cytochrome has a very low redox potential and acts as a carrier in the coupling of hydrogenase and thiosulfate reductase in extracts of Desulfovibrio gigas and Desulfovibrio desulfuricans (Norway strain) in contrast to D. gigas cytochrome c3 (molecular weight, 13,000). A comparison of the activities of the cytochrome c3 (molecular weight, 13,000) of D. gigas and that of D. desulfuricans in this reaction suggests that these homologous proteins can have different specificity in the electron transfer chain of these bacteria.

Amino Acids

[Isolation and characterization of rubredoxin from Acinetobacter calcoaceticus].

Acinetobacter calcoaceticus growing on long-chain n-alkanes contains a soluble iron-sulfur protein, which corresponds in its properties to a rubredoxin. It was prepared from the 50000 X g supernatant of ultrasonically treated cells using ion exchange chromatography on DEAE cellulose and gel filtration on Sephadex G-75. The isolated protein is pure electrophoretically, but yields two bands corresponding to molecular weights of 6000 and 12000 respectively. A content of 11 acidic against 6 basic amino acids is in line with the acidic character of the protein. The absence of acid-labile sulfur, content of 4 cysteine residues and one iron atom per polypeptide chain and the typical absorption maxima at gamma = 280, 380, and 490 nm exclude the presence of a ferredoxin. Involvement of the rubredoxin in the alkane hydroxylation is discussed.

Acinetobacter

The low temperature magnetic circular dichroism spectra of iron-sulphur proteins. I. Oxidised rubredoxin.

Variable temperature magnetic circular dichroism spectra have been measured on oxidised Clostridium pasteurianum rubredoxin. Evidence has been obtained for the presence of two one-electron charge-transfer transitions, sulphur to ferric ion, in the region 15 000 to 28 000 cm-1. The first moment of the lower energy band is consistent with it being the orbital transition t1 non-bonding sulphur orbital, to the 2 e ferric d-orbital. The magnitude of the spin-orbit coupling constant in the lower excited state has been determined and shown to be small compared with the axial distortion. The splitting of the low energy band observed in the absorption spectrum can therefore be equated directly with the axial distortion of the lowest excited charge-transfer state. Finally, the potential utility of making saturation experiments at very low temperatures has been examined.

Circular Dichroism