Abstract
A minigene encoding the C-terminal domain of the 2Fe rubredoxin of Pseudomonas oleovorans was created from the parental alk G gene contained in the expression plasmid pKK223-3. The vector directed the high-level production of the C-terminal domain of this rubredoxin; a simple procedure was used to purify the recombinant domain in the 1Fe form. The 1Fe form of the C-terminal domain was readily converted into the apoprotein and cadmium forms after precipitation with trichloroacetic acid and resolubilization in the presence or absence of cadmium chloride respectively. In steady-state assays, the recombinant 1Fe C-terminal domain is redox-active and able to transfer electrons from reduced rubredoxin reductase to cytochrome c. The absorption spectrum and dichroic features of the CD spectrum for the iron- and cadmium-substituted C-terminal domain are similar to those reported for the iron- and cadmium-substituted Desulfovibrio gigas rubredoxin [Henehen, Pountney, Zerbe and Vasak (1993) Protein Sci. 2, 1756-1764]. Difference absorption spectroscopy of the cadmium-substituted C-terminal domain revealed the presence of four Gaussian-resolved maxima at 202, 225, 240 and 276 nm; from Jørgensen's electronegativity theory, the 240 nm band is attributable to a CysS-Cd(II) charge-transfer excitation. Attempts to express the N-terminal domain of the 2Fe rubredoxin directly from a minigene were unsuccessful. However, the N-terminal domain was isolated through cleavage of an engineered 2Fe rubredoxin in which a factor Xa proteolysis site had been introduced into the putative interdomain linker. The N-terminal domain is characterized by absorption spectra typical of the 1Fe rubredoxins. The domain is folded as determined by CD and NMR spectroscopies and is redox-active. However, the N-terminal domain is less stable than the isolated C-terminal domain, a finding consistent with the known properties of the full-length 2Fe and cadmium-substituted Ps. oleovorans rubredoxin.
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- Adman E. T., Sieker L. C., Jensen L. H. Structure of rubredoxin from Desulfovibrio vulgaris at 1.5 A resolution. J Mol Biol. 1991 Jan 20;217(2):337–352. doi: 10.1016/0022-2836(91)90547-j. [DOI] [PubMed] [Google Scholar]
- Bachmayer H., Benson A. M., Yasunobu K. T., Garrard W. T., Whiteley H. R. Nonheme iron proteins. IV. Structural studies of Micrococcus aerogenes rubredoxin. Biochemistry. 1968 Mar;7(3):986–996. doi: 10.1021/bi00843a016. [DOI] [PubMed] [Google Scholar]
- Bachmayer H., Yasunobu K. T., Peel J. L., Mayhew S. Non-heme iron proteins. V. The amino acid sequence of rubredoxin from Peptostreptococcus elsdenii. J Biol Chem. 1968 Mar 10;243(5):1022–1030. [PubMed] [Google Scholar]
- Ballongue J., Amine J., Masion E., Petitdemange H., Gay R. Rôle de l'acétate et du butyrate dans l'induction de la NADH: rubrédoxine oxydoréductase chez Clostridium acetobutylicum. Biochimie. 1986 Apr;68(4):575–580. doi: 10.1016/s0300-9084(86)80202-4. [DOI] [PubMed] [Google Scholar]
- Blake P. R., Day M. W., Hsu B. T., Joshua-Tor L., Park J. B., Hare D. R., Adams M. W., Rees D. C., Summers M. F. Comparison of the X-ray structure of native rubredoxin from Pyrococcus furiosus with the NMR structure of the zinc-substituted protein. Protein Sci. 1992 Nov;1(11):1522–1525. doi: 10.1002/pro.5560011113. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Blake P. R., Park J. B., Bryant F. O., Aono S., Magnuson J. K., Eccleston E., Howard J. B., Summers M. F., Adams M. W. Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR. Biochemistry. 1991 Nov 12;30(45):10885–10895. doi: 10.1021/bi00109a012. [DOI] [PubMed] [Google Scholar]
- Blake P. R., Park J. B., Zhou Z. H., Hare D. R., Adams M. W., Summers M. F. Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus. Protein Sci. 1992 Nov;1(11):1508–1521. doi: 10.1002/pro.5560011112. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bruschi M. Non-heme iron proteins. The amino acid sequence of rubredoxin from Desulfovibrio vulgaris. Biochim Biophys Acta. 1976 May 20;434(1):4–17. doi: 10.1016/0005-2795(76)90030-1. [DOI] [PubMed] [Google Scholar]
- Bruschi M. The amino acid sequence of rubredoxin from the sulfate reducing bacterium, Desulfovibrio gigas. Biochem Biophys Res Commun. 1976 May 17;70(2):615–621. doi: 10.1016/0006-291x(76)91092-5. [DOI] [PubMed] [Google Scholar]
- Cavagnero S., Zhou Z. H., Adams M. W., Chan S. I. Response of rubredoxin from Pyrococcus furiosus to environmental changes: implications for the origin of hyperthermostability. Biochemistry. 1995 Aug 8;34(31):9865–9873. doi: 10.1021/bi00031a007. [DOI] [PubMed] [Google Scholar]
- Chen J. C., Mortenson L. E. Identification of six open reading frames from a region of the Azotobacter vinelandii genome likely involved in dihydrogen metabolism. Biochim Biophys Acta. 1992 Jun 15;1131(2):199–202. doi: 10.1016/0167-4781(92)90077-d. [DOI] [PubMed] [Google Scholar]
- Dauter Z., Wilson K. S., Sieker L. C., Moulis J. M., Meyer J. Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein. Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):8836–8840. doi: 10.1073/pnas.93.17.8836. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Eggink G., Engel H., Vriend G., Terpstra P., Witholt B. Rubredoxin reductase of Pseudomonas oleovorans. Structural relationship to other flavoprotein oxidoreductases based on one NAD and two FAD fingerprints. J Mol Biol. 1990 Mar 5;212(1):135–142. doi: 10.1016/0022-2836(90)90310-I. [DOI] [PubMed] [Google Scholar]
- Eggink G., van Lelyveld P. H., Arnberg A., Arfman N., Witteveen C., Witholt B. Structure of the Pseudomonas putida alkBAC operon. Identification of transcription and translation products. J Biol Chem. 1987 May 5;262(13):6400–6406. [PubMed] [Google Scholar]
- Frey M., Sieker L., Payan F., Haser R., Bruschi M., Pepe G., LeGall J. Rubredoxin from Desulfovibrio gigas. A molecular model of the oxidized form at 1.4 A resolution. J Mol Biol. 1987 Oct 5;197(3):525–541. doi: 10.1016/0022-2836(87)90562-6. [DOI] [PubMed] [Google Scholar]
- Geissdörfer W., Frosch S. C., Haspel G., Ehrt S., Hillen W. Two genes encoding proteins with similarities to rubredoxin and rubredoxin reductase are required for conversion of dodecane to lauric acid in Acinetobacter calcoaceticus ADP1. Microbiology. 1995 Jun;141(Pt 6):1425–1432. doi: 10.1099/13500872-141-6-1425. [DOI] [PubMed] [Google Scholar]
- Gomes C. M., Silva G., Oliveira S., LeGall J., Liu M. Y., Xavier A. V., Rodrigues-Pousada C., Teixeira M. Studies on the redox centers of the terminal oxidase from Desulfovibrio gigas and evidence for its interaction with rubredoxin. J Biol Chem. 1997 Sep 5;272(36):22502–22508. doi: 10.1074/jbc.272.36.22502. [DOI] [PubMed] [Google Scholar]
- Henehan C. J., Pountney D. L., Zerbe O., Vasák M. Identification of cysteine ligands in metalloproteins using optical and NMR spectroscopy: cadmium-substituted rubredoxin as a model [Cd(CysS)4]2- center. Protein Sci. 1993 Oct;2(10):1756–1764. doi: 10.1002/pro.5560021019. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hormel S., Walsh K. A., Prickril B. C., Titani K., LeGall J., Sieker L. C. Amino acid sequence of rubredoxin from Desulfovibrio desulfuricans strain 27774. FEBS Lett. 1986 May 26;201(1):147–150. doi: 10.1016/0014-5793(86)80588-9. [DOI] [PubMed] [Google Scholar]
- Jenney F. E., Jr, Verhagen M. F., Cui X., Adams M. W. Anaerobic microbes: oxygen detoxification without superoxide dismutase. Science. 1999 Oct 8;286(5438):306–309. doi: 10.1126/science.286.5438.306. [DOI] [PubMed] [Google Scholar]
- Kok M., Oldenhuis R., van der Linden M. P., Meulenberg C. H., Kingma J., Witholt B. The Pseudomonas oleovorans alkBAC operon encodes two structurally related rubredoxins and an aldehyde dehydrogenase. J Biol Chem. 1989 Apr 5;264(10):5442–5451. [PubMed] [Google Scholar]
- Lee H. J., Basran J., Scrutton N. S. Electron transfer from flavin to iron in the Pseudomonas oleovorans rubredoxin reductase-rubredoxin electron transfer complex. Biochemistry. 1998 Nov 3;37(44):15513–15522. doi: 10.1021/bi981853v. [DOI] [PubMed] [Google Scholar]
- Lee H. J., Lian L. Y., Scrutton N. S. Recombinant two-iron rubredoxin of Pseudomonas oleovorans: overexpression, purification and characterization by optical, CD and 113Cd NMR spectroscopies. Biochem J. 1997 Nov 15;328(Pt 1):131–136. doi: 10.1042/bj3280131. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lee W. Y., Brune D. C., LoBrutto R., Blankenship R. E. Isolation, characterization, and primary structure of rubredoxin from the photosynthetic bacterium, Heliobacillus mobilis. Arch Biochem Biophys. 1995 Apr 1;318(1):80–88. doi: 10.1006/abbi.1995.1207. [DOI] [PubMed] [Google Scholar]
- Lloyd D. Microbial ecology. How to avoid oxygen. Science. 1999 Oct 8;286(5438):249–249. doi: 10.1126/science.286.5438.249. [DOI] [PubMed] [Google Scholar]
- Lode E. T., Coon M. J. Enzymatic omega-oxidation. V. Forms of Pseudomonas oleovorans rubredoxin containing one or two iron atoms: structure and function in omega-hydroxylation. J Biol Chem. 1971 Feb 10;246(3):791–802. [PubMed] [Google Scholar]
- Lovenberg W., Sobel B. E. Rubredoxin: a new electron transfer protein from Clostridium pasteurianum. Proc Natl Acad Sci U S A. 1965 Jul;54(1):193–199. doi: 10.1073/pnas.54.1.193. [DOI] [PMC free article] [PubMed] [Google Scholar]
- May S. W., Kuo J. Y. Preparation and properties of cobalt(II) rubredoxin. Biochemistry. 1978 Aug 8;17(16):3333–3338. doi: 10.1021/bi00609a025. [DOI] [PubMed] [Google Scholar]
- Meyer J., Gagnon J., Sieker L. C., Van Dorsselaer A., Moulis J. M. Rubredoxin from Clostridium thermosaccharolyticum. Amino acid sequence, mass-spectrometric and preliminary crystallographic data. Biochem J. 1990 Nov 1;271(3):839–841. doi: 10.1042/bj2710839. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Peterson J. A., Basu D., Coon M. J. Enzymatic omega-oxidation. I. Electon carriers in fatty acid and hydrocarbon hydroxylation. J Biol Chem. 1966 Nov 10;241(21):5162–5164. [PubMed] [Google Scholar]
- Peterson J. A., Coon M. J. Enzymatic omega-oxidation. 3. Purification and properties of rubredoxin, a component of the omega-hydroxylation system of Pseudomonas oleovorans. J Biol Chem. 1968 Jan 25;243(2):329–334. [PubMed] [Google Scholar]
- Pountney D. L., Henehan C. J., Vasák M. Establishing isostructural metal substitution in metalloproteins using 1H NMR, circular dichroism, and Fourier transform infrared spectroscopy. Protein Sci. 1995 Aug;4(8):1571–1576. doi: 10.1002/pro.5560040815. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Saeki K., Yao Y., Wakabayashi S., Shen G. J., Zeikus J. G., Matsubara H. Ferredoxin and rubredoxin from Butyribacterium methylotrophicum: complete primary structures and construction of phylogenetic trees. J Biochem. 1989 Oct;106(4):656–662. doi: 10.1093/oxfordjournals.jbchem.a122912. [DOI] [PubMed] [Google Scholar]
- Seki Y., Seki S., Satoh M., Ikeda A., Ishimoto M. Rubredoxin from Clostridium perfringens: complete amino acid sequence and participation in nitrate reduction. J Biochem. 1989 Aug;106(2):336–341. doi: 10.1093/oxfordjournals.jbchem.a122854. [DOI] [PubMed] [Google Scholar]
- Shanklin J., Achim C., Schmidt H., Fox B. G., Münck E. Mössbauer studies of alkane omega-hydroxylase: evidence for a diiron cluster in an integral-membrane enzyme. Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):2981–2986. doi: 10.1073/pnas.94.7.2981. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shimizu F., Ogata M., Yagi T., Wakabayashi S., Matsubara H. Amino acid sequence and function of rubredoxin from Desulfovibrio vulgaris Miyazaki. Biochimie. 1989 Nov-Dec;71(11-12):1171–1177. doi: 10.1016/0300-9084(89)90020-5. [DOI] [PubMed] [Google Scholar]
- Sieker L. C., Stenkamp R. E., LeGall J. Rubredoxin in crystalline state. Methods Enzymol. 1994;243:203–216. doi: 10.1016/0076-6879(94)43016-0. [DOI] [PubMed] [Google Scholar]
- Stenkamp R. E., Sieker L. C., Jensen L. H. The structure of rubredoxin from Desulfovibrio desulfuricans strain 27774 at 1.5 A resolution. Proteins. 1990;8(4):352–364. doi: 10.1002/prot.340080409. [DOI] [PubMed] [Google Scholar]
- Ueda T., Coon M. J. Enzymatic oxidation. VII. Reduced diphosphopyridine nucleotide-rubredoxin reductase: properties and function as an electron carrier in hydroxylation. J Biol Chem. 1972 Aug 25;247(16):5010–5016. [PubMed] [Google Scholar]
- Wastl J., Duin E. C., Iuzzolino L., Dörner W., Link T., Hoffmann S., Sticht H., Dau H., Lingelbach K., Maier U. G. Eukaryotically encoded and chloroplast-located rubredoxin is associated with photosystem II. J Biol Chem. 2000 Sep 29;275(39):30058–30063. doi: 10.1074/jbc.M004629200. [DOI] [PubMed] [Google Scholar]
- Wastl J., Sticht H., Maier U. G., Rösch P., Hoffmann S. Identification and characterization of a eukaryotically encoded rubredoxin in a cryptomonad alga. FEBS Lett. 2000 Apr 14;471(2-3):191–196. doi: 10.1016/s0014-5793(00)01399-5. [DOI] [PubMed] [Google Scholar]
- Yoon K. S., Hille R., Hemann C., Tabita F. R. Rubredoxin from the green sulfur bacterium Chlorobium tepidum functions as an electron acceptor for pyruvate ferredoxin oxidoreductase. J Biol Chem. 1999 Oct 15;274(42):29772–29778. doi: 10.1074/jbc.274.42.29772. [DOI] [PubMed] [Google Scholar]