Preparation and X-ray crystallographic analysis of rubredoxin crystals from Desulfovibrio gigas to beyond ultra-high 0.68 Å resolution

Biochemical and Biophysical Research Communications

Volumn 308, Issue 4, 2003, Pages 684-688

  Chen, Chun Jung ^a   Liu, Ming Yih ^b   Chen, Yi Ting ^a   LeGall, Jean ^b  

^a NATIONAL SYNCHROTRON RADIATION RESEARCH CENTER   (Taiwan)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

Anaerobic; Crystallization; Desulfovibrio gigas; Iron sulfur cluster; Redox; Rubredoxin; Ultra high resolution

Indexed keywords

IRON; MONOMER; RUBREDOXIN; SULFUR;

AB INITIO CALCULATION; ARTICLE; CRYSTAL; CRYSTAL STRUCTURE; CRYSTALLIZATION; DESULFOVIBRIO; DESULFOVIBRIO GIGAS; DIFFRACTION; OPTICAL RESOLUTION; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY;

DESULFOVIBRIO; DESULFOVIBRIO GIGAS;

EID: 0041659272     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-291X(03)01463-3     Document Type: Article

References (29)

1. Lovenberg W., Sobel B.E. Rubredoxin: a new electron transfer protein from Clostridium pasteurianum. Proc. Natl. Acad. Sci. USA. 54:1965;193-199.
2. Ragsdale S.W., Ljungdahl L.G. Characterization of ferredoxin, flavodoxin, and rubredoxin from Clostridium formicoaceticum grown in media with high and low iron contents. J. Bacteriol. 157:1984;1-6.
3. Seki S., Ikeda A., Ishimoto M. Rubredoxin as intermediary electron carrier for nitrate reduction by NAD(P)H in Clostridium perfringens. J. Biochem. 103:1988;583-584.
4. Sieker L.C., Stenkemp R.E., LeGall J. Rubredoxin in crystalline state. Method Enzymol. 243:1994;203-216.
5. Aurisch H., Sorger D., Asperger O. Isolierung und charakterisieung eines rubredoxins aus Acinetobacter calcoaceticus. Acta Biol. Med. Germ. 35:1976;443-451.
6. 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. 243:1968;329-334.
7. Santos H., Fareleira P., Xavier A.V., Chen L., Liu M.-Y., LeGall J. Aerobic metabolism of carbon reserves by the "obligate anaerobe" Desulfovibrio gigas. Biochem. Biophys. Res. Commun. 195:1993;551-557.
8. Fareleira P., LeGall J., Xavier A.V., Santos H. Pathways of the utilization of carbon reserves in Desulfovibrio gigas under fermentative and respiratory conditions. J. Bacteriol. 179:1997;3972-3980.
9. Chen L., Liu M.-Y., LeGall J., Fareleira P., Santos H., Xavier A.V. Purification of characterization of an NADH-rubredoxin oxidoreductase involved in the utilization of oxygen by Desulfovibrio gigas. Eur. J. Biochem. 216:1993;443-448.
10. Moura J., Moura J.J.G., Santos M.H., Xavier A.V., LeGall J. Redox studies of rubredoxins from sulphate and sulphur reducing bacteria. FEBS Lett. 107:1979;419-421.
11. Chen L., Liu M.-Y., LeGall J., Fareleira P., Santos H., Xavier A.V. Rubredoxin oxidase, a new flavo-heme-protein, is the site of oxygen reduction to water by the "strict anaerobe" Desulfovibrio gigas. Biochem. Biophys. Res. Commun. 193:1993;100-105.
12. Gomes G.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 interaction with rubredoxin. J. Biol. Chem. 272:1997;22502-22508.
13. Frazao C., Silva G., Gomes C.M., Matias P., Coelho R., Sieker L.C., Macedo S., Liu M.-Y., Oliveira S., Teixeira M., Xavier A.V., Rodrigues-Pousada C., Carrondo M.A., LeGall J. Structure of a dioxygen reduction enzyme from Desulfovibrio gigas. Nat. Struct. Biol. 17:2000;1041-1045.
14. Ragsdale S.W., Ljungdahl L.G., DerVartanian D.V. Isolation of carbon monoxide dehydrogenase from Acetobacterium woodi and comparison of its properties with those of the Clostridium thermoaceticum enzyme. J. Bacteriol. 155:1982;1224-1237.
15. Eggink G., Lageveen R.G., Altenburg B., Witholt B. Controlled and functional expression of the Pseudomonas oleovorans alkane utilizing system in Psedomonas putida and Escherichia coli. J. Biol. Chem. 262:1987;17712-17718.
16. Eggink G., Engel H., Vriend G., Terpstra P., Witholt B. Rubredoxin reductase of Pseudomonas oleovorans. Structure relationship to other flavoprotein oxidoreductases based of one NAD and two FAD fingerprints. J. Mol. Biol. 212:1992;135-142.
17. Watenpaugh K.D., Sieker L.C., Jensen L.H. The binding of riboflavin-5'-phosphate in a flavoprotein: flavodoxin at 2.0-Angstrom resolution. Proc. Natl. Acad. Sci. USA. 70:1973;3857-383860.
18. Pierrot M., Haser R., Frey M., Bruschi M., LeGall J., Sieker L.C., Jensen L.H. Some comparisons between two crystallized anaerobic bacterial ruberdoxins from Desulfovibrio gigas and D. vulgaris. J. Mol. Biol. 107:1976;179-182.
19. 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. USA. 93:1996;8836-8840.
20. Frey M., Sieker L.C., Payan F., Haser R., Bruschi M., Pepe G., LeGall J. Rubredoxin from Desulfovibrio gigas. A molecular model of the oxidized form at 1.4. Å resolution J. Mol. Biol. 197:1994;524-525.
21. Stenkamp R.E., Sieker L.C., Jensen L.H. The structure of rubredoxin from Desulfovibrio desulfuricans strain 27774 at 1.5. Å resolution Proteins. 8:1990;352-364.
22. Dauter Z., Sieker L.C., Wilson K.S. Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0. Å with and without restraints Acta Crystallogr. B. 48:1992;42-59.
23. Bau R., Rees D.C., Kurtz D.M., Scott R.A., Huang H., Adams M.W.W., Eidsness M.K. Crystal structure of rubredoxin from Pyrococcus furiosus at 0.95. Å resolution J. Biol. Inorg. Chem. 3:1998;484.
24. LeGall J., Mazza G., Dragoni N. Biochim. Biophys. Acta. 99:1965;385-387.
25. Otwinowski Z., Minnor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
26. Mathews B.W. Solvent content of protein crystals. J. Mol. Biol. 33:1968;491-497.
27. Terwilliger T.C., Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr. D. 55:1999;849-861.
28. Sheldrick G.M., Schnider T.R. SHELX: high-resolution refinement. Methods Enzymol. 277:1997;319-343.
29. Bruschi M., LeGall J. Purification et propriétés d'une rubrédoxine isolée à partir de D. vulgaris (souche NCIB 8380). Biochim. Biophys. Acta. 263:1972;279-282.