Quaternary Structure of Flavorubredoxin as Revealed by Synchrotron Radiation Small-Angle X-Ray Scattering

Structure

Volumn 16, Issue 9, 2008, Pages 1428-1436

  Petoukhov, Maxim V ^a,b   Vicente, João B ^c   Crowley, Peter B ^c   Carrondo, Maria Arménia ^c   Teixeira, Miguel ^c   Svergun, Dmitri I ^a,b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b SHUBNIKOV INSTITUTE OF CRYSTALLOGRAPHY   (Russian Federation)

^c INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

Author keywords

PROTEINS

Indexed keywords

FLAVODOXIN; FLAVORUBREDOXIN; METALLOPROTEIN; NITRIC OXIDE REDUCTASE; RUBREDOXIN; UNCLASSIFIED DRUG;

ARTICLE; ESCHERICHIA COLI; IMAGE RECONSTRUCTION; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; RADIATION; X RAY CRYSTALLOGRAPHY;

CATALYTIC DOMAIN; ESCHERICHIA COLI PROTEINS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; SCATTERING, SMALL ANGLE; SYNCHROTRONS; TRANSCRIPTION FACTORS; X-RAY DIFFRACTION;

ESCHERICHIA COLI;

EID: 51049115518     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2008.06.009     Document Type: Article

References (48)

1. Andersen C.B., Becker T., Blau M., Anand M., Halic M., Balar B., Mielke T., Boesen T., Pedersen J.S., Spahn C.M., et al. Structure of eEF3 and the mechanism of transfer RNA release from the E-site. Nature 443 (2006) 663-668
2. Andersson J.O., Hirt R.P., Foster P.G., and Roger A.J. Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC Evol. Biol. 6 (2006) 27
3. Arnold K., Bordoli L., Kopp J., and Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22 (2006) 195-201
4. Bahadur R.P., Chakrabarti P., Rodier F., and Janin J. A dissection of specific and non-specific protein-protein interfaces. J. Mol. Biol. 336 (2004) 943-955
5. Bernado P., Mylonas E., Petoukhov M.V., Blackledge M., and Svergun D.I. Structural characterization of flexible proteins using small-angle X-ray scattering. J. Am. Chem. Soc. 129 (2007) 5656-5664
6. Brown R.E., Jarvis K.L., and Hyland K.J. Protein measurement using bicinchoninic acid: elimination of interfering substances. Anal. Biochem. 180 (1989) 136-139
7. Chen L., Liu M.Y., LeGall J., Fareleira P., Santos H., and Xavier A.V. Rubredoxin oxidase, a new flavo-hemo-protein, is the site of oxygen reduction to water by the "strict anaerobe" Desulfovibrio gigas. Biochem. Biophys. Res. Commun. 193 (1993) 100-105
8. Crowley P.B., and Ubbink M. Close encounters of the transient kind: protein interactions in the photosynthetic redox chain investigated by NMR spectroscopy. Acc. Chem. Res. 36 (2003) 723-730
9. Crowley P.B., and Carrondo M.A. The architecture of the binding site in redox protein complexes: implications for fast dissociation. Proteins 55 (2004) 603-612
10. DeLano, W.L. (2002). The PyMOL Molecular Graphics System (http://www.pymol.org/).
11. 2-scavenging flavodiiron protein in the human parasite Giardia intestinalis. J. Biol. Chem. 283 (2008) 4061-4068
12. Feigin L.A., and Svergun D.I. Structure Analysis by Small-Angle X-Ray and Neutron Scattering (1987), Plenum Press, New York
13. Fitzkee N.C., and Rose G.D. Reassessing random-coil statistics in unfolded proteins. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 12497-12502
14. Frazao C., Silva G., Gomes C.M., Matias P., Coelho R., Sieker L., Macedo S., Liu M.Y., Oliveira S., Teixeira M., et al. Structure of a dioxygen reduction enzyme from Desulfovibrio gigas. Nat. Struct. Biol. 7 (2000) 1041-1045
15. Gomes C.M., Silva G., Oliveira R., LeGall J., Liu M.-Y., Xavier A.V., Rodrigues-Pousada C., and Teixeira M. Studies on the redox centers of the terminal oxidase from Desulfovibrio gigas and evidence for its interaction with rubredoxin. J. Biol. Chem. 272 (1997) 22502-22508
16. Gomes C.M., Vicente J.B., Wasserfallen A., and Teixeira M. Spectroscopic studies and characterization of a novel electron-transfer chain from Escherichia coli involving a flavorubredoxin and its flavoprotein reductase partner. Biochemistry 39 (2000) 16230-16237
17. Gomes C.M., Giuffre A., Forte E., Vicente J.B., Saraiva L.M., Brunori M., and Teixeira M. A novel type of nitric-oxide reductase. Escherichia coli flavorubredoxin. J. Biol. Chem. 277 (2002) 25273-25276
18. Guinier A. La diffraction des rayons X aux tres petits angles; application a l'etude de phenomenes ultramicroscopiques. Ann. Phys. (Paris) 12 (1939) 161-237
19. Hagelueken G., Wiehlmann L., Adams T.M., Kolmar H., Heinz D.W., Tummler B., and Schubert W.D. Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA 104 (2007) 12276-12281
20. Konarev P.V., Volkov V.V., Sokolova A.V., Koch M.H.J., and Svergun D.I. PRIMUS-a Windows-PC based system for small-angle scattering data analysis. J. Appl. Crystallogr. 36 (2003) 1277-1282
21. Kozin M.B., and Svergun D.I. Automated matching of high- and low-resolution structural models. J. Appl. Crystallogr. 34 (2001) 33-41
22. Leys D., Basran J., Talfournier F., Sutcliffe M.J., and Scrutton N.S. Extensive conformational sampling in a ternary electron transfer complex. Nat. Struct. Biol. 10 (2003) 219-225
23. Petoukhov M.V., and Svergun D.I. Global rigid body modelling of macromolecular complexes against small-angle scattering data. Biophys. J. 89 (2005) 1237-1250
24. Ponstingl H., Kabir T., Gorse D., and Thornton J.M. Morphological aspects of oligomeric protein structures. Prog. Biophys. Mol. Biol. 89 (2005) 9-35
25. Porod G. General theory. In: Glatter O., and Kratky O. (Eds). Small-Angle X-Ray Scattering (1982), Academic Press, London 17-51
26. Rodrigues R., Vicente J.B., Felix R., Oliveira S., Teixeira M., and Rodrigues-Pousada C. Desulfovibrio gigas flavodiiron protein affords protection against nitrosative stress in vivo. J. Bacteriol. 188 (2006) 2745-2751
27. Roessle M.W., Klaering R., Ristau U., Robrahn B., Jahn D., Gehrmann T., Konarev P., Round A., Fiedler S., Hermes C., and Svergun D. Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory, Hamburg. J. Appl. Crystallogr. 40 (2007) S190-S194
28. Saraiva L.M., Vicente J.B., and Teixeira M. The role of the flavodiiron proteins in microbial nitric oxide detoxification. Adv. Microb. Physiol. 49 (2004) 77-129
29. Sarti P., Fiori P.L., Forte E., Rappelli P., Teixeira M., Mastronicola D., Sanciu G., Giuffre A., and Brunori M. Trichomonas vaginalis degrades nitric oxide and expresses a flavorubredoxin-type protein: a new pathogenic mechanism?. Cell. Mol. Life Sci. 61 (2004) 618-623
30. 2O. FEBS J. 274 (2007) 1588-1599
31. Silaghi-Dumitrescu R., Coulter E.D., Das A., Ljungdahl L.G., Jameson G.N., Huynh B.H., and Kurtz Jr. D.M. A flavodiiron protein and high molecular weight rubredoxin from Moorella thermoacetica with nitric oxide reductase activity. Biochemistry 42 (2003) 2806-2815
32. Silaghi-Dumitrescu R., Kurtz Jr. D.M., Ljungdahl L.G., and Lanzilotta W.N. X-ray crystal structures of Moorella thermoacetica FprA. Novel diiron site structure and mechanistic insights into a scavenging nitric oxide reductase. Biochemistry 44 (2005) 6492-6501
33. Silaghi-Dumitrescu R., Ng K.Y., Viswanathan R., and Kurtz Jr. D.M. A flavo-diiron protein from Desulfovibrio vulgaris with oxidase and nitric oxide reductase activities. Evidence for an in vivo nitric oxide scavenging function. Biochemistry 44 (2005) 3572-3579
34. Svergun D.I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25 (1992) 495-503
35. Svergun D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76 (1999) 2879-2886
36. Svergun D.I., Barberato C., and Koch M.H.J. CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28 (1995) 768-773
37. Svergun D.I., Petoukhov M.V., Koch M.H.J., and Koenig S. Crystal versus solution structures of thiamine diphosphate-dependent enzymes. J. Biol. Chem. 275 (2000) 297-302
38. Vicente J.B., and Teixeira M. Redox and spectroscopic properties of the Escherichia coli nitric oxide-detoxifying system involving flavorubredoxin and its NADH-oxidizing redox partner. J. Biol. Chem. 280 (2005) 34599-34608
39. Vicente J.B., Scandurra F.M., Rodrigues J.V., Brunori M., Sarti P., Teixeira M., and Giuffre A. Kinetics of electron transfer from NADH to the Escherichia coli nitric oxide reductase flavorubredoxin. FEBS J. 274 (2007) 677-686
40. Vicente J.B., Carrondo M.A., Teixeira M., and Frazão C. Flavodiiron proteins: nitric oxide and/or oxygen reductases. Handbook of Metalloproteins Volume 4 (2008), Wiley, New York in press
41. Victor B.L., Vicente J.B., Rodrigues R., Oliveira S., Rodrigues-Pousada C., Frazao C., Gomes C.M., Teixeira M., and Soares C.M. Docking and electron transfer studies between rubredoxin and rubredoxin:oxygen oxidoreductase. J. Biol. Inorg. Chem. 8 (2003) 475-488
42. Volkov V.V., and Svergun D.I. Uniqueness of ab initio shape determination in small angle scattering. J. Appl. Crystallogr. 36 (2003) 860-864
43. Volkov A.N., Ferrari D., Worrall J.A.R., Bonvin A.M., and Ubbink M. Solution structure and dynamics of the complex between cytochrome c and cytochrome c peroxidase determined by paramagnetic NMR. Protein Sci. 14 (2005) 799-811
44. Wasserfallen A., Ragettli S., Jouanneau Y., and Leisinger T. A family of flavoproteins in the domains Archaea and Bacteria. Eur. J. Biochem. 254 (1998) 325-332
45. Watenpaugh K.D., Sieker L.C., and Jensen L.H. Crystallographic refinement of rubredoxin at 1 × 2 Å degrees resolution. J. Mol. Biol. 138 (1980) 615-633
46. 5: a nuclear magnetic resonance study of a highly dynamic protein complex. Biochemistry 41 (2002) 11721-11730
47. Worrall J.A.R., Reinle W., Bernhardt R., and Ubbink M. Transient protein interactions studied by NMR spectroscopy: the case of cytochrome c and adrenodoxin. Biochemistry 42 (2003) 7068-7076
48. 1. Nature 392 (1998) 677-684