Skip to main content
PMC home page
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 1992 Nov;1(11):1494–1507. doi: 10.1002/pro.5560011111

X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.

M W Day 1, B T Hsu 1, L Joshua-Tor 1, J B Park 1, Z H Zhou 1, M W Adams 1, D C Rees 1
PMCID: PMC2142115  PMID: 1303768

Abstract

The structures of the oxidized and reduced forms of the rubredoxin from the archaebacterium, Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, have been determined by X-ray crystallography to a resolution of 1.8 A. Crystals of this rubredoxin grow in space group P2(1)2(1)2(1) with room temperature cell dimensions a = 34.6 A, b = 35.5 A, and c = 44.4 A. Initial phases were determined by the method of molecular replacement using the oxidized form of the rubredoxin from the mesophilic eubacterium, Clostridium pasteurianum, as a starting model. The oxidized and reduced models of P. furiosus rubredoxin each contain 414 nonhydrogen protein atoms comprising 53 residues. The model of the oxidized form contains 61 solvent H2O oxygen atoms and has been refined with X-PLOR and TNT to a final R = 0.178 with root mean square (rms) deviations from ideality in bond distances and bond angles of 0.014 A and 2.06 degrees, respectively. The model of the reduced form contains 37 solvent H2O oxygen atoms and has been refined to R = 0.193 with rms deviations from ideality in bond lengths of 0.012 A and in bond angles of 1.95 degrees. The overall structure of P. furiosus rubredoxin is similar to the structures of mesophilic rubredoxins, with the exception of a more extensive hydrogen-bonding network in the beta-sheet region and multiple electrostatic interactions (salt bridge, hydrogen bonds) of the Glu 14 side chain with groups on three other residues (the amino-terminal nitrogen of Ala 1; the indole nitrogen of Trp 3; and the amide nitrogen group of Phe 29). The influence of these and other features upon the thermostability of the P. furiosus protein is discussed.

Full Text

The Full Text of this article is available as a PDF (1.2 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. 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]
  2. 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]
  3. Barlow D. J., Thornton J. M. Ion-pairs in proteins. J Mol Biol. 1983 Aug 25;168(4):867–885. doi: 10.1016/s0022-2836(83)80079-5. [DOI] [PubMed] [Google Scholar]
  4. Becktel W. J., Schellman J. A. Protein stability curves. Biopolymers. 1987 Nov;26(11):1859–1877. doi: 10.1002/bip.360261104. [DOI] [PubMed] [Google Scholar]
  5. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. 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]
  8. Bryant F. O., Adams M. W. Characterization of hydrogenase from the hyperthermophilic archaebacterium, Pyrococcus furiosus. J Biol Chem. 1989 Mar 25;264(9):5070–5079. [PubMed] [Google Scholar]
  9. Brünger A. T., Krukowski A., Erickson J. W. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallogr A. 1990 Jul 1;46(Pt 7):585–593. doi: 10.1107/s0108767390002355. [DOI] [PubMed] [Google Scholar]
  10. Brünger A. T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 1987 Jan 23;235(4787):458–460. doi: 10.1126/science.235.4787.458. [DOI] [PubMed] [Google Scholar]
  11. Carter C. W., Jr, Kraut J., Freer S. T., Alden R. A. Comparison of oxidation-reduction site geometries in oxidized and reduced Chromatium high potential iron protein and oxidized Peptococcus aerogenes ferredoxin. J Biol Chem. 1974 Oct 10;249(19):6339–6346. [PubMed] [Google Scholar]
  12. Chothia C. Hydrophobic bonding and accessible surface area in proteins. Nature. 1974 Mar 22;248(446):338–339. doi: 10.1038/248338a0. [DOI] [PubMed] [Google Scholar]
  13. Chothia C., Lesk A. M. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986 Apr;5(4):823–826. doi: 10.1002/j.1460-2075.1986.tb04288.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Chothia C. The nature of the accessible and buried surfaces in proteins. J Mol Biol. 1976 Jul 25;105(1):1–12. doi: 10.1016/0022-2836(76)90191-1. [DOI] [PubMed] [Google Scholar]
  15. Dill K. A., Shortle D. Denatured states of proteins. Annu Rev Biochem. 1991;60:795–825. doi: 10.1146/annurev.bi.60.070191.004051. [DOI] [PubMed] [Google Scholar]
  16. Eisenberg D., McLachlan A. D. Solvation energy in protein folding and binding. Nature. 1986 Jan 16;319(6050):199–203. doi: 10.1038/319199a0. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Hecht M. H., Sturtevant J. M., Sauer R. T. Stabilization of lambda repressor against thermal denaturation by site-directed Gly----Ala changes in alpha-helix 3. Proteins. 1986 Sep;1(1):43–46. doi: 10.1002/prot.340010108. [DOI] [PubMed] [Google Scholar]
  19. Hope H. Cryocrystallography of biological macromolecules: a generally applicable method. Acta Crystallogr B. 1988 Feb 1;44(Pt 1):22–26. doi: 10.1107/s0108768187008632. [DOI] [PubMed] [Google Scholar]
  20. Hope H. Crystallography of biological macromolecules at ultra-low temperature. Annu Rev Biophys Biophys Chem. 1990;19:107–126. doi: 10.1146/annurev.bb.19.060190.000543. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Komine S., Yoshida K., Yamashita H., Masaki Z. Voiding dysfunction in patients with human T-lymphotropic virus type-1-associated myelopathy (HAM). Paraplegia. 1989 Jun;27(3):217–221. doi: 10.1038/sc.1989.32. [DOI] [PubMed] [Google Scholar]
  23. Lee B., Richards F. M. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971 Feb 14;55(3):379–400. doi: 10.1016/0022-2836(71)90324-x. [DOI] [PubMed] [Google Scholar]
  24. Livingstone J. R., Spolar R. S., Record M. T., Jr Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area. Biochemistry. 1991 Apr 30;30(17):4237–4244. doi: 10.1021/bi00231a019. [DOI] [PubMed] [Google Scholar]
  25. Matthews B. W., Nicholson H., Becktel W. J. Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc Natl Acad Sci U S A. 1987 Oct;84(19):6663–6667. doi: 10.1073/pnas.84.19.6663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. Miller S., Janin J., Lesk A. M., Chothia C. Interior and surface of monomeric proteins. J Mol Biol. 1987 Aug 5;196(3):641–656. doi: 10.1016/0022-2836(87)90038-6. [DOI] [PubMed] [Google Scholar]
  28. Perutz M. F. Electrostatic effects in proteins. Science. 1978 Sep 29;201(4362):1187–1191. doi: 10.1126/science.694508. [DOI] [PubMed] [Google Scholar]
  29. Privalov P. L. Cold denaturation of proteins. Crit Rev Biochem Mol Biol. 1990;25(4):281–305. doi: 10.3109/10409239009090612. [DOI] [PubMed] [Google Scholar]
  30. Privalov P. L., Gill S. J. Stability of protein structure and hydrophobic interaction. Adv Protein Chem. 1988;39:191–234. doi: 10.1016/s0065-3233(08)60377-0. [DOI] [PubMed] [Google Scholar]
  31. Privalov P. L. Stability of proteins: small globular proteins. Adv Protein Chem. 1979;33:167–241. doi: 10.1016/s0065-3233(08)60460-x. [DOI] [PubMed] [Google Scholar]
  32. Privalov P. L. Thermodynamic problems of protein structure. Annu Rev Biophys Biophys Chem. 1989;18:47–69. doi: 10.1146/annurev.bb.18.060189.000403. [DOI] [PubMed] [Google Scholar]
  33. Richards F. M. Areas, volumes, packing and protein structure. Annu Rev Biophys Bioeng. 1977;6:151–176. doi: 10.1146/annurev.bb.06.060177.001055. [DOI] [PubMed] [Google Scholar]
  34. Richardson J. S., Getzoff E. D., Richardson D. C. The beta bulge: a common small unit of nonrepetitive protein structure. Proc Natl Acad Sci U S A. 1978 Jun;75(6):2574–2578. doi: 10.1073/pnas.75.6.2574. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Richardson J. S. The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981;34:167–339. doi: 10.1016/s0065-3233(08)60520-3. [DOI] [PubMed] [Google Scholar]
  36. 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]
  37. 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]
  38. 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]
  39. Sieker L. C., Stenkamp R. E., Jensen L. H., Prickril B., LeGall J. Structure of rubredoxin from the bacterium Desulfovibrio desulfuricans. FEBS Lett. 1986 Nov 10;208(1):73–76. doi: 10.1016/0014-5793(86)81535-6. [DOI] [PubMed] [Google Scholar]
  40. Sturtevant J. M. Heat capacity and entropy changes in processes involving proteins. Proc Natl Acad Sci U S A. 1977 Jun;74(6):2236–2240. doi: 10.1073/pnas.74.6.2236. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Tanaka M., Haniu M., Matsueda G., Yasunobu K. T., Himes R. H., Akagi J. M., Barnes E. M., Devanathan T. The primary structure of the Clostridium tartarivorum ferredoxin, a heat-stable ferredoxin. J Biol Chem. 1971 Jun 25;246(12):3953–3960. [PubMed] [Google Scholar]
  42. Venkatachalam C. M. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers. 1968 Oct;6(10):1425–1436. doi: 10.1002/bip.1968.360061006. [DOI] [PubMed] [Google Scholar]
  43. Voordouw G. Cloning of genes encoding redox proteins of known amino acid sequence from a library of the Desulfovibrio vulgaris (Hildenborough) genome. Gene. 1988 Jul 15;67(1):75–83. doi: 10.1016/0378-1119(88)90010-8. [DOI] [PubMed] [Google Scholar]
  44. Watenpaugh K. D., Sieker L. C., Jensen L. H. The structure of rubredoxin at 1.2 A resolution. J Mol Biol. 1979 Jul 5;131(3):509–522. doi: 10.1016/0022-2836(79)90005-6. [DOI] [PubMed] [Google Scholar]
  45. Woolley K. J., Meyer T. E. The complete amino acid sequence of rubredoxin from the green phototrophic bacterium Chlorobium thiosulphatophilum strain PM. Eur J Biochem. 1987 Feb 16;163(1):161–166. doi: 10.1111/j.1432-1033.1987.tb10750.x. [DOI] [PubMed] [Google Scholar]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

RESOURCES