Skip to main content
The EMBO Journal logoLink to The EMBO Journal
. 1997 Mar 17;16(6):1181–1188. doi: 10.1093/emboj/16.6.1181

Projection structure of the cytochrome bo ubiquinol oxidase from Escherichia coli at 6 A resolution.

U Gohlke 1, A Warne 1, M Saraste 1
PMCID: PMC1169717  PMID: 9135135

Abstract

The haem-copper cytochrome oxidases are terminal catalysts of the respiratory chains in aerobic organisms. These integral membrane protein complexes catalyse the reduction of molecular oxygen to water and utilize the free energy of this reaction to generate a transmembrane proton gradient. Quinol oxidase complexes such as the Escherichia coli cytochrome bo belong to this superfamily. To elucidate the similarities as well as differences between ubiquinol and cytochrome c oxidases, we have analysed two-dimensional crystals of cytochrome bo by cryo-electron microscopy. The crystals diffract beyond 5 A. A projection map was calculated to a resolution of 6 A. All four subunits can be identified and single alpha-helices are resolved within the density for the protein complex. The comparison with the three-dimensional structure of cytochrome c oxidase shows the clear structural similarity within the common functional core surrounding the metal-binding sites in subunit I. It also indicates subtle differences which are due to the distinct subunit composition. This study can be extended to a three-dimensional structure analysis of the quinol oxidase complex by electron image processing of tilted crystals.

Full Text

The Full Text of this article is available as a PDF (898.0 KB).

Selected References

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

  1. Bullough P. A., Tulloch P. A. High-resolution spot-scan electron microscopy of microcrystals of an alpha-helical coiled-coil protein. J Mol Biol. 1990 Sep 5;215(1):161–173. doi: 10.1016/s0022-2836(05)80101-9. [DOI] [PubMed] [Google Scholar]
  2. Calhoun M. W., Hill J. J., Lemieux L. J., Ingledew W. J., Alben J. O., Gennis R. B. Site-directed mutants of the cytochrome bo ubiquinol oxidase of Escherichia coli: amino acid substitutions for two histidines that are putative CuB ligands. Biochemistry. 1993 Nov 2;32(43):11524–11529. doi: 10.1021/bi00094a008. [DOI] [PubMed] [Google Scholar]
  3. Castresana J., Lübben M., Saraste M., Higgins D. G. Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen. EMBO J. 1994 Jun 1;13(11):2516–2525. doi: 10.1002/j.1460-2075.1994.tb06541.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Castresana J., Saraste M. Evolution of energetic metabolism: the respiration-early hypothesis. Trends Biochem Sci. 1995 Nov;20(11):443–448. doi: 10.1016/s0968-0004(00)89098-2. [DOI] [PubMed] [Google Scholar]
  5. Chepuri V., Lemieux L., Au D. C., Gennis R. B. The sequence of the cyo operon indicates substantial structural similarities between the cytochrome o ubiquinol oxidase of Escherichia coli and the aa3-type family of cytochrome c oxidases. J Biol Chem. 1990 Jul 5;265(19):11185–11192. [PubMed] [Google Scholar]
  6. Crowther R. A., Henderson R., Smith J. M. MRC image processing programs. J Struct Biol. 1996 Jan-Feb;116(1):9–16. doi: 10.1006/jsbi.1996.0003. [DOI] [PubMed] [Google Scholar]
  7. Crum J., Gruys K. J., Frey T. G. Electron microscopy of cytochrome c oxidase crystals: labeling of subunit III with a monomaleimide undecagold cluster compound. Biochemistry. 1994 Nov 22;33(46):13719–13726. doi: 10.1021/bi00250a024. [DOI] [PubMed] [Google Scholar]
  8. Frey T. G. Cytochrome c oxidase: structural studies by electron microscopy of two-dimensional crystals. Microsc Res Tech. 1994 Mar 1;27(4):319–332. doi: 10.1002/jemt.1070270407. [DOI] [PubMed] [Google Scholar]
  9. García-Horsman J. A., Barquera B., Rumbley J., Ma J., Gennis R. B. The superfamily of heme-copper respiratory oxidases. J Bacteriol. 1994 Sep;176(18):5587–5600. doi: 10.1128/jb.176.18.5587-5600.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Haltia T., Finel M., Harms N., Nakari T., Raitio M., Wikström M., Saraste M. Deletion of the gene for subunit III leads to defective assembly of bacterial cytochrome oxidase. EMBO J. 1989 Dec 1;8(12):3571–3579. doi: 10.1002/j.1460-2075.1989.tb08529.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Haltia T., Semo N., Arrondo J. L., Goñi F. M., Freire E. Thermodynamic and structural stability of cytochrome c oxidase from Paracoccus denitrificans. Biochemistry. 1994 Aug 16;33(32):9731–9740. doi: 10.1021/bi00198a044. [DOI] [PubMed] [Google Scholar]
  12. Havelka W. A., Henderson R., Oesterhelt D. Three-dimensional structure of halorhodopsin at 7 A resolution. J Mol Biol. 1995 Apr 7;247(4):726–738. doi: 10.1006/jmbi.1995.0176. [DOI] [PubMed] [Google Scholar]
  13. Hendler R. W., Pardhasaradhi K., Reynafarje B., Ludwig B. Comparison of energy-transducing capabilities of the two- and three-subunit cytochromes aa3 from Paracoccus denitrificans and the 13-subunit beef heart enzyme. Biophys J. 1991 Aug;60(2):415–423. doi: 10.1016/S0006-3495(91)82067-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Ishizuka M., Machida K., Shimada S., Mogi A., Tsuchiya T., Ohmori T., Souma Y., Gonda M., Sone N. Nucleotide sequence of the gene coding for four subunits of cytochrome c oxidase from the thermophilic bacterium PS3. J Biochem. 1990 Nov;108(5):866–873. doi: 10.1093/oxfordjournals.jbchem.a123294. [DOI] [PubMed] [Google Scholar]
  15. Iwata S., Ostermeier C., Ludwig B., Michel H. Structure at 2.8 A resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature. 1995 Aug 24;376(6542):660–669. doi: 10.1038/376660a0. [DOI] [PubMed] [Google Scholar]
  16. Kita K., Kasahara M., Anraku Y. Formation of a membrane potential by reconstructed liposomes made with cytochrome b562-o complex, a terminal oxidase of Escherichia coli K12. J Biol Chem. 1982 Jul 25;257(14):7933–7935. [PubMed] [Google Scholar]
  17. Kita K., Konishi K., Anraku Y. Terminal oxidases of Escherichia coli aerobic respiratory chain. I. Purification and properties of cytochrome b562-o complex from cells in the early exponential phase of aerobic growth. J Biol Chem. 1984 Mar 10;259(5):3368–3374. [PubMed] [Google Scholar]
  18. Lappalainen P., Watmough N. J., Greenwood C., Saraste M. Electron transfer between cytochrome c and the isolated CuA domain: identification of substrate-binding residues in cytochrome c oxidase. Biochemistry. 1995 May 2;34(17):5824–5830. doi: 10.1021/bi00017a014. [DOI] [PubMed] [Google Scholar]
  19. Lemieux L. J., Calhoun M. W., Thomas J. W., Ingledew W. J., Gennis R. B. Determination of the ligands of the low spin heme of the cytochrome o ubiquinol oxidase complex using site-directed mutagenesis. J Biol Chem. 1992 Jan 25;267(3):2105–2113. [PubMed] [Google Scholar]
  20. Lübben M., Arnaud S., Castresana J., Warne A., Albracht S. P., Saraste M. A second terminal oxidase in Sulfolobus acidocaldarius. Eur J Biochem. 1994 Aug 15;224(1):151–159. doi: 10.1111/j.1432-1033.1994.tb20006.x. [DOI] [PubMed] [Google Scholar]
  21. Mather M. W., Springer P., Hensel S., Buse G., Fee J. A. Cytochrome oxidase genes from Thermus thermophilus. Nucleotide sequence of the fused gene and analysis of the deduced primary structures for subunits I and III of cytochrome caa3. J Biol Chem. 1993 Mar 15;268(8):5395–5408. [PubMed] [Google Scholar]
  22. Merritt E. A., Murphy M. E. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D Biol Crystallogr. 1994 Nov 1;50(Pt 6):869–873. doi: 10.1107/S0907444994006396. [DOI] [PubMed] [Google Scholar]
  23. Minagawa J., Mogi T., Gennis R. B., Anraku Y. Identification of heme and copper ligands in subunit I of the cytochrome bo complex in Escherichia coli. J Biol Chem. 1992 Jan 25;267(3):2096–2104. [PubMed] [Google Scholar]
  24. Puustinen A., Verkhovsky M. I., Morgan J. E., Belevich N. P., Wikstrom M. Reaction of the Escherichia coli quinol oxidase cytochrome bo3 with dioxygen: the role of a bound ubiquinone molecule. Proc Natl Acad Sci U S A. 1996 Feb 20;93(4):1545–1548. doi: 10.1073/pnas.93.4.1545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Saiki K., Mogi T., Anraku Y. Heme O biosynthesis in Escherichia coli: the cyoE gene in the cytochrome bo operon encodes a protoheme IX farnesyltransferase. Biochem Biophys Res Commun. 1992 Dec 30;189(3):1491–1497. doi: 10.1016/0006-291x(92)90243-e. [DOI] [PubMed] [Google Scholar]
  26. Saiki K., Nakamura H., Mogi T., Anraku Y. Probing a role of subunit IV of the Escherichia coli bo-type ubiquinol oxidase by deletion and cross-linking analyses. J Biol Chem. 1996 Jun 28;271(26):15336–15340. doi: 10.1074/jbc.271.26.15336. [DOI] [PubMed] [Google Scholar]
  27. Santana M., Kunst F., Hullo M. F., Rapoport G., Danchin A., Glaser P. Molecular cloning, sequencing, and physiological characterization of the qox operon from Bacillus subtilis encoding the aa3-600 quinol oxidase. J Biol Chem. 1992 May 25;267(15):10225–10231. [PubMed] [Google Scholar]
  28. Saraste M., Metso T., Nakari T., Jalli T., Lauraeus M., Van der Oost J. The Bacillus subtilis cytochrome-c oxidase. Variations on a conserved protein theme. Eur J Biochem. 1991 Jan 30;195(2):517–525. doi: 10.1111/j.1432-1033.1991.tb15732.x. [DOI] [PubMed] [Google Scholar]
  29. Saraste M. Structural features of cytochrome oxidase. Q Rev Biophys. 1990 Nov;23(4):331–366. doi: 10.1017/s0033583500005588. [DOI] [PubMed] [Google Scholar]
  30. Sato-Watanabe M., Itoh S., Mogi T., Matsuura K., Miyoshi H., Anraku Y. Stabilization of a semiquinone radical at the high-affinity quinone-binding site (QH) of the Escherichia coli bo-type ubiquinol oxidase. FEBS Lett. 1995 Oct 30;374(2):265–269. doi: 10.1016/0014-5793(95)01125-x. [DOI] [PubMed] [Google Scholar]
  31. Taha T. S., Ferguson-Miller S. Interaction of cytochrome c with cytochrome c oxidase studied by monoclonal antibodies and a protein modifying reagent. Biochemistry. 1992 Sep 22;31(37):9090–9097. doi: 10.1021/bi00152a053. [DOI] [PubMed] [Google Scholar]
  32. Trumpower B. L., Gennis R. B. Energy transduction by cytochrome complexes in mitochondrial and bacterial respiration: the enzymology of coupling electron transfer reactions to transmembrane proton translocation. Annu Rev Biochem. 1994;63:675–716. doi: 10.1146/annurev.bi.63.070194.003331. [DOI] [PubMed] [Google Scholar]
  33. Tsubaki M., Mogi T., Hori H., Hirota S., Ogura T., Kitagawa T., Anraku Y. Molecular structure of redox metal centers of the cytochrome bo complex from Escherichia coli. Spectroscopic characterizations of the subunit I histidine mutant oxidases. J Biol Chem. 1994 Dec 9;269(49):30861–30868. [PubMed] [Google Scholar]
  34. Tsukihara T., Aoyama H., Yamashita E., Tomizaki T., Yamaguchi H., Shinzawa-Itoh K., Nakashima R., Yaono R., Yoshikawa S. Structures of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 A. Science. 1995 Aug 25;269(5227):1069–1074. doi: 10.1126/science.7652554. [DOI] [PubMed] [Google Scholar]
  35. Tsukihara T., Aoyama H., Yamashita E., Tomizaki T., Yamaguchi H., Shinzawa-Itoh K., Nakashima R., Yaono R., Yoshikawa S. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Science. 1996 May 24;272(5265):1136–1144. doi: 10.1126/science.272.5265.1136. [DOI] [PubMed] [Google Scholar]
  36. Uno T., Mogi T., Tsubaki M., Nishimura Y., Anraku Y. Resonance Raman and Fourier transform infrared studies on the subunit I histidine mutants of the cytochrome bo complex in Escherichia coli. Molecular structure of redox metal centers. J Biol Chem. 1994 Apr 22;269(16):11912–11920. [PubMed] [Google Scholar]
  37. Unwin N. Nicotinic acetylcholine receptor at 9 A resolution. J Mol Biol. 1993 Feb 20;229(4):1101–1124. doi: 10.1006/jmbi.1993.1107. [DOI] [PubMed] [Google Scholar]
  38. Unwin P. N., Henderson R. Molecular structure determination by electron microscopy of unstained crystalline specimens. J Mol Biol. 1975 May 25;94(3):425–440. doi: 10.1016/0022-2836(75)90212-0. [DOI] [PubMed] [Google Scholar]
  39. Valpuesta J. M., Carrascosa J. L., Henderson R. Analysis of electron microscope images and electron diffraction patterns of thin crystals of phi 29 connectors in ice. J Mol Biol. 1994 Jul 22;240(4):281–287. doi: 10.1006/jmbi.1994.1445. [DOI] [PubMed] [Google Scholar]
  40. Valpuesta J. M., Henderson R., Frey T. G. Electron cryo-microscopic analysis of crystalline cytochrome oxidase. J Mol Biol. 1990 Jul 5;214(1):237–251. doi: 10.1016/0022-2836(90)90158-I. [DOI] [PubMed] [Google Scholar]
  41. Warne A., Wang D. N., Saraste M. Purification and two-dimensional crystallization of bacterial cytochrome oxidases. Eur J Biochem. 1995 Dec 1;234(2):443–451. doi: 10.1111/j.1432-1033.1995.443_b.x. [DOI] [PubMed] [Google Scholar]
  42. Welter R., Gu L. Q., Yu L., Yu C. A., Rumbley J., Gennis R. B. Identification of the ubiquinol-binding site in the cytochrome bo3-ubiquinol oxidase of Escherichia coli. J Biol Chem. 1994 Nov 18;269(46):28834–28838. [PubMed] [Google Scholar]
  43. Wilmanns M., Lappalainen P., Kelly M., Sauer-Eriksson E., Saraste M. Crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered dinuclear copper center. Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):11955–11959. doi: 10.1073/pnas.92.26.11955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. van der Oost J., Lappalainen P., Musacchio A., Warne A., Lemieux L., Rumbley J., Gennis R. B., Aasa R., Pascher T., Malmström B. G. Restoration of a lost metal-binding site: construction of two different copper sites into a subunit of the E. coli cytochrome o quinol oxidase complex. EMBO J. 1992 Sep;11(9):3209–3217. doi: 10.1002/j.1460-2075.1992.tb05398.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES