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. 2000 Nov;9(11):2068–2073. doi: 10.1110/ps.9.11.2068

Primary structure of a novel subunit in ba3-cytochrome oxidase from Thermus thermophilus.

T Soulimane 1, M E Than 1, M Dewor 1, R Huber 1, G Buse 1
PMCID: PMC2144504  PMID: 11152118

Abstract

The bax-type cytochrome c oxidase from Thermus thermophilus is known as a two subunit enzyme. Deduced from the crystal structure of this enzyme, we discovered the presence of an additional transmembrane helix "subunit IIa" spanning the membrane. The hydrophobic N-terminally blocked protein was isolated in high yield using high-performance liquid chromatography. Its complete amino acid sequence was determined by a combination of automated Edman degradation of both the deformylated and the cyanogen bromide cleaved protein and automated C-terminal sequencing of the native protein. The molecular mass of 3,794 Da as determined by MALDI-MS and by ESI requires the N-terminal methionine to be formylated and is in good agreement with the value calculated from the formylmethionine containing sequence (3,766.5 Da + 28 Da = 3,794.5 Da). This subunit consits of 34 residues forming one helix across the membrane (Lys5-Ala34), which corresponds in space to the first transmembrane helix of subunit II of the cytochrome c oxidases from Paracoccus denitrificans and bovine heart, however, with opposite polarity. It is 35% identical to subunit IV of the ba3-cytochrome oxidase from Natronobacterium pharaonis. The open reading frame encoding this new subunit IIa (cbaD) is located upstream of cbaB in the same operon as the genes for subunit I (cbaA) and subunit II (cbaB).

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Selected References

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  1. Buse G., Soulimane T., Dewor M., Meyer H. E., Blüggel M. Evidence for a copper-coordinated histidine-tyrosine cross-link in the active site of cytochrome oxidase. Protein Sci. 1999 May;8(5):985–990. doi: 10.1110/ps.8.5.985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. 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]
  3. Edman P., Begg G. A protein sequenator. Eur J Biochem. 1967 Mar;1(1):80–91. doi: 10.1007/978-3-662-25813-2_14. [DOI] [PubMed] [Google Scholar]
  4. Fee J. A., Choc M. G., Findling K. L., Lorence R., Yoshida T. Properties of a copper-containing cytochrome c1aa3 complex: a terminal oxidase of the extreme thermophile Thermus thermophilus HB8. Proc Natl Acad Sci U S A. 1980 Jan;77(1):147–151. doi: 10.1073/pnas.77.1.147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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]
  6. Giuffrè A., Forte E., Antonini G., D'Itri E., Brunori M., Soulimane T., Buse G. Kinetic properties of ba3 oxidase from Thermus thermophilus: effect of temperature. Biochemistry. 1999 Jan 19;38(3):1057–1065. doi: 10.1021/bi9815389. [DOI] [PubMed] [Google Scholar]
  7. Gold L., Stormo G. D. High-level translation initiation. Methods Enzymol. 1990;185:89–93. doi: 10.1016/0076-6879(90)85009-d. [DOI] [PubMed] [Google Scholar]
  8. Gross E., Morell J. L. The reaction of cyanogen bromide with S-methylcysteine: fragmentation of the peptide 14-29 of bovine pancreatic ribonuclease A. Biochem Biophys Res Commun. 1974 Aug 5;59(3):1145–1150. doi: 10.1016/s0006-291x(74)80098-7. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Keightley J. A., Zimmermann B. H., Mather M. W., Springer P., Pastuszyn A., Lawrence D. M., Fee J. A. Molecular genetic and protein chemical characterization of the cytochrome ba3 from Thermus thermophilus HB8. J Biol Chem. 1995 Sep 1;270(35):20345–20358. doi: 10.1074/jbc.270.35.20345. [DOI] [PubMed] [Google Scholar]
  11. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  12. Lübben M., Kolmerer B., Saraste M. An archaebacterial terminal oxidase combines core structures of two mitochondrial respiratory complexes. EMBO J. 1992 Mar;11(3):805–812. doi: 10.1002/j.1460-2075.1992.tb05117.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lübben M., Morand K. Novel prenylated hemes as cofactors of cytochrome oxidases. Archaea have modified hemes A and O. J Biol Chem. 1994 Aug 26;269(34):21473–21479. [PubMed] [Google Scholar]
  14. Lübben M., Warne A., Albracht S. P., Saraste M. The purified SoxABCD quinol oxidase complex of Sulfolobus acidocaldarius contains a novel haem. Mol Microbiol. 1994 Jul;13(2):327–335. doi: 10.1111/j.1365-2958.1994.tb00426.x. [DOI] [PubMed] [Google Scholar]
  15. Mattar S., Engelhard M. Cytochrome ba3 from Natronobacterium pharaonis--an archaeal four-subunit cytochrome-c-type oxidase. Eur J Biochem. 1997 Dec 1;250(2):332–341. doi: 10.1111/j.1432-1033.1997.0332a.x. [DOI] [PubMed] [Google Scholar]
  16. Nikaido K., Noguchi S., Sakamoto J., Sone N. The cbaAB genes for bo3-type cytochrome c oxidase in Bacillus stearothermophilus. Biochim Biophys Acta. 1998 May 11;1397(3):262–267. doi: 10.1016/s0167-4781(98)00043-8. [DOI] [PubMed] [Google Scholar]
  17. Ostermeier C., Harrenga A., Ermler U., Michel H. Structure at 2.7 A resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment. Proc Natl Acad Sci U S A. 1997 Sep 30;94(20):10547–10553. doi: 10.1073/pnas.94.20.10547. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Soulimane T., Buse G., Bourenkov G. P., Bartunik H. D., Huber R., Than M. E. Structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from thermus thermophilus. EMBO J. 2000 Apr 17;19(8):1766–1776. doi: 10.1093/emboj/19.8.1766. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Soulimane T., Gohlke U., Huber R., Buse G. Three-dimensional crystals of cytochrome-c oxidase from Thermus thermophilus diffracting to 3.8 A resolution. FEBS Lett. 1995 Jul 10;368(1):132–134. doi: 10.1016/0014-5793(95)00623-h. [DOI] [PubMed] [Google Scholar]
  20. Soulimane T., von Walter M., Hof P., Than M. E., Huber R., Buse G. Cytochrome-c552 from Thermus thermophilus: a functional and crystallographic investigation. Biochem Biophys Res Commun. 1997 Aug 28;237(3):572–576. doi: 10.1006/bbrc.1997.7041. [DOI] [PubMed] [Google Scholar]
  21. Than M. E., Hof P., Huber R., Bourenkov G. P., Bartunik H. D., Buse G., Soulimane T. Thermus thermophilus cytochrome-c552: A new highly thermostable cytochrome-c structure obtained by MAD phasing. J Mol Biol. 1997 Aug 29;271(4):629–644. doi: 10.1006/jmbi.1997.1181. [DOI] [PubMed] [Google Scholar]
  22. 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]
  23. 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]
  24. Yoshikawa S., Shinzawa-Itoh K., Nakashima R., Yaono R., Yamashita E., Inoue N., Yao M., Fei M. J., Libeu C. P., Mizushima T. Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase. Science. 1998 Jun 12;280(5370):1723–1729. doi: 10.1126/science.280.5370.1723. [DOI] [PubMed] [Google Scholar]
  25. Zimmermann B. H., Nitsche C. I., Fee J. A., Rusnak F., Münck E. Properties of a copper-containing cytochrome ba3: a second terminal oxidase from the extreme thermophile Thermus thermophilus. Proc Natl Acad Sci U S A. 1988 Aug;85(16):5779–5783. doi: 10.1073/pnas.85.16.5779. [DOI] [PMC free article] [PubMed] [Google Scholar]

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