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A predicted structure of the cytochrome c oxidase from Burkholderia pseudomallei

Mohd. Firdaus Mohd. Raih, and Ahmad Tarmidi Sailan, and Zulkeflie Zamrod, and Mohd. Noor Embi, and Rahmah Mohamed, (2003) A predicted structure of the cytochrome c oxidase from Burkholderia pseudomallei. Electronic Journal of Biotechnology, 6 (1). ISSN 07173458

Full text not available from this repository.

Official URL: http://www.ejbiotechnology.info/content/vol6/issue1/full/5/

Affiliations

Universiti Kebangsaan Malaysia, Centre for Gene Analysis and Technology
Universiti Kebangsaan Malaysia, Centre for Gene Analysis and Technology
Universiti Kebangsaan Malaysia, Centre for Gene Analysis and Technology
Universiti Kebangsaan Malaysia, Centre for Gene Analysis and Technology
Universiti Kebangsaan Malaysia, Centre for Gene Analysis and Technology

Abstract

Cytochrome c oxidase, the terminal enzyme of the respiratory chains of mitochondria and aerobic bacteria, catalyzes electron transfer from cytochrome c to molecular oxygen. The enzyme belongs to the haem-copper-containing oxidases superfamily. A recombinant plasmid carrying a 2.0 kb insert from a Burkholderia pseudomallei genomic library was subjected to automated DNA sequencing utilizing a primer walking strategy. Analysis of the 2002 bp insert revealed a 1536 bp open reading frame predicted to encode a putative cytochrome c oxidase. Further analysis using sequence alignments and tertiary structure analysis tools demonstrated that the hypothetical B. pseudomallei cytochrome c oxidase is similar to cytochrome c oxidases from other organisms such as Thermus thermophilus (36% protein sequence identity), Paracoccus denitrificans and bovine heart mitochondrial, the latter two which crystal structures available. The deduced 512 residue protein sequence includes the six canonical histidine residues involved in binding the low spin heme B and the binuclear center CuB/hemeA. The predicted tertiary structure of the hypothetical protein is consistent with previous models of electron transfer for cytochrome c oxidase.

Item Type:Journal
Additional Information:This work was funded by the Intensification of Research in Priority Areas (IRPA) grants IRPA 01-02-02-001 and IRPA-TOPDOWN 09-02-02-T001 provided by the Ministry of Science, Technology and the Environment, Malaysia.
Keywords:Burkholderia pseudomallei, cytochrome c oxidase, protein structure prediction, sequence alignments, structure-function extrapolation
Subjects:Q Science
ID Code:1894

ALTSCHUL, S.F.; THOMAS, L.M.; ALEJANDRO, A.S.; JINGHUI Z.; ZHENG Z.; WEBB, M. and DAVID, J.L. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, September 1997, vol. 25, no. 17, p. 3389-3402.

BIRNBOIM, H.C. and DOLY, J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Research, November 1979, vol. 7, no. 6, p. 1513-1523.

CLAROS, M.G. and VON HEIJNE, G. TopPred II: An improved software for membrane protein structure predictions. CABIOS, December 1994, vol. 10, no. 6, p. 685-686.

COLOVOS, C. and YEATES, T.O. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Science, September 1993, vol. 2, p. 1511-1519.

CSERZO, M.; WALLIN E.; SIMON, I.; VON HEIJNE, G. and ELOFSSON, A. prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Engineering, June 1997, vol. 10, no. 6, p. 673-676.

DANCE, D.A.B. Melioidosis. Current Opinion in Infectious Diseases, April 2002, vol. 15, no. 2, p. 127-132.

FERGUSON-MILLER, S. and BABCOCK, G.T. Heme/copper terminal oxidases. Chemical Reviews, November 1996, vol. 96, no. 7, p. 2889-2907.

FISCHER, D.; ELOFSSON, A.; RYCHLEWSKI, L.; PAZOS, F.; VALENCIA, A.; ROST, B.; ORTIZ, A.R. and DUNBRACK, R.L. Jr. CAFASP2: The second critical assessment of fully automated structure prediction methods. Proteins, 2001, vol. 45, Suppl. 5, p. 171-183.

FISCHER, D. Hybrid fold recognition: Combining sequence derived properties with evolutionary information. In: Pacific Symposium on Biocomputing, (January 4-9 2000 Hawaii), World Scientific, p. 119-130.

GARCIA-HORSMAN, J.A.; PUUSTINEN, A.; GENNIS, R.B. and WIKSTRÖM, M. Proton transfer in cytochrome ba3 ubiquinol oxidase of Escherichia coli: second-site mutations in subunit I that restore proton pumping in the mutant Asp-135 Asn. Biochemistry, April 1995, vol. 34, no. 13, p. 4428-4433.

HILL, B.C. Modelling the sequence of electron transfer reactions in the single turnover of reduced, mammalian cytochrome c oxidase with oxygen. Journal of Biological Chemistry, January 1994, vol. 28, no. 269, p. 2419-2425.

HIROKAWA, T.; BOON-CHIENG, S. and MITAKU, S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics, 1998, vol. 14, no. 4, p. 378-379.

IWATA, S.; OSTERMEIER, C.; LUDWIG, B. and MICHEL, H. Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature, August 1995, vol. 24, no. 376, p. 660-669.

JONES, D.T. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. Journal of Molecular Biology, April 1999, vol. 287, no. 4, p. 797-815.

JONES, D.T.; TAYLOR, W.R. and THORNTON, J.M. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry, March 1994, vol. 33, no. 10, p. 3038-3049.

JURETIC, D.; JERONCIC, A. and ZUCIC, D. Sequence analysis of membrane proteins with the web server SPLIT. Croatica Chemica Acta, 1999, vol. 72, no. 4, p. 975-997.

KELLEY, L.A.; MACCALLUM, R.M. and STERNBERG, M.J.E. Enhanced genome annotation using structural profiles in the Program 3D-PSSM. Journal of Molecular Biology, June 2000, vol. 299, no. 2, p. 501-522.

KROGH, A.; LARSSON, B.; VON HEIJNE, G. and SONNHAMMER, E.L.L. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. Journal of Molecular Biology, January 2001, vol. 305, no. 3, p. 567-580.

LASKOWSKI, R.A.; MACARTHUR, M.W.; MOSS, D.S. and THORNTON J.M. PROCHECK: a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 1993, vol. 26, p. 283-291.

LUKASHIN, A. and BORODOVSKY, M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Research, February 1998, vol. 26, no. 4, p. 1107-1115.

LUTHY, R.; BOWIE, J.U. and EISENBERG, D. Assessment of protein models with three-dimensional profiles. Nature, March 1992, vol. 356, p. 83-85.

MICHEL, H.; BEHR, J.; HARRENGA, A. and KANNT, A. Cytochrome c oxidase: structure and spectroscopy. Annual Reviews Biophysics and Biomolecular Structure, 1998, vol. 27, p. 329-356.

MOLLER, S.; CRONING, M.D. and APWEILER, R. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics, July 2001, vol. 17, no. 7, p. 646-653.

ROST, B.; SANDER, C. and SCHNEIDER, R. PHD-an automatic server for protein secondary structure prediction. CABIOS, February 1994, vol. 10, no. 1, p. 53-60.

SALI, A. and BLUNDELL, T.L. Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, December 1993, vol. 234, p. 779-815.

SOULIMANE, T.; BUSE, G.; BOURENKOV, G.P.; BARTUNIK, H.D.; HUBER, R. and THAN, M.E. Structure and mechanism of the aberrant ba3-cytochrome c oxidase from Thermus thermophilus. European Molecular Biology Organization Journal, April 2000, vol. 19, no. 8, p. 1766-1776.

THOMPSON, J.D.; HIGGINS, D.G. and GIBSON, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, November 1994, vol. 22, p. 4673-4680.

VRIEND, G. What if: a molecular modelling and drug design program. Journal of Molecular Graphics, March 1990, vol. 8, p. 52-56.

WITT, H. and LUDWIG, B. Isolation, analysis, and deletion of the gene coding for subunit IV of cytochrome c oxidase in Paracoccus denitrificans. Journal of Biological Chemistry, February 1997, vol. 272, no. 9, p. 5514-5517.

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