Advertisement

Intermolecular Interaction Study of Dissimilatory Sulfite Reductase (DsrAB) from Sulfur Oxidizing Proteobacteria Allchromatium vinosum

  • Semanti Ghosh
  • Angshuman Bagchi
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 340)

Abstract

Dissimilatory Sulfite Reductase (dSiR) is the main redox enzyme system utilized in sulfur metabolism in both sulfur oxidizing and reducing prokaryotes. Anoxygenic phototrophic bacteria Allochromatium vinosum produces elemental sulfur during sulfur cycle which is ultimately oxidized sulfate by DSR operon. Allochromatium vinosum encodes dsrAB reverse dSiR that oxidizes thiosulfate or elemental sulfur. DsrAB is a α2β2 hetero-tetrameric complex. In our present study, we first reported the three dimensional structure of DsrAB protein complex from Allochromatium vinosum and we also predicted the protein-protein interactions between DsrA and DsrB proteins. DsrAB is a major redox enzyme complex required in both sulfur oxidation and reduction processes so this structure function relationship investigation will help in researches to predict the biochemical mechanism of sulfur-oxidation. The importance of the study lies in the fact that sulfur metabolism pathways are used in waste remediation and bio-hydrogen production. This is the most important aspect of our analysis.

Keywords

Dsr operon DsrAB Allochromatium vinosum Homology modeling Protein-protein docking Active site interaction 

Notes

Acknowledgment

Ms. Semanti Ghosh is thankful to the University of Kalyani, West Bengal, India and University Grant Commission, India for the financial support. We would like to thank the Bioinformatics Infrastructure Facility and also the DST-PURSE program 2012–2015 going on in the Department of Biochemistry and Biophysics, University of Kalyani for their support.

References

  1. 1.
    Sasikala, C., Ramana, C.V.: Biotechnological potentials of anoxygenic phototrophic bacteria. 1. Production of single-cell protein, vitamins, ubiquinones, hormones, and enzymes and use in waste treatment. Adv. Appl. Microbiol. 41, 173–226 (1995)CrossRefGoogle Scholar
  2. 2.
    Sasikala, C., Ramana, C.V.: Biotechnological potentials of anoxygenic phototrophic bacteria. 2. Bio-polyesters, biopesticide, biofuel, and biofertilizer. Adv. Appl. Microbiol. 41, 227–278 (1995)CrossRefGoogle Scholar
  3. 3.
    Liebergesell, M., Steinbüchel, A.: New knowledge about the pha-locus and P (3HB) granule-associated proteins in Chromatium vinosum. Biotechnol. Lett. 18, 719–724 (1996)CrossRefGoogle Scholar
  4. 4.
    Sasikala, K., Ramana, C.V., Rao, P.R., Kovács, K.L.: Anoxygenic photosynthetic bacteria: physiology and advances in hydrogen production technology. Adv. Appl. Microbiol. 38, 211–295 (1993)CrossRefGoogle Scholar
  5. 5.
    Grein, F.: Biochemical, biophysical and functional analysis of the DsrMKJOP transmembrane complex from Allochromatium vinosum. PhD thesis. Rhenish Friedrich Wilhelm University, Bonn (2010)Google Scholar
  6. 6.
    Pott, A.S.: Dahl. C.: Sirohaem-sulfite reductase and other proteins encoded in the dsr locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur. Microbiology 144, 1881–1894 (1998)CrossRefGoogle Scholar
  7. 7.
    Dahl, C., Engels, S., Pott-Sperling, A.S., Schulte, A., Sander, J., Lübbe, Y., Oliver Deuster, O., Brune. D.C.: Novel genes of the dsr gene cluster and evidence for close interaction of Dsr Proteins during sulfur oxidation in the phototrophic sulfur bacterium Allochromatium vinosum. J. Bacteriol. 187, 1392–1404 (2005)Google Scholar
  8. 8.
    Dahl, C., Franz, B., Hensen, D., Kesselheim, A., Zigann, R.: Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: Identification of SoeABC as a major player and relevance of SoxYZ in the process. Microbiology 159, 2626–2638 (2013)CrossRefGoogle Scholar
  9. 9.
    Sanchez, O., Ferrera, I., Dahl, C., Mas, J.: In vivo role of APS reductase in the purple sulfur bacterium Allochromatium vinosum. Arch. Microbiol. 176, 301–305 (2001)CrossRefGoogle Scholar
  10. 10.
    Lübbe, Y.J., Youn, H., Timkovich, R., Dahl, C.: Siro (haem) amide in Allochromatium vinosum and relevance of DsrL and DsrN, a homolog of cobyrinic acid a, c-diamide synthase, for sulphur oxidation. FEMS Microbiol. Lett. 261, 194–202 (2006)CrossRefGoogle Scholar
  11. 11.
    Berman, H.M.: The Protein Data Bank: a historical perspective. Acta Crystallogr. A 64, 88–95 (2008)CrossRefGoogle Scholar
  12. 12.
    Altschul, S.F., Gish,W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. J. Mol. Biol. 215(3), 403–410 (1990)Google Scholar
  13. 13.
    Sali, A., Pottertone, L., Yuan, F., van Vlijmen, H., Karplus, M.: Evaluation of comparative protein modeling by MODELLER. Proteins 23, 318–326 (1995)CrossRefGoogle Scholar
  14. 14.
    Fiser, A., Kinh Gian Do, R., Sali, A.: Modeling of loops in protein structures. Protein Sci. 9, 1753–1773 (2000)Google Scholar
  15. 15.
    Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M.: CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comp. Chem. 4, 187–217 (1983)CrossRefGoogle Scholar
  16. 16.
    Lüthy, R., Bowie, J.U., Eisenberg, D.: Assessment of protein models with three-dimensional profiles. Nature 356(6364), 83–5 (1992)Google Scholar
  17. 17.
    Laskowski, R.A., McArthur, M.W., Moss, D.S., Thornton, J.M.: PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993)CrossRefGoogle Scholar
  18. 18.
    Ramachandran, G.N., Ramakrishnan, C., Sasisekharan, V.: Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7, 95–99 (1963)CrossRefGoogle Scholar
  19. 19.
    Structural Analysis and Verification Server, http://nihserver.mbi.ucla.edu/SAVES/
  20. 20.
    Chen, R., Weng, Z.: Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 47, 281–294 (2002)CrossRefGoogle Scholar
  21. 21.
    Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi, Active Site Prediction, http://www.scfbio-iitd.res.in/dock/ActiveSite_new.jsp
  22. 22.
    University Hamburg, Centre of Bioinformatics, DoGSiteScorer: Active Site Prediction and Analysis Server, http://dogsite.zbh.uni-hamburg.de/
  23. 23.
  24. 24.
    Pierce, B., Weng, Z.: ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 67, 1078–1086 (2007)CrossRefGoogle Scholar
  25. 25.
    Li, L., Chen, R., Weng, Z.: RDOCK: refinement of rigid-body protein docking predictions. Proteins 53, 693–707 (2003)CrossRefGoogle Scholar
  26. 26.
    Tina, K.G., Bhadra, R., Srinivasan, N.: PIC: Protein interaction calculator. Nucleic Acid Res. 35, Web server issue W473–W476 (2007)Google Scholar

Copyright information

© Springer India 2015

Authors and Affiliations

  1. 1.Department of Biochemistry and BiophysicsUniversity of KalyaniNadiaIndia

Personalised recommendations