Share This Article:

Structural analyses of the interactions of SoxY and SoxZ from thermo-neutrophilic Hydrogenobacter thermophilus

Abstract Full-Text HTML Download Download as PDF (Size:387KB) PP. 408-413
DOI: 10.4236/jbpc.2011.24047    3,951 Downloads   6,817 Views   Citations


Microbial redox reactions of inorganic sulfur compounds are one of the important reactions responsible for the recycling of this element to maintain the environmental sulfur balance. These reactions are carried out by phylogenetically diverse set of microorganisms. The sulfur oxidizing gene cluster (sox) of thermo-neutrophilic bacterium Hydrogenobacter thermophilus consists of soxYZAXB. The bacterium shows optimal thiosulfate oxidation activity at 60°C. There are practically no reports regarding the structural biology of the sulfur oxidation proc- ess in this organism. In the present context, we employed homology modeling to construct the three dimensional structures of SoxY and SoxZ from Hydrogenobacter thermophilus. With the help of docking simulations we have identified the amino acid residues of these proteins in- volved in the interactions. The thermodynamics of the protein-protein interactions have also been analyzed. The probable biochemical mechanism of the binding of thiosulfate has been elucidated. Our study provides a rational framework to understand the molecular mechanism of the sulfur oxidation biochemistry.

Conflicts of Interest

The authors declare no conflicts of interest.

Cite this paper

Bagchi, A. and Ghosh, T. (2011) Structural analyses of the interactions of SoxY and SoxZ from thermo-neutrophilic Hydrogenobacter thermophilus. Journal of Biophysical Chemistry, 2, 408-413. doi: 10.4236/jbpc.2011.24047.


[1] Freidrich, C.G. (1998) Physiology and genetics of sulfur- oxidizing bacteria. Advances in Microbial Physiology, 39, 235-289. doi:10.1016/S0065-2911(08)60018-1
[2] Le Faou A., et al. (1990) Thiosulfate, polythionates and elemental sulfur assimilation and reduction in the bacterial world. FEMS Microbiology Reviews, 6, 351-381. doi:10.1016/S0168-6445(05)80005-1
[3] Appia-Ayme C., et al. (2001) Cytochrome complex essential for photosynthetic oxidation of both thiosulfate and sulfide in Rhodovulum sulfidophilum. Journal of Bacteriology, 183, 6107-6118. doi:10.1128/JB.183.20.6107-6118.2001
[4] Freidrich C.G., et al. (2001) Oxidation of reduced inorganic sulfur compounds by bacteria: Emergence of a common mechanism? Applied and Environmental Microbiology, 67, 2873-2882. doi:10.1128/AEM.67.7.2873-2882.2001
[5] Bagchi A. and Ghosh T.C. (2006) Structural insight into the interactions of SoxV, SoxW and SoxS in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle. Biophysical Chemistry, 119, 7-13. doi:10.1016/j.bpc.2005.08.011
[6] Bagchi A., et al. (2005) Homology modeling of a transcriptional regulator SoxR of the lithotrophic sulfur oxidation (Sox) operon in α-proteobacteria. Journal of Biomolecular Structure & Dynamics, 22, 571-578.
[7] Bagchi A. and Roy P. (2005) Structural insight into SoxC and SoxD interaction and their role in electron transport process in the novel global sulfur cycle in Paracoccus pantotrophus. Biochemical and Biophysical Research Communications, 331, 1107-1103. doi:10.1016/j.bbrc.2005.04.028
[8] Rother D. and Friedrich C.G. (2002) The cytochrome complex SoxXA of Paracoccus pantotrophus is produced in Escherichia coli and functional in the reconstituted sulfur-oxidizing enzyme system. Biochimica et Biophysica Acta, 1598, 65-73.
[9] Hensen D., et al. (2006) Thiosulphate oxidation in the phototrophic sulphur bacterium Allochromatium vinosum. Molecular Microbiology, 62, 794-810. doi:10.1111/j.1365-2958.2006.05408.x
[10] Sano R., et al. (2010) Thiosulphate oxidation by a ther- mo-neutrophilic hydrogen-oxidizing bacterium, Hydroge- nobacter thermophilus. Bioscience, Biotechnology, and Biochemistry, 74, 892-894. doi:10.1271/bbb.90948
[11] Berman M.H., et al. (2000) The protein data bank. Nucleic Acids Research, 28, 235-242. doi:10.1093/nar/28.1.235
[12] Altschul S.F., et al. (1990) Basic local alignment search tool. Journal of Molecular Biology, 25, 403-410.
[13] Shi J., et al. (2001) FUGUE: Sequence-structure ho- mology recognition using environment-specific substitu- tion tables and structure-dependent gap penalties. Journal of Molecular Biology, 310, 243-257. doi:10.1006/jmbi.2001.4762
[14] Dauber-Osguthorpe P., et al. (1988) Structure and ener- getics of ligand binding to proteins: Escherichia coli di- hydrofolate reductase trimethoprim, a drug receptor sys- tem. Proteins, 4, 31-47. doi:10.1002/prot.340040106
[15] Sippl. M.J. (1993) Recognition of errors in three-dimen- sional structures in proteins. Proteins, 17, 355-362. doi:10.1002/prot.340170404
[16] Wiederstein M., et al. (2004) Evolutionary methods in Biotechnology, Wiley-VCH.
[17] Eisenberg D., et al. (1997) VERIFY3D: Assessment of protein models with three-dimensional profiles. Methods in Enzymology, 277, 396-404. doi:10.1016/S0076-6879(97)77022-8
[18] Laskowski R.A., et al. (1993) PROCHECK: A program to check the stereochemistry of protein structures. Jour- nal of Applied Crystallography, 26, 283-291. doi:10.1107/S0021889892009944
[19] Ramachandran G.N. and Sashisekharan V. (1968) Con- formation of polypeptides and proteins. Advances in Pro- tein Chemistry, 23, 283-438. doi:10.1016/S0065-3233(08)60402-7
[20] Vakser I.A. (1995) Protein docking for low-resolution structures. Protein Engineering, 8, 371-377. doi:10.1093/protein/8.4.371
[21] Mendel J.G., et al. (2001) Protein docking using con- tinuum electrostatics and geometric fit. Protein Engineer- ing, 14, 105-113. doi:10.1093/protein/14.2.105
[22] Chen R., et al. (2003) ZDOCK: An initial-stage protein docking algorithms. Proteins, 51, 82-87.
[23] Comeau S.R., et al. (2004) ClusPro: An automated dock- ing and discrimination method for the prediction of pro- tein complexes. Bioinformatics, 20, 45-50. doi:10.1093/bioinformatics/btg371
[24] van der Spoel D., et al. (2005) GROMACS: Fast, flexible and free. Journal of Computational Chemistry, 26, 1701- 1718. doi:10.1002/jcc.20291
[25] Hess B., et al. (1997) LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18, 1463-1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
[26] Essmann U., et al. (1995) A smooth particle mesh Ewald method. Journal of Chemical Physics, 105, 8577-8593. doi:10.1063/1.470117
[27] Lavigne P., et al. (2000) Structure-based thermodynamic analysis of the dissociation of protein phosphatase-1 cata- lytic subunit and microcystin-LR docked complexes. Pro- tein Science, 9, 252-264. doi:10.1110/ps.9.2.252

comments powered by Disqus

Copyright © 2019 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.