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Structural insight into the mode of interactions of SoxL from Allochromatium vinosum in the global sulfur oxidation cycle

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Abstract

Microbial redox reactions of inorganic sulfur compounds are one of the important reactions for the recycling of sulfur to maintain the environmental sulfur balance. These reactions are carried out by phylogenetically diverse microorganisms. The sulfur oxidizing gene cluster (sox) of α-proteobacteria, Allochromatium vinosum comprises two divergently transcribed units. The central players of this process are SoxY, SoxZ and SoxL. SoxY is sulfur compound binder which binds to sulfur anions with the help of SoxZ. SoxL is a rhodanese like protein, which then cleaves off the sulfur substrate from the SoxYZ complex to recycle the SoxY and SoxZ. In the present work, homology modeling has been employed to build the three dimensional structures of SoxY, SoxZ and SoxL. With the help of docking simulations the amino acid residues of these proteins involved in the interactions have been identified. The interactions between the SoxY, SoxZ and SoxL proteins are mediated mainly through hydrogen bonding. Strong positive fields created by the SoxZ and SoxL proteins are found to be responsible for the binding and removal of the sulfur anion. The probable biochemical mechanism of sulfur anion oxidation process has been identified.

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Acknowledgments

The help and support rendered by Prof. Tapash Chandra Ghosh of Bioinformatics Center, Bose Institute, AJC Bose Centenary Building, P1/12 CIT Scheme VII M, Kolkata 700 054, India are duly acknowledgement here. The author is also thankful to the DBT sponsored Bioinformatics Infrastructure Facility in the Department of Biochemistry and Biophysics, University of Kalyani for the necessary support. Finally, the author would like to thank the anonymous referee for the valuable comments to make the manuscript better.

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  1. Department of Biochemistry and Biophysics, University of Kalyani, Nadia, Kalyani, 741235, India

    Angshuman Bagchi

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  1. Angshuman Bagchi
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Correspondence to Angshuman Bagchi.

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Fig. S1

[For web version (supplementary material)]: Ribbon representation of modeled SoxY. α-Helices and β-sheets are shown as helices and ribbons, respectively. The rest are shown as loops (DOC 155 kb)

Fig. S2

[For web version (supplementary material)]: Ribbon representation of modeled SoxZ. β-Sheets are shown as ribbons. The rest are shown as loops (DOC 122 kb)

Fig. S3

[For web version (supplementary material)]: Ribbon representation of modeled SoxL. α-Helices and β-sheets are shown as helices and ribbons, respectively. The rest are shown as loops (DOC 118 kb)

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Bagchi, A. Structural insight into the mode of interactions of SoxL from Allochromatium vinosum in the global sulfur oxidation cycle. Mol Biol Rep 39, 10243–10248 (2012). https://doi.org/10.1007/s11033-012-1900-9

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  • DOI: https://doi.org/10.1007/s11033-012-1900-9

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