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Computational Molecular Biology
2013, Vol.3, No.1, 1-5 http://cmb.sophiapublisher.com
Research Report
Open Access
Structural Analysis of the Mode of Interactions of SoxB Protein with SoxYZ
Complex from
Allochromatium vinosum
in the Global Sulfur Oxidation Cycle
Sujay Ray , Angshuman Bagchi
Department of Biochemistry and Biophysics University of Kalyani, Kalyani, Nadia, India
Corresponding Author email: angshuman_bagchi@yahoo.com;
Author
Computational Molecular Biology, 2013, Vol.3, No.1 doi: 10.5376/cmb.2013.01.0003
Copyright
© 2013 Bagchi et al. This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Microbial redox reaction is a very essential reaction to maintain for the recycling of sulphur to maintain the
environmental sulphur balance. These oxidation process is conducted by a large number of phylogenitically diversed sulphur
oxidizing bacteria. The sox gene cluster of α-proteobacteria,
Allochromacium vinosum
(
A.vinosum
or
A.vino
) are mainly responsible
for microbial redox reaction. The main proteins of this process are SoxY, SoxZ and SoxB. SoxY binds to sulfur anions with the help
of SoxZ. SoxB is a heterodimeric protein, which then hydrolytically releases one molecule of sulfate to yield a SoxY-persulfide. In
the present work, homology modeling has been used to build the three dimensional structures of SoxY, SoxZ. Due to large sequence
length only 5’-nucleotidase C-terminal domain of SoxB has been modelled by homology modeling. With the help of protein-protein
docking complex structure of SoxYZB is formed and using Protein interaction calculator (P.I.C) webserver the amino acid residues of
these proteins involved in the interactions have been identified. The interactions between the SoxY, SoxZ and 5'-nucleotidase,
C-terminal domain of SoxB proteins are mediated mainly through hydrogen bonding. The probable biophysical mechanism of SoxB
interaction with SoxYZ complex has been identified.
Keywords
Docking simulations; Environmental sulphur balance; Homology modelling; Sox operon; Sulphur oxidation
Background
Oxidation-reduction reaction is an important
mechanism to maintain natural sulphur cycle. The
thiosulphate , tetrathionate ,sulphide are the major
sources of sulphur for oxidation-reduction reaction.
Thiosulphate is an environmentally abundant sulphur
compound which fulfils an important role to maintain
environmental sulphur balance. Thiosulphate oxidation is
mainly governed by multienzyme complex (Sox)
which is present in phylogenetically diverse set of
microorganism (Meyer et al., 2007; Freidrich et al.,
2005 ). However the bio-molecular mechanism of the
sulphur oxidation process by the Sox multi-enzyme
complex is not well understood.
Allochromatium vinosum
(
A.vino
) is a α-proteobacteria
accumulates water insoluble sulphur inside the
periplasm during the oxidation of reduced sulphur
compounds such as thiosulfate or sulphide. Three
periplasmic Sox proteins encoded by the
SoxB
,
SoxXAK
, and
SoxYZ
genes are mainly responsible
thiosulphate oxidation in the
A.vino
. The molecular
mechanism proposed for the oxidation of thiosulfate
in
A.vino
reveals that thiosulfate gets coupled to the
carboxy terminal cysteine residue of SoxY bound to
SoxZ and the whole process is facilitated by SoxXA.
SoxB then comes into play and cleaves the
SoxY-thiosulfate hydrolytically adduct to release a
molecule of sulphate (Bagchi, 2012). It was
documented that SoxB of
A.vino
reacted productively
with SoxYZ complex (Welte et al., 2009). However
the details of interactions between SoxB and SoxYZ
protein complex at the residue level are yet to be
explored.
Computational
Molecular Biology
Preferred citation for this article:
Bagchi et al., 2013, Structural Analysis of the Mode of Interactions of SoxB Protein with SoxYZ Complex from
Allochromatium vinosum
in the Global
Sulfur Oxidation Cycle, Computational Molecular Biology, Vol.3, No.1 1-5 (doi: 10.5376/cmb.2013.03.0001)
Received: 12 Jun., 2013
|
Accepted: 19 Jun., 2013
|
Published: 28 Aug., 2013