Structural basis for the oxidation of thiosulfate by a sulfur cycle enzyme (original) (raw)
Related papers
Journal of Biological Chemistry, 2009
SoxB is an essential component of the bacterial Sox sulfur oxidation pathway. SoxB contains a di-manganese(II) site and is proposed to catalyze the release of sulfate from a protein-bound cysteine S-thiosulfonate. A direct assay for SoxB activity is described. The structure of recombinant Thermus thermophilus SoxB was determined by X-ray crystallography to a resolution of 1.5Å. Structures were also determined for SoxB in complex with the substrate analogue thiosulfate, and in complex with the product sulfate. A mechanistic model for SoxB based on these structures is proposed.
Novel domain packing in the crystal structure of a thiosulphate-oxidizing enzyme
Biochemical Society Transactions, 2002
A key component of the oxidative biogeochemical sulphur cycle involves the utilization by bacteria of reduced inorganic sulphur compounds as electron donors to photosynthetic or respiratory electron transport chains. The SoxAX protein of the photosynthetic bacterium Rhodovulum sulfidophilum is a heterodimeric c-type cytochrome that is involved in the oxidation of thiosulphate and sulphide. The recently solved crystal structure of the SoxAX complex represents the first structurally characterized example of a productive electron transfer complex between haemoproteins where both partners adopt the c-type cytochrome fold. The packing of c-type cytochrome domains both within SoxA and at the interface between the subunits of the complex has been compared with other examples and found to be unique.
Journal of Biological Chemistry, 2011
The sulfur cycle enzyme sulfane dehydrogenase SoxCD is an essential component of the sulfur oxidation (Sox) enzyme system of Paracoccus pantotrophus. SoxCD catalyzes a six electron oxidation reaction within the Sox cycle. SoxCD is a α 2 β 2 heterotetrameric complex of the molybdenum cofactor-containing SoxC protein and the diheme c-type cytochrome SoxD with the heme domains D 1 and D 2 . SoxCD 1 misses the heme-2 domain D 2 and is catalytically as active as SoxCD. The crystal structure of SoxCD 1 was resolved at 1.33 Å. The substrate of SoxCD is the outer (sulfane) sulfur of Cys110-persulfide located at the C-terminal peptide swinging arm of SoxY of the SoxYZ carrier complex. The SoxCD 1 substrate funnel towards the molybdopterin is narrow and partially shielded by side chain residues of SoxD 1 . For access of the sulfane-sulfur of SoxY-Cys110 persulfide we propose that (i) the blockage by SoxD-Arg98 is opened via interaction with the carboxy terminus of SoxY and (ii) the C-terminal peptide VTIGGCGG of SoxY provides interactions with the entrance path such that the cysteine bound persulfide is optimally positioned near the molybdenum atom. The subsequent oxidation reactions of the sulfane-sulfur are initiated by the nucleophilic attack of the persulfide anion on the molybdenum atom which is, in turn, reduced. The close proximity of heme-1 to the molybdopterin allows easy acceptance of the electrons. Since SoxYZ, SoxXA and SoxB are already structurally characterized, with SoxCD 1 the structures of all key enzymes of the Sox cycle are known with atomic resolution.
Applied and Environmental Microbiology, 2013
During chemolithoautotrophic thiosulfate oxidation, the phylogenetically diverged proteobacteria Paracoccus pantotrophus, Tetrathiobacter kashmirensis, and Thiomicrospira crunogena rendered steady enrichment of 34 S in the end product sulfate, with overall fractionation ranging between ؊4.6‰ and ؉5.8‰. The fractionation kinetics of T. crunogena was essentially similar to that of P. pantotrophus, albeit the former had a slightly higher magnitude and rate of 34 S enrichment. In the case of T. kashmirensis, the only significant departure of its fractionation curve from that of P. pantotrophus was observed during the first 36 h of thiosulfate-dependent growth, in the course of which tetrathionate intermediate formation is completed and sulfate production starts. The almost-identical 34 S enrichment rates observed during the peak sulfate-producing stage of all three processes indicated the potential involvement of identical S-S bond-breaking enzymes. Concurrent proteomic analyses detected the hydrolase SoxB (which is known to cleave terminal sulfone groups from SoxYZ-bound cysteine S-thiosulfonates, as well as cysteine S-sulfonates, in P. pantotrophus) in the actively sulfate-producing cells of all three species. The inducible expression of soxB during tetrathionate oxidation, as well as the second leg of thiosulfate oxidation, by T. kashmirensis is significant because the current Sox pathway does not accommodate tetrathionate as one of its substrates. Notably, however, no other Sox protein except SoxB could be detected upon matrix-assisted laser desorption ionization mass spectrometry analysis of all such T. kashmirensis proteins as appeared to be thiosulfate inducible in 2-dimensional gel electrophoresis. Instead, several other redox proteins were found to be at least 2-fold overexpressed during thiosulfate-or tetrathionate-dependent growth, thereby indicating that there is more to tetrathionate oxidation than SoxB alone.
The Journal of biological chemistry, 2015
Although the oxidative condensation of two thiosulfate anions to tetrathionate constitutes a well-documented and significant part of the natural sulfur cycle little is known about the enzymes catalyzing this reaction. In the purple sulfur bacterium Allochromatium vinosum, the reaction is catalyzed by the periplasmic diheme c-type cytochrome thiosulfate dehydrogenase (TsdA). Here, we report the crystal structure of the 'as-isolated' form of A. vinosum TsdA to 1.98 Å resolution, and those of several redox states of the enzyme to different resolutions. The protein contains two typical class I c-type cytochrome domains wrapped around two hemes axially coordinated by His-53/Cys-96 and His-164/Lys-208. These domains are very similar suggesting a gene duplication event during evolution. A ligand switch from Lys-208 to Met-209 is observed upon reduction of the enzyme. Cys-96 is an essential residue for catalysis with the specific activity of the enzyme being completely abolished in ...
Biophysical Chemistry, 2006
Microbial redox reactions involving inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically diverse prokaryotes, some of which also take part in the extraction of metal ions from their sulfur containing ores. These sulfur oxidizers oxidize inorganic sulfur compounds like sulfide, thiosulfate etc. to produce reductants that are used for carbon dioxide fixation or in respiratory electron transfer chains. The sulfur oxidizing gene cluster (sox) of a-Proteobacteria comprises of at least 15 genes, forming two transcriptional units, viz., soxSR and soxVWXYZABCDEFGH. SoxV is known to be a CcdA homolog involved in the transport of reductants from cytoplasm to periplasm. SoxW and SoxS are periplasmic thioredoxins, which (SoxW) interact with SoxV and thereby help in the redox reactions. We have employed homology modeling to construct the three-dimensional structures of the SoxV, SoxW and SoxS proteins from Rhodovulum sulfidophilum. With the help of docking and molecular dynamics simulations we have identified the amino acid residues of these proteins involved in the interaction. The probable biochemical mechanism of the transport of reductants through the interactions of these proteins has also been investigated. Our study provides a rational basis to interpret the molecular mechanism of the biochemistry of sulfur anion oxidation reactions by these ecologically important organisms.
Microbial redox reactions of inorganic sulfur compounds play a vital role in balancing the turnover of this element in the environment. These vital reactions are carried out by the enzyme system encoded by the sox operon. The central player of the sulfur oxidation biochemistry is the SoxY–Z protein complex. Another protein called SoxF having sulfide dehydrogenase activity has the ability to reactivate the inactivated SoxY–Z protein complex. This SoxF protein is obtained from the sox operon of Chlorobium tepidium. In the present work an attempt has been made to understand the structural details of the activity of SoxF protein. A plausible biochemical mechanism has been predicted regarding the involvement of the SoxF protein in biological sulfur anion oxidation process. Since this is the first report regarding the structural biology of SoxF protein this study may shed light in the hitherto unknown molecular biochemistry of sulfur anion oxidation by sox operon.
Acta Crystallographica Section F-structural Biology and Crystallization Communications, 2006
The 22 kDa SoxYZ protein complex from the green sulfur bacterium Chlorobium limicola f. thiosulfatophilum is a central player in the sulfuroxidizing (Sox) enzyme system of the organism by activating thiosulfate for oxidation by SoxXA and SoxB. It has been proposed that SoxYZ exists as a heterodimer or heterotetramer, but the properties and role of the individual components of the complex thus far remain unknown. Here, the heterologous expression, purification, and the crystallization of stable tetrameric SoxY are reported. Crystals of SoxY diffract to 2.15 Å resolution and belong to space group C222 1 , with unit-cell parameters a = 41.22, b = 120.11, c = 95.30 Å . MIRAS data from Pt 2+ -and Hg 2+ -derivatized SoxY crystals resulted in an interpretable electron-density map at 3 Å resolution after density modification.
Chemolithotrophic bacteria oxidize various sulfur species for energy and electrons, thereby operationalizing biogeochemical sulfur cycles in nature. The best-studied pathway of bacterial sulfur-chemolithotrophy, involving direct oxidation of thiosulfate to sulfate (without any free intermediate) by the SoxXAYZBCD multienzyme system, is apparently the exclusive mechanism of thiosulfate oxidation in facultatively chemolithotrophic alphaproteobacteria. Here we explore the molecular mechanisms of sulfur oxidation in the thiosulfate- and tetrathionate-oxidizing alphaproteobacteriumParacoccus thiocyanatusSST, and compare them with the prototypical Sox process characterized inParacoccus pantotrophus. Our results revealed the unique case where, an alphaproteobacterium has Sox as its secondary pathway of thiosulfate oxidation, converting ∼10% of the thiosulfate supplied whilst 90% of the substrate is oxidized via a Tetrathionate-Intermediate pathway. Knock-out mutation, followed by the study...