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discounted EARLY registration ends Dec 31, 2014
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discounted EARLY registration ends Dec 31, 2014
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MetaCyc Pathway: sulfite oxidation I (sulfite oxidoreductase)

Enzyme View:

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Degradation/Utilization/Assimilation Inorganic Nutrients Metabolism Sulfur Compounds Metabolism Sulfite Oxidation
Generation of Precursor Metabolites and Energy Chemoautotrophic Energy Metabolism

Some taxa known to possess this pathway include ? : Acidianus ambivalens , Acidithiobacillus ferrooxidans , Beggiatoa , Paracoccus denitrificans , Paracoccus versutus , Starkeya novella , Sulfitobacter , Sulfitobacter pontiacus , Sulfobacillus thermosulfidooxidans , Thiobacillus thioparus

Expected Taxonomic Range: Firmicutes , Proteobacteria , Thermoprotei

Summary:
General Background

Sulfite plays a key role in oxidative sulfur metabolism. It is derived from multiple sources: First, sulfite is the main intermediate in the oxidation of sulfur compounds to sulfate [Kappler01]. In purple sulfur bacteria such as Allochromatium vinosum, the oxidation of hydrogen sulfide and thiosulfate results in formation of intracellular sulfur globules, which are oxidized to sulfite by the Dsr system (see superpathway of sulfide oxidation (phototrophic sulfur bacteria)).

A second source for sulfite is the desulfonation of organic compounds by enzymes like EC 2.3.3.15, sulfoacetaldehyde acetyltransferase (Xsc) (see sulfoacetaldehyde degradation I).

A third source of sulfite is extracellular sulfite retrieved from the environment. Free sulfite in the periplasm (which most likely exists as bisulfite) is bound to the SoxYZ protein complex in the form of [a SoxY protein]-L-cysteine-S-sulfinate. The binding acts to shield components of the periplasm from chemical reactions with sulfite, and may also be required for delivering the sulfite to a transporter that exports it into the cytoplasm for oxidation [Dahl13]. Some microorganisms (such as Sulfitobacter species) can use sulfite as their sole electron source [Sorokin95, Pukall99].

Enzymes that catalyze the direct oxidation of sulfite to sulfate are molybdenum hydroxylases, and belong to the sulfite oxidase family, which includes both sulfite-oxidizing enzymes and plant assimilatory nitrate reductases (such as the sulfite oxidase of Arabidopsis thaliana col). The best characterized members of this family are sulfite oxidases from avian and mammalian sources. However, these enzymes differ from the bacterial enzymes in that they can use oxygen as an electron acceptor (see EC 1.8.3.1, sulfite oxidase).

Some sulfite oxidizing enzyme are located in the periplasm. The best characterized enzyme from this group is sulfite dehydrogenase (SOR) from Starkeya novella, which contains a molybdopyranopterin cofactor (this pathway). Another well-characterized periplasmic enzyme is the Sox enzyme system (such as that from Paracoccus pantotrophus). It has been shown that this system can oxidize sulfite independently from the presence of the SoxCD component (a molybdohemoprotein), but it is not clear whether the Sox system functions in vivo as sulfite-oxidizing enzymes [Friedrich00, Lu84, Friedrich01]).

Other enzyme systems that oxidize sulfite are located in the cytoplasm. Two general mechanisms for sulfite oxidation in the cytoplasm have been described: a direct oxidation by a membrane-bound iron-sulfur molybdoprotein (EC 1.8.2.1, sulfite dehydrogenase, as described in sulfite oxidation V (SoeABC)), and an indirect, AMP-dependent oxidation via the intermediate adenosine 5'-phosphosulfate (APS) (see sulfite oxidation II and sulfite oxidation III) [Kappler01]. The direct oxidation route is much more prevalent, but the two mechanisms are present simultaneously in many organisms, including β and γ proteobacteria (Thiobacillus thioparus, Allochromatium vinosum, Thiobacillus denitrificans, Beggiatoa), green sulfur bacteria (Chlorobium), Gram-positive bacteria (Sulfobacillus thermosulfidooxidans) and even archaea (Acidianus ambivalens) [Kappler01].

While many organisms possess only the direct mechanism, the only examples for organisms that possess only the non-direct mechanism are found in the bacterial endosymbionts of invertebrates [Nelson95].

About This Pathway

The SorAB protein from the α-proteobacterium Starkeya novella is the best characterized periplasmic sulfite:acceptor oxidoreductase. It is a heterodimer, with a large subunit that binds a molybdopyranopterin cofactor and a smaller monoheme cytochrome c subunit [Kappler00].

During catalysis electrons are transferred to the single heme c552 located on the smaller subunit, and passed to a cytochrome c550 which is believed to be the enzyme's natural electron acceptor [Yamanaka81]. The enzyme exhibits a Ping Pong mechanism (similarly to eukaryotic SORs), and is non-competitively inhibited by sulfate. A structure revealed that the short distance between the two redox centers in the protein complex allows for rapid electron transfer via tunnelling. A potential site of electron transfer to an external acceptor cytochrome c was identified on the SorB subunit [Kappler05].

Superpathways: superpathway of sulfide oxidation (Acidithiobacillus ferrooxidans) , superpathway of sulfur metabolism (Desulfocapsa sulfoexigens) , superpathway of sulfide oxidation (Starkeya novella) , superpathway of sulfur oxidation (Acidianus ambivalens)

Variants: sulfite oxidation II , sulfite oxidation III , sulfite oxidation IV , sulfite oxidation V (SoeABC) , superpathway of thiosulfate metabolism (Desulfovibrio sulfodismutans)

Credits:
Created 04-Aug-2006 by Caspi R , SRI International
Revised 25-Feb-2014 by Caspi R , SRI International


References

Bagchi05: Bagchi A, Ghosh TC (2005). "A structural study towards the understanding of the interactions of SoxY, SoxZ, and SoxB, leading to the oxidation of sulfur anions via the novel global sulfur oxidizing (sox) operon." Biochem Biophys Res Commun 335(2);609-15. PMID: 16084835

Dahl13: Dahl C, Franz B, Hensen D, Kesselheim A, Zigann R (2013). "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(Pt 12);2626-38. PMID: 24030319

Friedrich00: Friedrich CG, Quentmeier A, Bardischewsky F, Rother D, Kraft R, Kostka S, Prinz H (2000). "Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17." J Bacteriol 182(17);4677-87. PMID: 10940005

Friedrich01: Friedrich CG, Rother D, Bardischewsky F, Quentmeier A, Fischer J (2001). "Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism?." Appl Environ Microbiol 67(7);2873-82. PMID: 11425697

Kappler00: Kappler U, Bennett B, Rethmeier J, Schwarz G, Deutzmann R, McEwan AG, Dahl C (2000). "Sulfite:Cytochrome c oxidoreductase from Thiobacillus novellus. Purification, characterization, and molecular biology of a heterodimeric member of the sulfite oxidase family." J Biol Chem 275(18);13202-12. PMID: 10788424

Kappler01: Kappler U, Dahl C (2001). "Enzymology and molecular biology of prokaryotic sulfite oxidation." FEMS Microbiol Lett 203(1);1-9. PMID: 11557133

Kappler05: Kappler U, Bailey S (2005). "Molecular basis of intramolecular electron transfer in sulfite-oxidizing enzymes is revealed by high resolution structure of a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit." J Biol Chem 280(26);24999-5007. PMID: 15863498

Lu84: Lu, W.P., Kelly, D.P. (1984). "Properties and role of sulphite:cytochrome c oxidoreductase purified from Thiobacillus versutus (A2)." J. Gen. Microbiol. 130(7):1683-1692.

Nelson95: Nelson, D.C., Hagen, K.D. (1995). "Physiology and biochemistry of symbiotic and free-living chemoautotrophic sulfur bacteria." Am. Zool. 35: 91-101.

Pukall99: Pukall R, Buntefuss D, Fruhling A, Rohde M, Kroppenstedt RM, Burghardt J, Lebaron P, Bernard L, Stackebrandt E (1999). "Sulfitobacter mediterraneus sp. nov., a new sulfite-oxidizing member of the alpha-Proteobacteria." Int J Syst Bacteriol 49 Pt 2;513-9. PMID: 10319472

Quentmeier01: Quentmeier A, Friedrich CG (2001). "The cysteine residue of the SoxY protein as the active site of protein-bound sulfur oxidation of Paracoccus pantotrophus GB17." FEBS Lett 503(2-3);168-72. PMID: 11513876

Quentmeier03: Quentmeier A, Hellwig P, Bardischewsky F, Grelle G, Kraft R, Friedrich CG (2003). "Sulfur oxidation in Paracoccus pantotrophus: interaction of the sulfur-binding protein SoxYZ with the dimanganese SoxB protein." Biochem Biophys Res Commun 312(4);1011-8. PMID: 14651972

Sorokin95: Sorokin, D.Y. (1995). "Sulfitobacter pontiacus gen. nov., sp. nov. - a new heterotrophic bacterium from the Black Sea, specialized on sulfite oxidation." Mikrobiologiya 64:354-365.

Yamanaka81: Yamanaka, T., Yoshioka, T., Kimura, K. (1981). "Purification of sulphite cytocrome c reductase of Thiobacillus novellus and reconstitution of its sulphite oxidase system with the purified constituents." Plant and Cell Physiol.,22(4):631-622.

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Ambler91: Ambler RP (1991). "Sequence variability in bacterial cytochromes c." Biochim Biophys Acta 1058(1);42-7. PMID: 1646017

Frederiksen03: Frederiksen TM, Finster K (2003). "Sulfite-oxido-reductase is involved in the oxidation of sulfite in Desulfocapsa sulfoexigens during disproportionation of thiosulfate and elemental sulfur." Biodegradation 14(3);189-98. PMID: 12889609

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Lyric70: Lyric RM, Suzuki I (1970). "Enzymes involved in the metabolism of thiosulfate by Thiobacillus thioparus. I. Survey of enzymes and properties of sulfite: cytochrome c oxidoreductase." Can J Biochem 48(3);334-43. PMID: 5438321

Nakamura95: Nakamura, K., Yoshikawa, H., Okubo, S., Kurosawa, H., Amano, Y. (1995). "Purification and properties of membrane-bound sulfite dehydrogenase from Thiobacillus thiooxidans." JCM 7814. Biosci. Biotechnol. Biochem. 59: 11-15.

Suzuki94a: Suzuki, I. (1994). "Sulfite:cytochrome c oxidoreductase of Thiobacilli." Methods Enzymol. 243(32):447-454.

Toghrol83: Toghrol F, Southerland WM (1983). "Purification of Thiobacillus novellus sulfite oxidase. Evidence for the presence of heme and molybdenum." J Biol Chem 258(11);6762-6. PMID: 6853504

Zimmermann99: Zimmermann P, Laska S, Kletzin A (1999). "Two modes of sulfite oxidation in the extremely thermophilic and acidophilic archaeon acidianus ambivalens." Arch Microbiol 172(2);76-82. PMID: 10415168


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sat Dec 20, 2014, BIOCYC14B.