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discounted EARLY registration ends Dec 31, 2014
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discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Enzyme: (SoxCD)2

Species: Paracoccus pantotrophus

Component of: Sox enzyme system (extended summary available)

Subunit composition of (SoxCD)2 = [(SoxC)(SoxD)]2
         SoxCD = (SoxC)(SoxD)

Summary:
Sulfur dehydrogenase, (SoxCD)2, is an essential part of the Sox enzyme system of the chemotrophic bacterium Paracoccus pantotrophus. (SoxCD)2 is an α2β2 complex composed of the molybdoprotein SoxC and the hybrid diheme c-type cytochrome SoxD

(SoxCD)2 is proposed to successively oxidize the outer sulfur atom bound to SoxY-S-thiocysteine, using three water molecules and forming SoxY-cyteine-S-sulfate. During the process, six-electrons are transferred to a cytochreome c [Bardischewsky05, Friedrich01].

Locations: periplasmic space

Molecular Weight of Multimer: 180 kD (experimental) [Bardischewsky05]

Gene-Reaction Schematic: ?

GO Terms:

Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space [Friedrich00]

Credits:
Created 31-Aug-2006 by Caspi R , SRI International


Enzymatic reaction of: SoxCD sulfane hydrogenase ((SoxCD)2)

a [SoxY protein]-S-thiocysteine + 6 an oxidized c-type cytochrome + 3 H2O <=> a [SoxY protein]-L-cysteine-S-sulfate + 6 a reduced c-type cytochrome + 7 H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

In Pathways: thiosulfate oxidation III (multienzyme complex)


Subunit of: Sox enzyme system

Synonyms: thiosulfate-oxidizing multi-enzyme system, TOMES

Species: Paracoccus pantotrophus

Subunit composition of Sox enzyme system = [(SoxX)(SoxA)][SoxB][([SoxC][SoxD])2][(SoxY)(SoxZ)]
         SoxXA = (SoxX)(SoxA) (extended summary available)
         (SoxCD)2 = ([SoxC][SoxD])2 (summary available)
                 SoxCD = (SoxC)(SoxD)
         SoxYZ = (SoxY)(SoxZ) (extended summary available)

Summary:
Paracoccus pantotrophus posseses a periplasmic enzyme complex known as the Sox enzyme system (for sulfur oxidation) that is able to oxidize thiosulfate to sulfate with no intermediates [Friedrich00].

The genes, soxXYZABCD, part of the sox gene cluster, encode 4 proteins which can be combined in vitro to reconstitute an active Sox enzyme complex. The four proteins encoded by these seven genes are SoxXA, SoxYZ, SoxB, and SoxCD. SoxXA is a heterodimeric c-type cytochrome; SoxYZ is a heterodimeric protein that binds thiosulfate covalently. SoxB is a monomer that contains two manganese atoms [Wodara97]. SoxCD is an α2β2 heterotetramer composed of two units each of SoxC, a molybdenum cofactor-containing subunit, and SoxD, a diheme c-type cytochrome [Quentmeier00].

An in vitro reconstituted Sox system mediates not only thiosulfate, but also sulfite-, S0-, and hydrogen sulfide-dependent cytochrome c reduction [Wodara97, Rother01]. Sulfite oxidation occurs as described in the following equation, and results in the transfer of only 2 electrons per mol substrate:

sulfite + H2O = sulfate + 2e- + 2H+

In addition, sulfite oxidation does not require the presence of the SoxCD protein.

Based on these results, a model has been proposed for the mechanism of the Sox system [Friedrich01]. According to this model, the first step is the SoxXA-mediated binding of thiosulfate or sulfite to a cysteine residue of SoxY. When thiosulfate binds, the resulting SoxY-thiocysteine-S-sulfate is then hydrolyzed by SoxB, liberating a sulfate, and forming a SoxY-S-thiocysteine. SoxCD would then successively oxidize the outer sulfur atom, using three water molecules and forming SoxY-cyteine-S-sulfate. Finally, the second sulfate group is hydrolyzed by SoxB, bringing the cysteine residue of SoxY to its initial condition.

Locations: periplasmic space

GO Terms:

Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space [Friedrich00]

Credits:
Created 10-Aug-1999 by Pellegrini-Toole A , Marine Biological Laboratory
Revised 31-Aug-2006 by Caspi R , SRI International


Enzymatic reaction of: Sox enzyme system

2 sulfate[in] + 11 H+[in] + 8 e- <=> thiosulfate[in] + 5 H2O[in]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.


Subunit of SoxCD: SoxC

Synonyms: sulfur dehydrogenase

Gene: soxC Accession Number: G-307 (MetaCyc)

Locations: periplasmic space

Molecular Weight: 47.339 kD (from nucleotide sequence)

Molecular Weight: 43.442 kD (experimental) [Bardischewsky05]

GO Terms:

Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space [Friedrich00]

Summary:
SoxC is one of the subunits of (SoxCD)2, an essential part of the Sox enzyme system of the chemotrophic bacterium Paracoccus pantotrophus.

The soxC gene encodes a 430-amino-acid polypeptide that includes a signal peptide of 40 amino acids with a RR motif present in periplasmic proteins. The mature soxC gene product exhibits high amino acid sequence similarity to the eukaryotic molybdoenzyme sulfite oxidase and to nitrate reductase [Wodara97].

(SoxCD)2 is proposed to successively oxidize the outer sulfur atom bound to SoxY-S-thiocysteine using three water molecules and forming SoxY-cyteine-S-sulfate. During the process, six-electrons are transferred to a cytochreome c [Bardischewsky05, Friedrich01].


Subunit of SoxCD: SoxD

Synonyms: cytochrome c

Gene: soxD Accession Number: G-306 (MetaCyc)

Locations: periplasmic space

Molecular Weight: 39.983 kD (from nucleotide sequence) [Wodara97]

Molecular Weight: 37.637 kD (experimental) [Bardischewsky05]

GO Terms:

Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space [Friedrich00]

Summary:
SoxD of Paracoccus pantotrophus is a periplasmic hybrid cytochrome of 384 amino acids with two heme domains. Both heme domains are linked by a proline-alanine-rich intervening sequence of about 35 amino acids [Wodara97]. SoxD is one of the subunits of (SoxCD)2, an essential part of the Sox enzyme system of the chemotrophic bacterium Paracoccus pantotrophus.

Amino acid sequence analysis identified the heme-1 domain of SoxD proteins to be specific for sulfur dehydrogenases and to contain a novel ProCysMetXaaAspCys motif. The heme-2 domain is related to various cytochromes c2[Bardischewsky05]

The heme-1 domain is crucial for catalytic activity, electron yield, and transfer of the electrons to the cytoplasmic membrane, while the heme-2 domain mediates the tetrameric structure of sulfur dehydrogenase [Bardischewsky05].


References

Bardischewsky05: Bardischewsky F, Quentmeier A, Rother D, Hellwig P, Kostka S, Friedrich CG (2005). "Sulfur dehydrogenase of Paracoccus pantotrophus: the heme-2 domain of the molybdoprotein cytochrome c complex is dispensable for catalytic activity." Biochemistry 44(18);7024-34. PMID: 15865447

Franz07: Franz B, Lichtenberg H, Hormes J, Modrow H, Dahl C, Prange A (2007). "Utilization of solid "elemental" sulfur by the phototrophic purple sulfur bacterium Allochromatium vinosum: a sulfur K-edge X-ray absorption spectroscopy study." Microbiology 153(Pt 4);1268-74. PMID: 17379736

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

Quentmeier00: Quentmeier A, Kraft R, Kostka S, Klockenkamper R, Friedrich CG (2000). "Characterization of a new type of sulfite dehydrogenase from Paracoccus pantotrophus GB17." Arch Microbiol 173(2);117-25. PMID: 10795683

Rother01: Rother D, Henrich HJ, Quentmeier A, Bardischewsky F, Friedrich CG (2001). "Novel genes of the sox gene cluster, mutagenesis of the flavoprotein SoxF, and evidence for a general sulfur-oxidizing system in Paracoccus pantotrophus GB17." J Bacteriol 183(15);4499-508. PMID: 11443084

Steudel00: Steudel, R. (2000). "The chemical sulfur cycle." Environmental Technologies to Treat Sulfur Pollution, pp. 1-31. Edited by P. N. L. Lens & L. Hulshof Pol. London: IWA Publishing.

Wodara97: Wodara C, Bardischewsky F, Friedrich CG (1997). "Cloning and characterization of sulfite dehydrogenase, two c-type cytochromes, and a flavoprotein of Paracoccus denitrificans GB17: essential role of sulfite dehydrogenase in lithotrophic sulfur oxidation." J Bacteriol 1997;179(16);5014-23. PMID: 9260941


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 Tue Nov 25, 2014, biocyc13.