Sulfide:quinone reductase

Sulfide:quinone reductase (EC 1.8.5.4) is an enzyme with systematic name sulfide:quinone oxidoreductase.[1][2][3][4][5][6] This enzyme catalyses the following chemical reaction

n HS− + n quinone polysulfide + n quinol
Sulfide:quinone reductase
Identifiers
EC number1.8.5.4
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum

Sulfide:quinone reductase contains FAD. Ubiquinone, plastoquinone or menaquinone can act as acceptor in different species.

The Enzyme Commission number for sulfide:quinone oxidoreductase is 1.8.5.’. The Enzyme Commission (EC) number indicates that the protein is an oxidoreductase (indicated by 1). The oxidoreductase reacts with a sulfur molecule in this case sulfide to donate electrons (indicated by 8). The donated electrons are accepted by a quinone (indicated by 5). [7]There are multiple sulfide:quinone oxidoreductases that are found in bacteria, archaea, and eukaryotes, but the function highlighted in the EC numbers 1.8.5.’. are all constant except for the final digit with is 4 in bacteria and 8 in eukaryotic mitochondria. [8][7]

Crystalline structure

The SQR in Aquifex aeolicus is composed of three subunits with a negatively charged hydrophilic side exposed to the periplasmic space and a hydrophobic region that integrates into the cell’s plasma membrane. The active site of the protein is composed of an FAD cofactor covalently linked by a thioether bond to the enzyme. On the si side of the FAD the sulfide reacts and donates its electrons to FAD, while the re side of FAD is connected to a disulfide bridge and donates electrons to the quinone. 2, 3 The quinone is surrounded by Phe-385 and Ile-346. Both amino acids are located in the hydrophobic region of the plasma membrane and are conserved among all sulfide: quinone oxidoreductases. [9]


Reaction Pathway

In Aquifex aeolicus, sulfide:quinone reductase is an integral monotopic protein, so the protein penetrates into the hydrophobic region of the plasma membrane. The SQR reaction takes place in two half reactions, sulfide oxidation and quinone reduction. The active site of SQR is composed of a region that interacts with the periplasmic space and sulfide connected by a FAD cofactor and a trisulfide bridge to a quinone. FAD receives two electrons from sulfide and transfers the electrons one at time to the quinone. The amino acids surrounding the quinone are all hydrophobic. Also, there is a highly conserved region of uncharged amino acids, phenylalanine and isoleucine, that surround the benzene ring of the quinone.[10]

Sulfide:quinone oxidoreductase is a member of the flavoprotein disulfide reductase (FDR) superfamily. FDRs are typically characterized as being dimeric or two subunit proteins, but sulfide quinone oxidoreductase is a trimeric protein. The main purpose of SQR is to detoxify sulfide. Sulfide is a toxic chemical that inhibits enzymatic reactions, especially those with metal cofactors. Most notably, sulfide inhibits cytochrome oxidase found in the electron transport chain. SQR oxidizes sulfide and produces non-toxic products. [11]

Where does sulfide:quinone oxidoreductase fit into metabolism?

As mentioned previously, sulfide:quinone oxidoreductase is an integral protein that enters the plasma membrane (or inner mitochondrial membrane) of cells. [12] The plasma membrane is the site of the electron transport chain for respiration. [13] The electron transport chain depends on two factors 1) ability of a membrane to store an ion gradient  2) the ability of an organism to pump hydrogen ions against a gradient (from low to high concentration). [12] Sulfide:quinone oxidoreductase enhances the formation of an ion gradient by donating two electrons to the quinone.[13] Once the electrons are in the quinone of SQR, they are transported to the quinone pool.[12] The quinone pool is located inside the hydrophobic region of the plasma membrane and plays a role in transporting hydrogen ions to the periplasm. From the quinone pool, electrons travel to cytochrome c oxidase where oxygen is waiting as the final electron acceptor.[12][13]

The aforementioned pathway seems rather foreign until you realize that electrons from carbon sources react in a similar fashion to those in sulfide. There are two main differences between the carbon pathway and the sulfur pathway. The first being that sulfur in this case sulfide skips glycolysis and the tricarboxylic acid cycle (TCA), while the carbon pathway requires both cycles to store electrons in NADH. [10] [14]The second difference is that electrons from sulfide are donated to SQR, while the electrons from NADH are donated to the NADH:quinone oxidoreductase. [14] In both cases, the electrons are shuttled to the quinone pool, then to cytochrome c oxidase where the final electron acceptor is waiting. [14] The reason why sulfide:quinone oxidoreductase is such a conserved protein is because SQR enhances energy conservation and synthesis ATP when carbon sources are depleted, but the main incentive to conserve SQR is to detoxify sulfide.[10][14]

References
  1. Arieli B, Shahak Y, Taglicht D, Hauska G, Padan E (February 1994). "Purification and characterization of sulfide-quinone reductase, a novel enzyme driving anoxygenic photosynthesis in Oscillatoria limnetica". The Journal of Biological Chemistry. 269 (8): 5705–11. PMID 8119908.
  2. Reinartz M, Tschäpe J, Brüser T, Trüper HG, Dahl C (July 1998). "Sulfide oxidation in the phototrophic sulfur bacterium Chromatium vinosum". Archives of Microbiology. 170 (1): 59–68. doi:10.1007/s002030050615. PMID 9639604.
  3. Nübel T, Klughammer C, Huber R, Hauska G, Schütz M (April 2000). "Sulfide:quinone oxidoreductase in membranes of the hyperthermophilic bacterium Aquifex aeolicus (VF5)". Archives of Microbiology. 173 (4): 233–44. doi:10.1007/s002030000135. PMID 10816041.
  4. Brito JA, Sousa FL, Stelter M, Bandeiras TM, Vonrhein C, Teixeira M, Pereira MM, Archer M (June 2009). "Structural and functional insights into sulfide:quinone oxidoreductase". Biochemistry. 48 (24): 5613–22. doi:10.1021/bi9003827. PMID 19438211.
  5. Cherney MM, Zhang Y, Solomonson M, Weiner JH, James MN (April 2010). "Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification". Journal of Molecular Biology. 398 (2): 292–305. doi:10.1016/j.jmb.2010.03.018. PMID 20303979.
  6. Marcia M, Langer JD, Parcej D, Vogel V, Peng G, Michel H (November 2010). "Characterizing a monotopic membrane enzyme. Biochemical, enzymatic and crystallization studies on Aquifex aeolicus sulfide:quinone oxidoreductase". Biochimica et Biophysica Acta (BBA) - Biomembranes. 1798 (11): 2114–23. doi:10.1016/j.bbamem.2010.07.033. PMID 20691146.
  7. "BRENDA - Information on EC 1.8.5.4 - bacterial sulfide:quinone reductase". www.brenda-enzymes.org. Retrieved 2020-10-17.
  8. "BRENDA - Information on EC 1.8.5.8 - eukaryotic sulfide quinone oxidoreductase". www.brenda-enzymes.org. Retrieved 2020-10-17.
  9. Brito, José A.; Sousa, Filipa L.; Stelter, Meike; Bandeiras, Tiago M.; Vonrhein, Clemens; Teixeira, Miguel; Pereira, Manuela M.; Archer, Margarida (2009-06-23). "Structural and Functional Insights into Sulfide:Quinone Oxidoreductase,". Biochemistry. 48 (24): 5613–5622. doi:10.1021/bi9003827. ISSN 0006-2960.
  10. Marcia, Marco; Ermler, Ulrich; Peng, Guohong; Michel, Hartmut (2009-06-16). "The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration". Proceedings of the National Academy of Sciences. 106 (24): 9625–9630. doi:10.1073/pnas.0904165106. ISSN 0027-8424. PMID 19487671.
  11. "Characterizing a monotopic membrane enzyme. Biochemical, enzymatic and crystallization studies on Aquifex aeolicus sulfide:quinone oxidoreductase". Biochimica et Biophysica Acta (BBA) - Biomembranes. 1798 (11): 2114–2123. 2010-11-01. doi:10.1016/j.bbamem.2010.07.033. ISSN 0005-2736.
  12. van der Stel, Anne-Xander; Wösten, Marc M. S. M. (2019-07-30). "Regulation of Respiratory Pathways in Campylobacterota: A Review". Frontiers in Microbiology. 10. doi:10.3389/fmicb.2019.01719. ISSN 1664-302X. PMC 6682613. PMID 31417516.
  13. Nübel, Tobias; Klughammer, Christof; Huber, Robert; Hauska, Günter; Schütz, Michael (2000-04-01). "Sulfide:quinone oxidoreductase in membranes of the hyperthermophilic bacterium Aquifex aeolicus (VF5)". Archives of Microbiology. 173 (4): 233–244. doi:10.1007/s002030000135. ISSN 1432-072X.
  14. Kracke, Frauke; Vassilev, Igor; Krömer, Jens O. (2015-06-11). "Microbial electron transport and energy conservation – the foundation for optimizing bioelectrochemical systems". Frontiers in Microbiology. 6. doi:10.3389/fmicb.2015.00575. ISSN 1664-302X. PMC 4463002. PMID 26124754.
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