Sulfide:quinone oxidoreductase

 

Catalyses the oxidation of sulfides, such as hydrogen sulfide, with the help of a quinone to form sulfur globules. Consecutive reaction cycles lead to the accumulation of a polysulfide product on the active site Cys residues; these products are released when they exceed a critical length, typically as cyclooctasulfur. This is an important step in anoxygenic bacterial photosynthesis.

 

Reference Protein and Structure

Sequence
Q7ZAG8 UniProt (1.8.5.4) IPR023753 (Sequence Homologues) (PDB Homologues)
Biological species
Acidianus ambivalens (Archaea) Uniprot
PDB
3h8i - The first X-ray structure of a sulfide:quinone oxidoreductase: Insights into sulfide oxidation mechanism (2.65 Å) PDBe PDBsum 3h8i
Catalytic CATH Domains
3.50.50.60 CATHdb (see all for 3h8i)
Cofactors
Fadh2(2-) (1)
Click To Show Structure

Enzyme Reaction (EC:1.8.5.4)

1,4-benzoquinones
CHEBI:132124ChEBI
+
hydron
CHEBI:15378ChEBI
+
hydrosulfide
CHEBI:29919ChEBI
→
sulfur atom
CHEBI:26833ChEBI
+
hydroquinones
CHEBI:24646ChEBI
Alternative enzyme names: Sqr (gene name), Sulfide:quinone reductase,

Enzyme Mechanism

Introduction

This enzyme has the highest activity with caldariella quinone and decylubiquinone, and lower activity with naphtoquinones. The substrate hydrogen sulfide is deprotonated by Asp353, activating the sulfur as a nucleophile towards the protein disulfide bridge. The anionic Cys178A attacks the C4 position of FAD, initiating protonation of the N5 position. The Cys350 dithiolate acts as a nucleophile towards the enzyme cofactor adduct, forming a three centre sulfur intermediate and the reduced form of FAD. Ubiquinone, the physiological electron acceptor accepts a hydride from reduced FAD, regenerating the cofactor for the next round of sulfide oxidiation. Only the first four steps are shown, but this enzyme catalyses several successive rounds of catalysis, until the polysulfide product on the active site Cys residues exceeds a critical length.

Catalytic Residues Roles

UniProt PDB* (3h8i)
Cys178, Cys350 Cys178A, Cys350A In the ground state of the protein, Cys350 and Cys178 are covalently attached in a disulfide bond. During the course of the reaction both residues act via covalent catalysis. Cys178 becomes attached to the FAD cofactor and is finally added back onto the Cys350, which during the course of the reaction accepts the substrate sulfur atom. covalently attached, nucleofuge, nucleophile, activator, electrofuge, electrophile
Asp215, Asp353 Asp215A, Asp353A Forms a proton relay chain that ultimately deprotonates the substrate hydrogen sulfide; both residues act as a general acid/base. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, activator
Cys129 Cys129A Forms a covalent bond with the FAD cofactor, enhancing its redox potential. covalently attached, activator
Lys386 Lys386A Helps stabilise the negative charge in the active site. This residue possibly acts as a general acid/base in the regeneration of the FAD cofactor stage of the reaction. activator
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, bimolecular nucleophilic substitution, overall reactant used, enzyme-substrate complex formation, bimolecular nucleophilic addition, cofactor used, intermediate formation, enzyme-substrate complex cleavage, hydride transfer, overall product formed, native state of cofactor regenerated

References

  1. Brito JA et al. (2009), Biochemistry, 48, 5613-5622. Structural and Functional Insights into Sulfide:Quinone Oxidoreductase,. DOI:10.1021/bi9003827. PMID:19438211.
  2. Cherney MM et al. (2010), J Mol Biol, 398, 292-305. Crystal Structure of Sulfide:Quinone Oxidoreductase from Acidithiobacillus ferrooxidans: Insights into Sulfidotrophic Respiration and Detoxification. DOI:10.1016/j.jmb.2010.03.018. PMID:20303979.
  3. Marcia M et al. (2009), Proc Natl Acad Sci U S A, 106, 9625-9630. The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration. DOI:10.1073/pnas.0904165106. PMID:19487671.

Step 1. The substrate hydrogen sulfide is deprotonated by Asp353, activating the sulfur as a nucleophile towards the protein disulfide bridge. The sulfide oxidation occurs on the re face of the FAD cofactor [PMID:19438211].

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp353A activator, hydrogen bond acceptor
Asp215A activator
Cys350A activator
Cys178A activator
Cys129A covalently attached
Asp353A proton donor, proton acceptor
Cys350A electrophile
Cys178A nucleofuge
Cys350A electrofuge
Asp215A proton acceptor
Asp353A proton relay

Chemical Components

proton transfer, ingold: bimolecular nucleophilic substitution, overall reactant used, enzyme-substrate complex formation

Step 2. The anionic Cys178A attacks the C4 position of FAD, initiating protonation of the N5 position.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp215A hydrogen bond donor
Cys350A activator, covalently attached
Cys178A activator
Asp353A hydrogen bond donor, hydrogen bond acceptor
Cys129A covalently attached
Cys178A nucleophile

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer, cofactor used, intermediate formation

Step 3. The Cys350 dithiolate acts as a nucleophile towards the enzyme cofactor adduct, forming a three centre sulfur intermediate and the reduced form of FAD. The steric bulk brought about by the presence of an elongated sulfur chain attached Cys350A directs the anionic Cys178A towards nucleophilic attack at Cys350A, reforming the active site disulfide bridge.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp215A activator
Cys350A activator, covalently attached
Cys178A activator, covalently attached
Asp353A activator, hydrogen bond acceptor, hydrogen bond donor
Cys129A activator, covalently attached
Asp353A proton acceptor
Asp215A proton donor
Asp353A proton relay
Cys178A electrofuge
Asp353A proton donor
Cys178A electrophile

Chemical Components

ingold: bimolecular nucleophilic substitution, proton transfer, cofactor used, enzyme-substrate complex cleavage, intermediate formation

Step 4. Ubiquinone, the physiological electron acceptor accepts a hydride from reduced FAD, regenerating the cofactor for the next round of sulfide oxidiation. While potential proton donors to the ubiquinone identified in Acidithiobacillus ferrooxidans are conserved in the Acidianus ambivalens homolouge listed here, no general base to the FAD cofactor has been suggested in either case [PMID:20303979].

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp215A hydrogen bond acceptor
Cys350A covalently attached
Cys178A covalently attached
Asp353A hydrogen bond donor
Lys386A activator
Cys129A covalently attached

Chemical Components

hydride transfer, proton transfer, overall reactant used, overall product formed, native state of cofactor regenerated
Download: Image, Marvin File

Step 1. The substrate hydrogen sulfide is deprotonated by Asp353, activating the sulfur as a nucleophile towards the protein disulfide bridge. The sulfide oxidation occurs on the re face of the FAD cofactor [PMID:19438211].

Step 2. The anionic Cys178A attacks the C4 position of FAD, initiating protonation of the N5 position.

Step 3. The Cys350 dithiolate acts as a nucleophile towards the enzyme cofactor adduct, forming a three centre sulfur intermediate and the reduced form of FAD. The steric bulk brought about by the presence of an elongated sulfur chain attached Cys350A directs the anionic Cys178A towards nucleophilic attack at Cys350A, reforming the active site disulfide bridge.

Step 4. Ubiquinone, the physiological electron acceptor accepts a hydride from reduced FAD, regenerating the cofactor for the next round of sulfide oxidiation. While potential proton donors to the ubiquinone identified in Acidithiobacillus ferrooxidans are conserved in the Acidianus ambivalens homolouge listed here, no general base to the FAD cofactor has been suggested in either case [PMID:20303979].

Products.

Contributors

Sophie T. Williams, Gemma L. Holliday, Amelia Brasnett