Sulfite oxidase

 

Sulfite oxidase (SO) catalyses the terminal reaction in the oxidative degradation of the sulfur-containing amino acids cysteine and methionine specifically the oxidation of sulfite to sulfate by the transfer of an oxygen to the lone pair of electrons on the substrate. It is a member of the molybdopterin oxidoreductase family of proteins that contain a single pterin cofactor ligated to Mo(VI) and two oxo ligands. SO also contains a heme b molecule which is part of the electron transfer pathway from the molybdenum centre to the final electron acceptor (in this case ferrocytochrome c).

 

Reference Protein and Structure

Sequence
P07850 UniProt (1.8.3.1) IPR008335 (Sequence Homologues) (PDB Homologues)
Biological species
Gallus gallus (Chicken) Uniprot
PDB
1sox - SULFITE OXIDASE FROM CHICKEN LIVER (1.9 Å) PDBe PDBsum 1sox
Catalytic CATH Domains
3.90.420.10 CATHdb 3.10.120.10 CATHdb (see all for 1sox)
Cofactors
Heme b (1), Moo2-molybdopterin cofactor(2−) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:1.8.3.1)

sulfite
CHEBI:17359ChEBI
+
water
CHEBI:15377ChEBI
+
iron(3+)
CHEBI:29034ChEBI
→
sulfate
CHEBI:16189ChEBI
+
iron(2+)
CHEBI:29033ChEBI
+
hydron
CHEBI:15378ChEBI

Enzyme Mechanism

Introduction

This protein requires both Heme and a molybdenum (VI) centre to be catalytically active. The sulfite substrate initiates a nucleophilic attack on one of the oxo ligands of the Mo(VI) centre, reducing the Mo to +4. This forms the sulfate product, which is displaced from the active site by water. Deprotonation of the new water ligand initiates the transfer of a single electron from the Mo centre to heme and then to an external electron acceptor. This occurs twice to regenerate the oxo ligand and Mo(VI) centre.

Catalytic Residues Roles

UniProt PDB* (1sox)
Cys185 Cys185A Forms part of the Molybdenum binding site. metal ligand
His40, His65 His40A, His65A Forms part of the heme binding site as the axial ligands to the iron ion. Not shown in the reaction diagrams for clarity. metal ligand
Arg138 Arg138A Prevents formation of a blocked non-catalytic form of the enzyme. steric role
Tyr322 Tyr322A Acts as a general acid/base as part of a proton relay chain from bulk solvent to the active site. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
*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

bimolecular nucleophilic addition, overall reactant used, cofactor used, intermediate formation, bimolecular nucleophilic substitution, coordination to a metal ion, decoordination from a metal ion, overall product formed, electron transfer, proton transfer, proton relay, electron relay, native state of cofactor regenerated, intermediate terminated, native state of enzyme regenerated

References

  1. Feng C et al. (2003), J Biol Chem, 278, 2913-2920. Role of Conserved Tyrosine 343 in Intramolecular Electron Transfer in Human Sulfite Oxidase. DOI:10.1074/jbc.m210374200. PMID:12424234.
  2. Caldararu O et al. (2018), Sci Rep, 8, 4684-. QM/MM study of the reaction mechanism of sulfite oxidase. DOI:10.1038/s41598-018-22751-6. PMID:29549261.
  3. Davis AC et al. (2014), Metallomics, 6, 1664-1670. Kinetic results for mutations of conserved residues H304 and R309 of human sulfite oxidase point to mechanistic complexities. DOI:10.1039/c4mt00099d. PMID:24968320.
  4. van Severen MC et al. (2014), J Biol Inorg Chem, 19, 1165-1179. A quantum-mechanical study of the reaction mechanism of sulfite oxidase. DOI:10.1007/s00775-014-1172-z. PMID:24957901.
  5. Davis AC et al. (2013), Dalton Trans, 42, 3043-3049. Effects of mutating aromatic surface residues of the heme domain of human sulfite oxidase on its heme midpoint potential, intramolecular electron transfer, and steady-state kinetics. DOI:10.1039/c2dt31508d. PMID:22975842.
  6. Klein EL et al. (2012), Inorg Chem, 51, 1408-1418. Identity of the exchangeable sulfur-containing ligand at the Mo(V) center of R160Q human sulfite oxidase. DOI:10.1021/ic201643t. PMID:22225516.
  7. Astashkin AV et al. (2012), J Phys Chem B, 116, 1942-1950. Determination of the distance between the Mo(V) and Fe(III) heme centers of wild type human sulfite oxidase by pulsed EPR spectroscopy. DOI:10.1021/jp210578f. PMID:22229742.
  8. Enemark JH et al. (2011), Faraday Discuss, 148, 249-67; discussion 299. Implications for the mechanism of sulfite oxidizing enzymes from pulsed EPR spectroscopy and DFT calculations for "difficult" nuclei. PMID:21322488.
  9. Johnson-Winters K et al. (2010), Biochemistry, 49, 7242-7254. Elucidating the catalytic mechanism of sulfite oxidizing enzymes using structural, spectroscopic, and kinetic analyses. DOI:10.1021/bi1008485. PMID:20666399.
  10. Qiu JA et al. (2010), Biochemistry, 49, 3989-4000. The structures of the C185S and C185A mutants of sulfite oxidase reveal rearrangement of the active site. DOI:10.1021/bi1001954. PMID:20356030.
  11. Emesh S et al. (2009), Biochemistry, 48, 2156-2163. Intramolecular electron transfer in sulfite-oxidizing enzymes: elucidating the role of a conserved active site arginine. DOI:10.1021/bi801553q. PMID:19226119.
  12. Astashkin AV et al. (2008), J Am Chem Soc, 130, 8471-8480. Structural Studies of the Molybdenum Center of the Pathogenic R160Q Mutant of Human Sulfite Oxidase by Pulsed EPR Spectroscopy and17O and33S Labeling. DOI:10.1021/ja801406f. PMID:18529001.
  13. Raitsimring AM et al. (2008), Inorganica Chim Acta, 361, 941-946. Studies of the Mo(V) center of the Y343F mutant of human sulfite oxidase by variable frequency pulsed EPR spectroscopy. DOI:10.1016/j.ica.2007.05.023. PMID:18496596.
  14. Neumann M et al. (2008), FEBS J, 275, 5678-5689. Heavy metal ions inhibit molybdoenzyme activity by binding to the dithiolene moiety of molybdopterin in Escherichia coli. DOI:10.1111/j.1742-4658.2008.06694.x. PMID:18959753.
  15. Karakas E et al. (2005), J Biol Chem, 280, 33506-33515. Structural insights into sulfite oxidase deficiency. DOI:10.1074/jbc.M505035200. PMID:16048997.
  16. Wilson HL et al. (2004), J Biol Chem, 279, 15105-15113. The Role of Tyrosine 343 in Substrate Binding and Catalysis by Human Sulfite Oxidase. DOI:10.1074/jbc.m314288200. PMID:14729666.
  17. Feng C et al. (2003), Biochemistry, 42, 12235-12242. Essential Role of Conserved Arginine 160 in Intramolecular Electron Transfer in Human Sulfite Oxidase†. DOI:10.1021/bi0350194. PMID:14567685.
  18. Rudolph MJ et al. (2003), Acta Crystallogr D Biol Crystallogr, 59, 1183-1191. The 1.2 Å structure of the human sulfite oxidase cytochromeb5domain. DOI:10.1107/s0907444903009934. PMID:12832761.
  19. Kisker C et al. (1997), Annu Rev Biochem, 66, 233-267. MOLYBDENUM-COFACTOR–CONTAINING ENZYMES:Structure and Mechanism. DOI:10.1146/annurev.biochem.66.1.233. PMID:9242907.
  20. Kisker C et al. (1997), Cell, 91, 973-983. Molecular Basis of Sulfite Oxidase Deficiency from the Structure of Sulfite Oxidase. DOI:10.1016/s0092-8674(00)80488-2. PMID:9428520.

Step 1. Sulfite initiates a nucleophilic attack upon one of the oxo groups coordinated to the Mo(VI) centre in an addition reaction, resulting in a two electron reduction of the centre to Mo(IV). It seems very likely that only one of the two oxygen ligands is the catalytically labile oxygen, whereas the other oxygen cannot be attacked owing to steric hindrance in the active site of the enzyme [PMID:9242907].

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Catalytic Residues Roles

Residue Roles
Arg138A steric role
Cys185A metal ligand
His40A metal ligand
His65A metal ligand

Chemical Components

ingold: bimolecular nucleophilic addition, overall reactant used, cofactor used, intermediate formation

Step 2. Water displaces the sulfate as a ligand to the Mo(IV) centre.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Cys185A metal ligand
His40A metal ligand
His65A metal ligand

Chemical Components

ingold: bimolecular nucleophilic substitution, overall reactant used, coordination to a metal ion, decoordination from a metal ion, intermediate formation, overall product formed

Step 3. Water deprotonates Tyr322, which deprotonates the Mo-bound water causing a single electron to be transferred from the Mo(IV) centre to Haem and thence to ferricyrochrome C.

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Catalytic Residues Roles

Residue Roles
Tyr322A hydrogen bond acceptor, hydrogen bond donor, proton relay
Cys185A metal ligand
His40A metal ligand
His65A metal ligand
Tyr322A proton donor, proton acceptor

Chemical Components

electron transfer, proton transfer, overall reactant used, intermediate formation, overall product formed, proton relay, electron relay, cofactor used, native state of cofactor regenerated

Step 4. Water deprotonates Tyr322, which deprotonates the Mo-bound hydroxide causing a single electron to be transferred from the Mo(V) centre to Haem and thence to ferricyrochrome C and regenerating the cofactor.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr322A hydrogen bond acceptor, hydrogen bond donor, proton relay
Cys185A metal ligand
His40A metal ligand
His65A metal ligand
Tyr322A proton donor, proton acceptor

Chemical Components

electron transfer, proton transfer, overall reactant used, cofactor used, native state of cofactor regenerated, intermediate terminated, overall product formed, proton relay, electron relay, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Sulfite initiates a nucleophilic attack upon one of the oxo groups coordinated to the Mo(VI) centre in an addition reaction, resulting in a two electron reduction of the centre to Mo(IV). It seems very likely that only one of the two oxygen ligands is the catalytically labile oxygen, whereas the other oxygen cannot be attacked owing to steric hindrance in the active site of the enzyme [PMID:9242907].

Step 2. Water displaces the sulfate as a ligand to the Mo(IV) centre.

Step 3. Water deprotonates Tyr322, which deprotonates the Mo-bound water causing a single electron to be transferred from the Mo(IV) centre to Haem and thence to ferricyrochrome C.

Step 4. Water deprotonates Tyr322, which deprotonates the Mo-bound hydroxide causing a single electron to be transferred from the Mo(V) centre to Haem and thence to ferricyrochrome C and regenerating the cofactor.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Christian Drew, Craig Porter, Amelia Brasnett