Succinate dehydrogenase (ubiquinone)

 

succinate dehydrogenase is a flavoprotein complex containing iron-sulfur centres. The enzyme is found in the inner mitochondrial membrane in eukaryotes and the plasma membrane of many aerobic or facultative bacteria. It catalyses succinate oxidation in the citric acid cycle and transfers the electrons to quinones in the membrane, thus constituting a part of the aerobic respiratory chain (known as complex II). In vivo the enzyme uses the quinone found in the organism - eukaryotic enzymes utilize ubiquinone, bacterial enzymes utilise ubiquinone or menaquinone, and archaebacterial enzymes from the Sulfolobus genus use caldariellaquinone.

 

Reference Protein and Structure

Sequence
Q9YHT1 UniProt (1.3.5.1) IPR011281 (Sequence Homologues) (PDB Homologues)
Biological species
Gallus gallus (Chicken) Uniprot
PDB
1yq4 - Avian respiratory complex ii with 3-nitropropionate and ubiquinone (2.33 Å) PDBe PDBsum 1yq4
Catalytic CATH Domains
3.50.50.60 CATHdb 3.90.700.10 CATHdb (see all for 1yq4)
Cofactors
Fadh2(2-) (1), Di-mu-sulfido-diiron(2+) (1), Tetra-mu3-sulfido-tetrairon (1), Tri-mu-sulfido-mu3-sulfido-triiron(0) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:1.3.5.1)

fumarate(2-)
CHEBI:29806ChEBI
+
ubiquinol
CHEBI:17976ChEBI
→
ubiquinones
CHEBI:16389ChEBI
+
succinate(2-)
CHEBI:30031ChEBI
Alternative enzyme names: Complex II, Succinate dehydrogenase (ubiquinone), Succinate dehydrogenase complex, Succinic dehydrogenase, SDH, Succinate:ubiquinone oxidoreductase,

Enzyme Mechanism

Introduction

Ubiquinol acts as a two electron donor to the FAD cofactor, forming anionic FADH. The FADH N5 acts as a hydride donor to the polarised double bond in fumarate. A proton is simultaneously abstracted from Arg297 to saturate the double bond, forming succinate. The catalytic acid/base is reprotonated by a solvent molecule.

Catalytic Residues Roles

UniProt PDB* (1yq4)
Gln295, Glu310 Gln251A, Glu266A Help activate the Arg297 to act as a general acid/base. hydrogen bond acceptor, electrostatic stabiliser, steric role
Arg341 Arg297A Acts as a general acid/base. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
His297, His408, Arg452, Leu307, Phe174 His253A, His364A, Arg408A, Leu263A, Phe130A The presence of residues which hydrogen bond to the two carboxylate groups of fumarate, and of bulky, non-polar residues imposes a twisted conformation within the substrate. This increases the ground state energy towards that of the transition state, while also aligning the double bond between the hydride donating FAD and proton donating Arg297 hydrogen bond donor, steric role, electrostatic stabiliser
*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, electron transfer, cofactor used, overall reactant used, overall product formed, inferred reaction step, hydride transfer, bimolecular nucleophilic addition, unimolecular elimination by the conjugate base, bond polarisation, rate-determining step, native state of enzyme regenerated

References

  1. Huang LS et al. (2006), J Biol Chem, 281, 5965-5972. 3-Nitropropionic Acid Is a Suicide Inhibitor of Mitochondrial Respiration That, upon Oxidation by Complex II, Forms a Covalent Adduct with a Catalytic Base Arginine in the Active Site of the Enzyme. DOI:10.1074/jbc.m511270200. PMID:16371358.
  2. Oyedotun KS et al. (2007), Biochim Biophys Acta, 1767, 1436-1445. The Saccharomyces cerevisiae succinate dehydrogenase does not require heme for ubiquinone reduction. DOI:10.1016/j.bbabio.2007.09.008. PMID:18028869.
  3. Zhang J et al. (2006), Proc Natl Acad Sci U S A, 103, 16212-16217. Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool. DOI:10.1073/pnas.0604567103. PMID:17050691.
  4. Horsefield R et al. (2006), J Biol Chem, 281, 7309-7316. Structural and Computational Analysis of the Quinone-binding Site of Complex II (Succinate-Ubiquinone Oxidoreductase). DOI:10.1074/jbc.m508173200. PMID:16407191.
  5. Mowat CG et al. (2001), Biochemistry, 40, 12292-12298. Kinetic and Crystallographic Analysis of the Key Active Site Acid/Base Arginine in a Soluble Fumarate Reductase†. DOI:10.1021/bi011360h. PMID:11591148.
  6. Taylor P et al. (1999), Nat Struct Biol, 6, 1108-1112. Structural and mechanistic mapping of a unique fumarate reductase. DOI:10.1038/70045. PMID:10581550.

Step 1.

Ubiquinol acts as a two electron donor to the FAD cofactor, forming anionic FADH.

The electrons donated by the biological reducing agent ubiquinol tunnel from the ubiquinol binding site, through the iron-sulfur clusters to the active site [PMI:16371358]. In the absence of ubiquinol, the 3Fe4S centre is left with a net positive charge [PMID:17050691].

For the related enzyme fumarate reductase, studies in E. Coli have identified residues which are thought to enhance the redox activity of ubiquinone by hydrogen bonding to the C1 carbonyl. group While they have not been shown to act as bases, the residues are conserved, including within the gallus gallus succinate dehydrogenase described here, as Trp157B and Ser39C, and could therefore be involved in activating the ubiquinol co-substrate [PMID:16407191].

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His364A hydrogen bond donor
His253A hydrogen bond donor
Gln251A hydrogen bond acceptor
Arg297A hydrogen bond donor
Arg408A hydrogen bond donor
Glu266A hydrogen bond acceptor

Chemical Components

proton transfer, electron transfer, cofactor used, overall reactant used, overall product formed, inferred reaction step

Step 2. The FADH N5 acts as a hydride donor to the polarised double bond in fumarate. A proton is simultaneously abstracted from Arg297 to saturate the double bond, forming succinate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His364A hydrogen bond donor, steric role, electrostatic stabiliser
His253A hydrogen bond donor, steric role, electrostatic stabiliser
Gln251A electrostatic stabiliser, hydrogen bond acceptor, steric role
Arg297A hydrogen bond donor
Arg408A hydrogen bond donor, electrostatic stabiliser, steric role
Leu263A steric role
Glu266A electrostatic stabiliser, hydrogen bond acceptor, steric role
Phe130A steric role
Arg297A proton donor

Chemical Components

hydride transfer, proton transfer, ingold: bimolecular nucleophilic addition, ingold: unimolecular elimination by the conjugate base, bond polarisation, cofactor used, overall product formed, overall reactant used, rate-determining step

Step 3. The catalytic acid/base is reprotonated by a solvent molecule.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His364A hydrogen bond donor
His253A hydrogen bond donor
Gln251A hydrogen bond acceptor
Arg297A hydrogen bond donor, hydrogen bond acceptor
Arg408A hydrogen bond donor
Glu266A hydrogen bond acceptor
Arg297A proton acceptor

Chemical Components

proton transfer, native state of enzyme regenerated, inferred reaction step
Download: Image, Marvin File

Step 1.

Ubiquinol acts as a two electron donor to the FAD cofactor, forming anionic FADH.

The electrons donated by the biological reducing agent ubiquinol tunnel from the ubiquinol binding site, through the iron-sulfur clusters to the active site [PMI:16371358]. In the absence of ubiquinol, the 3Fe4S centre is left with a net positive charge [PMID:17050691].

For the related enzyme fumarate reductase, studies in E. Coli have identified residues which are thought to enhance the redox activity of ubiquinone by hydrogen bonding to the C1 carbonyl. group While they have not been shown to act as bases, the residues are conserved, including within the gallus gallus succinate dehydrogenase described here, as Trp157B and Ser39C, and could therefore be involved in activating the ubiquinol co-substrate [PMID:16407191].

Step 2. The FADH N5 acts as a hydride donor to the polarised double bond in fumarate. A proton is simultaneously abstracted from Arg297 to saturate the double bond, forming succinate.

Step 3. The catalytic acid/base is reprotonated by a solvent molecule.

Products.

Contributors

Sophie T. Williams, Gemma L. Holliday