Succinate---CoA ligase (ADP-forming)

 

Succinyl-CoA synthetase (SCS) catalyses the reversible interchange of ADP, succinyl-CoA and inorganic phosphate with ATP succinate and CoA via a phosphorylated histidine intermediate. The enzyme has two subunit types with the catalysis occurring in an alpha/beta dimer. The alpha subunit is thought to bind CoA, and holds the phosphorylated His residue. It has been proposed that the beta sub unit confers nucleotide specificity.

 

Reference Protein and Structure

Sequences
P0AGE9 UniProt (6.2.1.5)
P0A836 UniProt (6.2.1.5) IPR005810 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1cqj - CRYSTAL STRUCTURE OF DEPHOSPHORYLATED E. COLI SUCCINYL-COA SYNTHETASE (2.9 Å) PDBe PDBsum 1cqj
Catalytic CATH Domains
3.40.50.261 CATHdb 3.30.470.20 CATHdb (see all for 1cqj)
Click To Show Structure

Enzyme Reaction (EC:6.2.1.5)

coenzyme A(4-)
CHEBI:57287ChEBI
+
succinate(2-)
CHEBI:30031ChEBI
+
ATP(4-)
CHEBI:30616ChEBI
→
ADP(3-)
CHEBI:456216ChEBI
+
hydrogenphosphate
CHEBI:43474ChEBI
+
succinyl-CoA(5-)
CHEBI:57292ChEBI
Alternative enzyme names: A-SCS, A-STK (adenin nucleotide-linked succinate thiokinase), STK, Succinate thiokinase, Succinic thiokinase, Succinyl coenzyme A synthetase, Succinyl coenzyme A synthetase (adenosine diphosphate-forming), Succinyl-CoA synthetase, Succinyl-CoA synthetase (ADP-forming),

Enzyme Mechanism

Introduction

The epsilon N atom of His 246 acts as a nucleophile towards the phosphoryl moiety of the nucleotide substrate (either ATP or GTP). The phosphorylated residue now acts as a phosphate donor to the succinate substrate, forming a non-covalently bound succinyl phosphate. The activated carbonyl, with a phospho-ester leaving group is activated towards nucleophilic attack by CoA, forming the succinyl-CoA product and phosphate.

Catalytic Residues Roles

UniProt PDB* (1cqj)
His247 His246A Acts as a nucleophile towards the nucleoside substrate, accepting a phosphate which is then donated to the succinate substrate, activating it towards attack by the bound CoA. Hydrogen bonding between the delta N and the residues Glu197* and Glu208 ensure the epsilon N is unprotonated, enhancing its nucleophilicity. covalent catalysis, electrostatic stabiliser
Tyr109 Tyr109B The residue hydrogen bonds to Glu197(B), ensuring it is correctly aligned to interact with the phosphorylating His 246. electrostatic stabiliser, steric role
Glu209, Glu197 Glu208A, Glu197B The residue hydrogen bonds with the phosphorylating His 246, influencing its pKa and ensuring the nucleophilic nitrogen is not protonated. modifies pKa, 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

References

  1. Fraser ME et al. (2002), Biochemistry, 41, 537-546. Two Glutamate Residues, Glu 208α and Glu 197β, Are Crucial for Phosphorylation and Dephosphorylation of the Active-Site Histidine Residue in Succinyl-CoA Synthetase†. DOI:10.1021/bi011518y. PMID:11781092.
  2. Hidber E et al. (2007), Acta Crystallogr D Biol Crystallogr, 63, 876-884. Participation of Cys123α ofEscherichia colisuccinyl-CoA synthetase in catalysis. DOI:10.1107/s0907444907029319. PMID:17642514.
  3. Joyce MA et al. (2000), Biochemistry, 39, 17-25. ADP-Binding Site ofEscherichia coliSuccinyl-CoA Synthetase Revealed by X-ray Crystallography†,‡. DOI:10.1021/bi991696f. PMID:10625475.

Step 1.

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Catalytic Residues Roles

Residue Roles
His246A electrostatic stabiliser
Glu208A electrostatic stabiliser
Glu197B electrostatic stabiliser
Tyr109B electrostatic stabiliser
His246A covalent catalysis
Glu208A modifies pKa
Glu197B modifies pKa
Tyr109B steric role

Chemical Components

Step 1.

Contributors

James W. Murray, Craig Porter, Gemma L. Holliday