Dihydrolipoyllysine-residue succinyltransferase

 

The alpha-ketoglutarate dehydrogenase complex (KGDC), also known as the oxoglutarate dehydrogenase complex (OGDC), is composed of multiple copies of three enzymes: oxoglutarate dehydrogenase (E1o), dihydrolipoamide succinyltransferase (E2o), and dihydrolipoamide dehydrogenase (E3o). The E2o component of the KGDC is a modular protein that is composed of one lipoyl domain at the N-terminus, followed by an E1o- and/or E3o-binding domain, and then by a carboxyl terminal catalytic domain. Although the catalytic domain forms trimers, the enzyme forms the octahedral inner core of the multienzyme complex, an aggregation of 24 subunits arranged with 432 point group symmetry. The substrate (dihydrolipoamide) is covalently bound to a specific lysine residue in the lipoyl domain. The enzyme catalyses the transfer of a succinyl group from the S-succinyldihydrolipoyl moiety to coenzyme A.

 

Reference Protein and Structure

Sequence
P0AFG6 UniProt (2.3.1.61) IPR006255 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1c4t - CATALYTIC DOMAIN FROM TRIMERIC DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE (3.0 Å) PDBe PDBsum 1c4t
Catalytic CATH Domains
3.30.559.10 CATHdb (see all for 1c4t)
Click To Show Structure

Enzyme Reaction (EC:2.3.1.61)

N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysine(1-) residue
CHEBI:83120ChEBI
+
coenzyme A(4-)
CHEBI:57287ChEBI
→
succinyl-CoA(5-)
CHEBI:57292ChEBI
+
N(6)-[(R)-dihydrolipoyl]-L-lysine residue
CHEBI:83100ChEBI
Alternative enzyme names: Dihydrolipoamide S-succinyltransferase, Dihydrolipoamide succinyltransferase, Dihydrolipoic transsuccinylase, Dihydrolipolyl transsuccinylase, Dihydrolipoyl transsuccinylase, Lipoate succinyltransferase (Escherichia coli), Lipoic transsuccinylase, Lipoyl transsuccinylase, Succinyl-CoA:dihydrolipoamide S-succinyltransferase, Succinyl-CoA:dihydrolipoate S-succinyltransferase, Lipoate succinyltransferase, Enzyme-dihydrolipoyllysine:succinyl-CoA S-succinyltransferase, Succinyl-CoA:enzyme-6-N-(dihydrolipoyl)lysine S-succinyltransferase,

Enzyme Mechanism

Introduction

The first step is the deprotonation of the thiol group of coenzyme A by the active site residue His375. The activated thiolate attacks the carbonyl carbon of the succinylated dihydrolipoyl moiety to form a tetrahedral intermediate, which is stabilised by Thr323'. The collapse of the tetrahedral intermediate results in the succinylation of coenzyme A, and the protonation of the dihydrolipoyl moiety.

Catalytic Residues Roles

UniProt PDB* (1c4t)
Thr324 Thr323(152)C Thr323 stabilises the tetrahedral intermediate. electrostatic stabiliser, polar interaction
His376 His375(204)A His375 deprotonates the thiol group of coenzyme A to form the nucleophile thiolate. activator, proton acceptor, proton donor
*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, overall reactant used, bimolecular nucleophilic addition, intermediate formation, unimolecular elimination by the conjugate base, intermediate terminated, overall product formed, native state of enzyme regenerated

References

  1. Knapp JE et al. (2000), Protein Sci, 9, 37-48. Expression, purification, and structural analysis of the trimeric form of the catalytic domain of the Escherichia coli dihydrolipoamide succinyltransferase. DOI:10.1110/ps.9.1.37. PMID:10739245.
  2. Perham RN (2000), Annu Rev Biochem, 69, 961-1004. Swinging Arms and Swinging Domains in Multifunctional Enzymes: Catalytic Machines for Multistep Reactions. DOI:10.1146/annurev.biochem.69.1.961. PMID:10966480.
  3. Knapp JE et al. (1998), J Mol Biol, 280, 655-668. Crystal structure of the truncated cubic core component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex. DOI:10.1006/jmbi.1998.1924. PMID:9677295.

Step 1. His275 deprotonates the thiol group.

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Catalytic Residues Roles

Residue Roles
Thr323(152)C electrostatic stabiliser
His375(204)A activator
Thr323(152)C polar interaction
His375(204)A proton acceptor

Chemical Components

proton transfer, overall reactant used

Step 2. Activated thiolate performs a nucleophilic attack on the carbonyl carbon on the succinyl dihydrolipoyl moiety to form a tetrahedral intermediate stabilised by Thr323.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Thr323(152)C electrostatic stabiliser
Thr323(152)C polar interaction

Chemical Components

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

Step 3. Tetrahedral intermediate collapse which sees the succinyl group transferred to CoA.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Thr323(152)C electrostatic stabiliser, polar interaction

Chemical Components

ingold: unimolecular elimination by the conjugate base, intermediate terminated, overall product formed

Step 4. His375 protonates the dihydrolipoyl moiety.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His375(204)A proton donor

Chemical Components

proton transfer, overall product formed, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. His275 deprotonates the thiol group.

Step 2. Activated thiolate performs a nucleophilic attack on the carbonyl carbon on the succinyl dihydrolipoyl moiety to form a tetrahedral intermediate stabilised by Thr323.

Step 3. Tetrahedral intermediate collapse which sees the succinyl group transferred to CoA.

Step 4. His375 protonates the dihydrolipoyl moiety.

Products.

Contributors

Gemma L. Holliday, Morwenna Hall