Function and Biology

Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, post-decarboxylation intermediate from pyruvate (2-hydroxyethyl-ThDP)

Source organism: Mycobacterium smegmatis
Biochemical function: oxoglutarate dehydrogenase (succinyl-transferring) activity
Biological process: oxidation-reduction process
Cellular component: not assigned

EC 1.2.4.2: Oxoglutarate dehydrogenase (succinyl-transferring)

Reaction catalysed:
2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO(2).
Comments:
  • It is a component of the multienzyme 2-oxoglutarate dehydrogenase complex in which multiple copies of it are bound to a core of molecules of EC 2.3.1.61, which also binds multiple copies of EC 1.8.1.4.
  • It does not act on free lipoamide or lipoyllysine, but only on the lipoyllysine residue in EC 2.3.1.61.
Systematic name:
2-oxoglutarate:[dihydrolipoyllysine-residue succinyltransferase]-lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-succinylating)
Alternative Name(s):
  • 2-ketoglutarate dehydrogenase
  • 2-oxoglutarate dehydrogenase
  • 2-oxoglutarate: lipoate oxidoreductase
  • 2-oxoglutarate:lipoamide 2-oxidoreductase (decarboxylating and acceptor-succinylating)
  • Alpha-ketoglutarate dehydrogenase
  • Alpha-ketoglutaric acid dehydrogenase
  • Alpha-ketoglutaric dehydrogenase
  • Alpha-oxoglutarate dehydrogenase
  • AKGDH
  • OGDC
  • Ketoglutaric dehydrogenase
  • Oxoglutarate decarboxylase
  • Oxoglutarate dehydrogenase
  • Oxoglutarate dehydrogenase (lipoamide)

EC 4.1.1.71: 2-oxoglutarate decarboxylase

Reaction catalysed:
2-oxoglutarate = succinate semialdehyde + CO(2).
Comments:
  • Highly specific.
Systematic name:
2-oxoglutarate carboxy-lyase (succinate-semialdehyde-forming)
Alternative Name(s):
  • Alpha-ketoglutarate decarboxylase
  • Alpha-ketoglutaric decarboxylase
  • Oxoglutarate decarboxylase
  • Pre-2-oxoglutarate decarboxylase
  • 2-oxoglutarate carboxy-lyase

EC 2.2.1.5: 2-hydroxy-3-oxoadipate synthase

Reaction catalysed:
2-oxoglutarate + glyoxylate = 2-hydroxy-3-oxoadipate + CO(2).
Comments:
  • The product decarboxylates to 5-hydroxy-4-oxopentanoate.
  • The enzyme can decarboxylate 2-oxoglutarate.
  • Acetaldehyde can replace glyoxylate.
  • Formerly EC 4.1.3.15.
Systematic name:
2-oxoglutarate:glyoxylate succinaldehydetransferase (decarboxylating)
Alternative Name(s):
  • 2-hydroxy-3-oxoadipate glyoxylate-lyase (carboxylating)
  • Alpha-ketoglutaric-glyoxylic carboligase
  • Oxoglutarate:glyoxylate carboligase
  • 2-hydroxy-3-oxoadipate synthetase
  • Oxoglutarate: glyoxylate carboligase

EC 2.3.1.61: Dihydrolipoyllysine-residue succinyltransferase

Reaction catalysed:
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)- (S-succinyldihydrolipoyl)lysine.
Comments:
  • A multimer (24-mer) of this enzyme forms the core of the multienzyme complex, and binds tightly both EC 1.2.4.2 and EC 1.8.1.4.
  • The lipoyl group of this enzyme is reductively succinylated by EC 1.2.4.2, and the only observed direction catalyzed by EC 2.3.1.61 is that where this succinyl group is passed to coenzyme A.
Systematic name:
Succinyl-CoA:enzyme-N(6)-(dihydrolipoyl)lysine S-succinyltransferase
Alternative Name(s):
  • 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

Sequence families

Pfam Protein families (Pfam)
PF02779
Domain description: Transketolase, pyrimidine binding domain
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
1 copy of Pfam domain PF02779 (Transketolase, pyrimidine binding domain) in Multifunctional 2-oxoglutarate metabolism enzyme in PDB 3zhv.

PF16870
Domain description: 2-oxoglutarate dehydrogenase C-terminal
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
1 copy of Pfam domain PF16870 (2-oxoglutarate dehydrogenase C-terminal) in Multifunctional 2-oxoglutarate metabolism enzyme in PDB 3zhv.

PF00676
Domain description: Dehydrogenase E1 component
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
1 copy of Pfam domain PF00676 (Dehydrogenase E1 component) in Multifunctional 2-oxoglutarate metabolism enzyme in PDB 3zhv.

InterPro InterPro annotations
IPR011603
Domain description: 2-oxoglutarate dehydrogenase E1 component
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
IPR029061
Domain description: Thiamin diphosphate-binding fold
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
IPR001017
Domain description: Dehydrogenase, E1 component
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
IPR005475
Domain description: Transketolase-like, pyrimidine-binding domain
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
IPR031717
Domain description: Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme

Structure domains

CATH CATH domains
3.40.50.970
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: Rossmann fold
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
1 copy of CATH domain 3.40.50.970 (Rossmann fold) in Multifunctional 2-oxoglutarate metabolism enzyme in PDB 3zhv.
1.10.287.1150
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Helix Hairpins
Homology: TPP helical domain
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
1 copy of CATH domain 1.10.287.1150 (Helix Hairpins) in Multifunctional 2-oxoglutarate metabolism enzyme in PDB 3zhv.