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

Source organism: Mycolicibacterium smegmatis
Biochemical function: thiamine pyrophosphate binding
Biological process: tricarboxylic acid cycle
Cellular component: not assigned

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EC 4.1.1.71: 2-oxoglutarate decarboxylase

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

EC 2.3.1.61: Dihydrolipoyllysine-residue succinyltransferase

Reaction catalysed:
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
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
  • Enzyme-dihydrolipoyllysine:succinyl-CoA S-succinyltransferase
  • Lipoate succinyltransferase
  • Lipoate succinyltransferase (Escherichia coli)
  • Lipoic transsuccinylase
  • Lipoyl transsuccinylase
  • Succinyl-CoA:dihydrolipoamide S-succinyltransferase
  • Succinyl-CoA:dihydrolipoate S-succinyltransferase
  • Succinyl-CoA:enzyme-6-N-(dihydrolipoyl)lysine S-succinyltransferase

EC 2.2.1.5: 2-hydroxy-3-oxoadipate synthase

Reaction catalysed:
2-oxoglutarate + glyoxylate = 2-hydroxy-3-oxoadipate + CO(2)
Systematic name:
2-oxoglutarate:glyoxylate succinaldehydetransferase (decarboxylating)
Alternative Name(s):
  • 2-hydroxy-3-oxoadipate glyoxylate-lyase (carboxylating)
  • 2-hydroxy-3-oxoadipate synthetase
  • Alpha-ketoglutaric-glyoxylic carboligase
  • Oxoglutarate: glyoxylate carboligase
  • Oxoglutarate:glyoxylate carboligase

EC 1.2.4.2: Oxoglutarate dehydrogenase (succinyl-transferring)

Reaction catalysed:
2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO(2)
Systematic name:
2-oxoglutarate:[dihydrolipoyllysine-residue succinyltransferase]-lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-succinylating)
Alternative Name(s):
  • 2-ketoglutarate dehydrogenase
  • 2-oxoglutarate dehydrogenase
  • 2-oxoglutarate:lipoamide 2-oxidoreductase (decarboxylating and acceptor-succinylating)
  • 2-oxoglutarate:lipoate oxidoreductase
  • AKGDH
  • Alpha-ketoglutarate dehydrogenase
  • Alpha-ketoglutaric acid dehydrogenase
  • Alpha-ketoglutaric dehydrogenase
  • Alpha-oxoglutarate dehydrogenase
  • Ketoglutaric dehydrogenase
  • OGDC
  • Oxoglutarate decarboxylase
  • Oxoglutarate dehydrogenase
  • Oxoglutarate dehydrogenase (lipoamide)

GO terms

Sequence families

Pfam Protein families (Pfam)
PF16870
Domain description: 2-oxoglutarate dehydrogenase C-terminal
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
The deposited structure of PDB entry 3zhv contains 4 copies of Pfam domain PF16870 (2-oxoglutarate dehydrogenase C-terminal) in Multifunctional 2-oxoglutarate metabolism enzyme. Showing 1 copy in chain A.

PF02779
Domain description: Transketolase, pyrimidine binding domain
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
The deposited structure of PDB entry 3zhv contains 4 copies of Pfam domain PF02779 (Transketolase, pyrimidine binding domain) in Multifunctional 2-oxoglutarate metabolism enzyme. Showing 1 copy in chain A.

PF00676
Domain description: Dehydrogenase E1 component
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
The deposited structure of PDB entry 3zhv contains 4 copies of Pfam domain PF00676 (Dehydrogenase E1 component) in Multifunctional 2-oxoglutarate metabolism enzyme. Showing 1 copy in chain A.

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
IPR031717
Domain description: Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
IPR042179
Domain description: Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
IPR005475
Domain description: Transketolase-like, pyrimidine-binding domain
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
IPR001017
Domain description: Dehydrogenase, E1 component
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme

Structure domains

CATH CATH domains
3.40.50.11610
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
The deposited structure of PDB entry 3zhv contains 4 copies of CATH domain 3.40.50.11610 (Rossmann fold) in Multifunctional 2-oxoglutarate metabolism enzyme. Showing 1 copy in chain A.
3.40.50.12470
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: Rossmann fold
Occurring in:
  1. Multifunctional 2-oxoglutarate metabolism enzyme
The deposited structure of PDB entry 3zhv contains 4 copies of CATH domain 3.40.50.12470 (Rossmann fold) in Multifunctional 2-oxoglutarate metabolism enzyme. Showing 1 copy in chain A.
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
The deposited structure of PDB entry 3zhv contains 4 copies of CATH domain 3.40.50.970 (Rossmann fold) in Multifunctional 2-oxoglutarate metabolism enzyme. Showing 1 copy in chain A.
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
The deposited structure of PDB entry 3zhv contains 4 copies of CATH domain 1.10.287.1150 (Helix Hairpins) in Multifunctional 2-oxoglutarate metabolism enzyme. Showing 1 copy in chain A.

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