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3zhs

X-ray diffraction
2.1Å resolution

Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, first post-decarboxylation intermediate from alpha-ketoglutarate

Released:
Model geometry
Fit model/data

Function and Biology Details

Reactions catalysed:
[N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H(+) = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CO2., N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H(+) = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CO2., N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H(+) = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CO2., N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H(+) = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CO2.]
[glyoxylate + 2-oxoglutarate + H(+) = 2-hydroxy-3-oxoadipate + CO2., glyoxylate + 2-oxoglutarate + H(+) = 2-hydroxy-3-oxoadipate + CO2., glyoxylate + 2-oxoglutarate + H(+) = 2-hydroxy-3-oxoadipate + CO2., glyoxylate + 2-oxoglutarate + H(+) = 2-hydroxy-3-oxoadipate + CO2.]
[N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + succinyl-CoA = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CoA., N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + succinyl-CoA = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CoA., N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + succinyl-CoA = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CoA., N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + succinyl-CoA = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CoA.]
[2-oxoglutarate + H(+) = succinate semialdehyde + CO2., 2-oxoglutarate + H(+) = succinate semialdehyde + CO2., 2-oxoglutarate + H(+) = succinate semialdehyde + CO2., 2-oxoglutarate + H(+) = succinate semialdehyde + CO2.]
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
PDBe Complex ID:
PDB-CPX-106428 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Multifunctional 2-oxoglutarate metabolism enzyme Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 868 amino acids
Theoretical weight: 97.17 KDa
Source organism: Mycolicibacterium smegmatis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0R2B1 (Residues: 361-1227; Coverage: 71%)
Gene names: MSMEG_5049, MSMEI_4922, kgd, sucA
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand TD6 4 x TD6
2 bound ligands:
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P1
Unit cell:
a: 80.846Å b: 83.713Å c: 159.94Å
α: 99.89° β: 99.03° γ: 100.2°
R-values:
R R work R free
0.202 0.2 0.228
Expression system: Escherichia coli BL21(DE3)