› 8p5r

X-ray diffraction
4.56Å resolution

Crystal structure of full-length, homohexameric 2-oxoglutarate dehydrogenase KGD from Mycobacterium smegmatis in complex with GarA

Released:
DOI: 10.2210/pdb8p5r/pdb
PDB entry 8p5r coloured by chain, front view.
PDB entry 8p5r coloured by chain, side view.
PDB entry 8p5r coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Primary publication:
High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.
Yang L, Wagner T, Mechaly A, Boyko A, Bruch EM, Megrian D, Gubellini F, Alzari PM, Bellinzoni M
OpenAccess logo Nat Commun 14 4851 (2023)
PMID: 37563123

Function and Biology Details

Reactions catalysed: 
2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO(2)
2-oxoglutarate + glyoxylate = 2-hydroxy-3-oxoadipate + CO(2)
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
2-oxoglutarate = succinate semialdehyde + CO(2)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-226626 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Multifunctional 2-oxoglutarate metabolism enzyme Chains: A, B, C, D, E, F, N, O, P, Q
Molecule details ›
Chains: A, B, C, D, E, F, N, O, P, Q
Length: 1250 amino acids
Theoretical weight: 138.55 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0R2B1 (Residues: 2-1227; Coverage: 100%)
Gene names: MSMEG_5049, MSMEI_4922, kgd, sucA
Sequence domains:
Glycogen accumulation regulator GarA Chains: G, H, I, J, K, L
Molecule details ›
Chains: G, H, I, J, K, L
Length: 158 amino acids
Theoretical weight: 16.6 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0QYG2 (Residues: 1-158; Coverage: 100%)
Gene names: MSMEG_3647, MSMEI_3561, garA
Sequence domains: FHA domain

Ligands and Environments


Cofactor: Ligand TPP 6 x TPP
2 bound ligands:
Ligand MG 6 x MG
Ligand CA 8 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P65
Unit cell:
a: 325.75Å b: 325.75Å c: 396.944Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.2 0.198 0.229
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

Cellular localization of the hybrid pyruvate/2-oxoglutarate dehydrogenase complex in the actinobacterium Corynebacterium glutamicum.
Sundermeyer et al. (2023)

1 mention without citation

High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.
Yang et al. (2023)