› 8p5u

Electron Microscopy
2.17Å resolution

Single particle cryo-EM structure of homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum with Coenzyme A bound to the E2o domain

Released:
DOI: 10.2210/pdb8p5u/pdb
PDB entry 8p5u coloured by chain, front view.
PDB entry 8p5u coloured by chain, side view.
PDB entry 8p5u coloured by chain, top view.
Source organism: Corynebacterium glutamicum ATCC 13032
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
Related structures: EMD-17453

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-569674 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-oxoglutarate dehydrogenase E1/E2 component Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 1223 amino acids
Theoretical weight: 134.97 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8NRC3 (Residues: 1-1221; Coverage: 100%)
Gene names: Cgl1129, cg1280, odhA
Sequence domains:

Ligands and Environments


Cofactor: Ligand TPP 6 x TPP

Cofactor: Ligand COA 6 x COA

Cofactor: Ligand ACO 6 x ACO
1 bound ligand:
Ligand MG 6 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.17Å
Relevant EMDB volumes: EMD-17453
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)