3dva

X-ray diffraction
2.35Å resolution

Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex

Released:

Function and Biology Details

Reactions catalysed:
Pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO(2)
Acetyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-acetyldihydrolipoyl)lysine
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-146012 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Pyruvate dehydrogenase E1 component subunit alpha Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 369 amino acids
Theoretical weight: 41.48 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P21873 (Residues: 1-369; Coverage: 100%)
Gene name: pdhA
Sequence domains: Dehydrogenase E1 component
Structure domains: Rossmann fold
Pyruvate dehydrogenase E1 component subunit beta Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 325 amino acids
Theoretical weight: 35.5 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P21874 (Residues: 1-325; Coverage: 100%)
Gene name: pdhB
Sequence domains:
Structure domains:
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex Chains: I, J
Molecule details ›
Chains: I, J
Length: 428 amino acids
Theoretical weight: 46.39 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P11961 (Residues: 1-428; Coverage: 100%)
Gene name: pdhC
Sequence domains:
Structure domains: E3-binding domain

Ligands and Environments


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

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P21
Unit cell:
a: 68.673Å b: 232.294Å c: 91.936Å
α: 90° β: 91.2° γ: 90°
R-values:
R R work R free
0.192 0.19 0.247
Expression system: Escherichia coli