› 3exg

X-ray diffraction
3.01Å resolution

Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex

Released:
DOI: 10.2210/pdb3exg/pdb
PDB entry 3exg coloured by chain, front view.
PDB entry 3exg coloured by chain, side view.
PDB entry 3exg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops.
Kato M, Wynn RM, Chuang JL, Tso SC, Machius M, Li J, Chuang DT
Structure 16 1849-59 (2008)
PMID: 19081061

Function and Biology Details

Reaction catalysed: 
Pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140174 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial Chains: 1, 3, 5, A, C, E, G, I, K, M, O, Q, S, U, W, Y
Molecule details ›
Chains: 1, 3, 5, A, C, E, G, I, K, M, O, Q, S, U, W, Y
Length: 382 amino acids
Theoretical weight: 42.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P08559 (Residues: 30-390; Coverage: 93%)
Gene names: PDHA1, PHE1A
Sequence domains: Dehydrogenase E1 component
Structure domains: Rossmann fold
Pyruvate dehydrogenase E1 component subunit beta, mitochondrial Chains: 2, 4, 6, B, D, F, H, J, L, N, P, R, T, V, X, Z
Molecule details ›
Chains: 2, 4, 6, B, D, F, H, J, L, N, P, R, T, V, X, Z
Length: 329 amino acids
Theoretical weight: 35.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P11177 (Residues: 31-359; Coverage: 92%)
Gene names: PDHB, PHE1B
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand K 16 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P1
Unit cell:
a: 119.278Å b: 128.29Å c: 228.41Å
α: 90.14° β: 90.05° γ: 90.02°
R-values:
R R work R free
0.192 0.189 0.253
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Regulation of pyruvate metabolism and human disease.
Gray et al. (2014)
13 more

1 mention without citation

Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops.
Kato et al. (2008)