› 3exh

X-ray diffraction
2.44Å resolution

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

Released:
DOI: 10.2210/pdb3exh/pdb
PDB entry 3exh coloured by chain, front view.
PDB entry 3exh coloured by chain, side view.
PDB entry 3exh 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-140173 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial Chains: A, E
Molecule details ›
Chains: A, E
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: B, D, F, H
Molecule details ›
Chains: B, D, F, H
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:
Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial Chains: C, G
Molecule details ›
Chains: C, G
Length: 382 amino acids
Theoretical weight: 42.63 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

Ligands and Environments


Cofactor: Ligand TPP 4 x TPP
3 bound ligands:
Ligand MN 4 x MN
Ligand K 4 x K
Ligand GOL 5 x GOL
1 modified residue:
Ligand SEP 2 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-D
Spacegroup: C2
Unit cell:
a: 257.064Å b: 115.612Å c: 127.592Å
α: 90° β: 113.64° γ: 90°
R-values:
R R work R free
0.167 0.165 0.211
Expression system: Escherichia coli

Quick links

Citations

14 review citations

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

3 mentions without citation

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