› 6cer

X-ray diffraction
2.69Å resolution

Human pyruvate dehydrogenase complex E1 component V138M mutation

Released:
DOI: 10.2210/pdb6cer/pdb
PDB entry 6cer coloured by chain, front view.
PDB entry 6cer coloured by chain, side view.
PDB entry 6cer coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Pyruvate dehydrogenase complex deficiency is linked to regulatory loop disorder in the αV138M variant of human pyruvate dehydrogenase.
Whitley MJ, Arjunan P, Nemeria NS, Korotchkina LG, Park YH, Patel MS, Jordan F, Furey W
J Biol Chem 293 13204-13213 (2018)
PMID: 29970614

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: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 365 amino acids
Theoretical weight: 40.75 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: 331 amino acids
Theoretical weight: 36.09 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


Cofactor: Ligand TPP 4 x TPP
1 bound ligand:
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P21
Unit cell:
a: 121.76Å b: 123.919Å c: 128.279Å
α: 90° β: 118.12° γ: 90°
R-values:
R R work R free
0.194 0.192 0.234
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Unstructured regions of large enzymatic complexes control the availability of metabolites with signaling functions.
Skalidis et al. (2020)
5 other articles

1 mention without citation

Pyruvate dehydrogenase complex deficiency is linked to regulatory loop disorder in the αV138M variant of human pyruvate dehydrogenase.
Whitley et al. (2018)