› 1zy8

X-ray diffraction
2.59Å resolution

The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide dehydrogenase-binding protein (didomain) subcomplex of human pyruvate dehydrogenase complex.

Released:
DOI: 10.2210/pdb1zy8/pdb
PDB entry 1zy8 coloured by chain, ensemble of 2 models, front view.
PDB entry 1zy8 coloured by chain, ensemble of 2 models, side view.
PDB entry 1zy8 coloured by chain, ensemble of 2 models, top view.
Source organism: Homo sapiens
Primary publication:
How dihydrolipoamide dehydrogenase-binding protein binds dihydrolipoamide dehydrogenase in the human pyruvate dehydrogenase complex.
Ciszak EM, Makal A, Hong YS, Vettaikkorumakankauv AK, Korotchkina LG, Patel MS
J Biol Chem 281 648-55 (2006)
PMID: 16263718

Function and Biology Details

Reaction catalysed: 
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126249 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Dihydrolipoyl dehydrogenase, mitochondrial Chains: A, B, C, D, E, F, G, H, I, J
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J
Length: 474 amino acids
Theoretical weight: 50.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09622 (Residues: 36-509; Coverage: 93%)
Gene names: DLD, GCSL, LAD, PHE3
Sequence domains:
Structure domains:
Pyruvate dehydrogenase protein X component, mitochondrial Chains: K, L, M, N, O
Molecule details ›
Chains: K, L, M, N, O
Length: 229 amino acids
Theoretical weight: 24.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O00330 (Residues: 54-274; Coverage: 44%)
Gene names: PDHX, PDX1
Sequence domains:
Structure domains: E3-binding domain

Ligands and Environments


Cofactor: Ligand FAD 10 x FAD
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 168.79Å b: 186.91Å c: 217.54Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.275 0.208 0.276
Expression systems:
  • Escherichia coli
  • Escherichia coli BL21

Quick links

Citations

11 review citations

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

8 mentions without citation

The pyruvate dehydrogenase complexes: structure-based function and regulation.
Patel et al. (2014)
7 more