› 3rnm

X-ray diffraction
2.4Å resolution

The crystal structure of the subunit binding of human dihydrolipoamide transacylase (E2b) bound to human dihydrolipoamide dehydrogenase (E3)

Released:
DOI: 10.2210/pdb3rnm/pdb
PDB entry 3rnm coloured by chain, front view.
PDB entry 3rnm coloured by chain, side view.
PDB entry 3rnm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and thermodynamic basis for weak interactions between dihydrolipoamide dehydrogenase and subunit-binding domain of the branched-chain alpha-ketoacid dehydrogenase complex.
Brautigam CA, Wynn RM, Chuang JL, Naik MT, Young BB, Huang TH, Chuang DT
J Biol Chem 286 23476-88 (2011)
PMID: 21543315

Function and Biology Details

Reactions catalysed: 
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH
2-methylpropanoyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-(2-methylpropanoyl)dihydrolipoyl)lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140718 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Dihydrolipoyl dehydrogenase, mitochondrial Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 495 amino acids
Theoretical weight: 52.65 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:
Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial Chains: E, F
Molecule details ›
Chains: E, F
Length: 58 amino acids
Theoretical weight: 6.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P11182 (Residues: 165-213; Coverage: 10%)
Gene names: BCATE2, BCKDHE2, DBT
Sequence domains: e3 binding domain
Structure domains: E3-binding domain

Ligands and Environments


Cofactor: Ligand FAD 4 x FAD
2 bound ligands:
Ligand BME 4 x BME
Ligand NHE 4 x NHE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 84.136Å b: 112.308Å c: 122.545Å
α: 90° β: 91.4° γ: 90°
R-values:
R R work R free
0.184 0.181 0.24
Expression system: Escherichia coli

Quick links

Citations

5 review citations

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

4 mentions without citation

Insight to the interaction of the dihydrolipoamide acetyltransferase (E2) core with the peripheral components in the Escherichia coli pyruvate dehydrogenase complex via multifaceted structural approaches.
Chandrasekhar et al. (2013)
3 more