› 1umc

X-ray diffraction
2.4Å resolution

branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methylpentanoate

Released:
DOI: 10.2210/pdb1umc/pdb
PDB entry 1umc coloured by chain, front view.
PDB entry 1umc coloured by chain, side view.
PDB entry 1umc coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
Ligand-induced conformational changes and a reaction intermediate in branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8, as revealed by X-ray crystallography.
Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N
J Mol Biol 337 1011-33 (2004)
PMID: 15033367

Function and Biology Details

Reaction catalysed: 
3-methyl-2-oxobutanoate + [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine = [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] S-(2-methylpropanoyl)dihydrolipoyllysine + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178208 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
2-oxoisovalerate dehydrogenase subunit alpha Chains: A, C
Molecule details ›
Chains: A, C
Length: 367 amino acids
Theoretical weight: 41.51 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SLR4 (Residues: 1-367; Coverage: 100%)
Gene name: TTHA0229
Sequence domains: Dehydrogenase E1 component
Structure domains: Rossmann fold
2-oxoisovalerate dehydrogenase subunit beta Chains: B, D
Molecule details ›
Chains: B, D
Length: 324 amino acids
Theoretical weight: 35.18 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SLR3 (Residues: 1-324; Coverage: 100%)
Gene name: TTHA0230
Sequence domains:
Structure domains:

Ligands and Environments


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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44B2
Spacegroup: C2221
Unit cell:
a: 127.197Å b: 247.216Å c: 137.557Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.172 0.206
Expression system: Escherichia coli

Quick links

Citations

20 citation in other articles

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