› 2w93

X-ray diffraction
1.6Å resolution

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide

Released:
DOI: 10.2210/pdb2w93/pdb
PDB entry 2w93 coloured by chain, front view.
PDB entry 2w93 coloured by chain, side view.
PDB entry 2w93 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Allosteric Activation of Pyruvate Decarboxylases. A Never-Ending Story.
Konig S, Spinka M, Kutter S
J Mol Catal B Enzym 61 100- (2014)

Function and Biology Details

Reactions catalysed: 
Phenylpyruvate = phenylacetaldehyde + CO(2)
(3S)-3-methyl-2-oxopentanoate = 2-methylbutanal + CO(2)
3-(indol-3-yl)pyruvate = 2-(indol-3-yl)acetaldehyde + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138889 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyruvate decarboxylase isozyme 1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 563 amino acids
Theoretical weight: 61.57 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P06169 (Residues: 1-563; Coverage: 100%)
Gene names: L2104, PDC1, YLR044C
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand TPP 4 x TPP
2 bound ligands:
Ligand MG 4 x MG
Ligand PY0 8 x PY0
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X12
Spacegroup: P1
Unit cell:
a: 73.05Å b: 79.22Å c: 109.09Å
α: 89.23° β: 73.32° γ: 62.43°
R-values:
R R work R free
0.181 0.181 0.213
Expression system: Escherichia coli

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