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Literature summary for 4.1.1.1 extracted from

  • Balakrishnan, A.; Gao, Y.; Moorjani, P.; Nemeria, N.S.; Tittmann, K.; Jordan, F.
    Bifunctionality of the thiamin diphosphate cofactor: assignment of tautomeric/ionization states of the 4-aminopyrimidine ring when various intermediates occupy the active sites during the catalysis of yeast pyruvate decarboxylase (2012), J. Am. Chem. Soc., 134, 3873-3885.
    View publication on PubMedView publication on EuropePMC

Protein Variants

Protein Variants Comment Organism
C221E/C222A site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme Saccharomyces cerevisiae
D28A site-directed mutagenesis of the active site residue, the mutant shows reduced activity compared to the wild-type enzyme Saccharomyces cerevisiae
D28N site-directed mutagenesis of the active site residue, the mutant shows reduced activity compared to the wild-type enzyme Saccharomyces cerevisiae
E477Q site-directed mutagenesis of the active site residue, the mutant shows reduced activity compared to the wild-type enzyme Saccharomyces cerevisiae
E51A site-directed mutagenesis of the active site residue, the mutant shows reduced activity compared to the wild-type enzyme,and the mutant is no longer capable of forming a hydrogen bond with cofactor thiamine diphosphate Saccharomyces cerevisiae
E51D site-directed mutagenesis of the active site residue, the mutant is still capable of forming a hydrogen bond with cofactor thiamine diphosphate, albeit weaker, and shows reduced activity compared to the wild-type enzyme Saccharomyces cerevisiae
E51N site-directed mutagenesis of the active site residue, the mutant is still capable of forming a hydrogen bond with cofactor thiamine diphosphate, albeit weaker, and shows reduced activity compared to the wild-type enzyme Saccharomyces cerevisiae
E51Q site-directed mutagenesis of the active site residue, the mutant is still capable of forming a hydrogen bond with cofactor thiamine diphosphate, albeit weaker, and shows reduced activity compared to the wild-type enzyme Saccharomyces cerevisiae
E91D site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme Saccharomyces cerevisiae

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information transient state, pre-steady-state, and steady-state complex formations of substrate/intermediate and thiamine diphosphate cofactor and of kinetics of wild-type and mutant enzymes, overview Saccharomyces cerevisiae
0.72
-
pyruvate per subunit, pH 6.0, 30°C, mutant E51A Saccharomyces cerevisiae
1.1
-
pyruvate per subunit, pH 6.0, 30°C, wild-type enzyme Saccharomyces cerevisiae
1.47
-
pyruvate per subunit, pH 6.0, 30°C, mutant C221E/C222A Saccharomyces cerevisiae
1.66
-
pyruvate per subunit, pH 6.0, 30°C, mutant D28A Saccharomyces cerevisiae
1.79
-
pyruvate per subunit, pH 6.0, 30°C, mutant E91D Saccharomyces cerevisiae
3.02
-
pyruvate per subunit, pH 6.0, 30°C, mutant E477Q Saccharomyces cerevisiae
14.9
-
pyruvate per subunit, pH 6.0, 30°C, mutant E51Q Saccharomyces cerevisiae
23.1
-
pyruvate per subunit, pH 6.0, 30°C, mutant E51D Saccharomyces cerevisiae
31.5
-
pyruvate per subunit, pH 6.0, 30°C, mutant E51N Saccharomyces cerevisiae

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Saccharomyces cerevisiae

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
pyruvate Saccharomyces cerevisiae
-
acetaldehyde + CO2
-
?

Organism

Organism UniProt Comment Textmining
Saccharomyces cerevisiae
-
-
-

Reaction

Reaction Comment Organism Reaction ID
a 2-oxo carboxylate = an aldehyde + CO2 mechanism of catalytic cycle of yeast pyruvate decarboxylase, overview. Pyruvate and analogues induce active site asymmetry in the wild-type yeast enzyme and mutant variants. The rare 1',4'-iminopyrimidine thiamine diphosphate tautomer participates in formation of thiamine diphosphate-bound intermediates. Propionylphosphinate also binds at the regulatory site and its binding is reflected by catalytic events at the active site 20 A away. The yeast enzyme stabilizes an electrostatic model for the 4'-aminopyrimidinium ionization state, an important contribution of the protein to catalysis Saccharomyces cerevisiae

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
pyruvate
-
Saccharomyces cerevisiae acetaldehyde + CO2
-
?

Subunits

Subunits Comment Organism
dimer or tetramer a tight dimer, known as the functional dimer, is the minimal catalytically active unit, two of these functional dimers assemble into a loose tetramer in the quaternary structure Saccharomyces cerevisiae

Synonyms

Synonyms Comment Organism
yeast pyruvate decarboxylase
-
Saccharomyces cerevisiae
YPDC
-
Saccharomyces cerevisiae

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30
-
assay at Saccharomyces cerevisiae

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.0024
-
pyruvate per subunit, pH 6.0, 30°C, mutant E51N Saccharomyces cerevisiae
0.0043
-
pyruvate per subunit, pH 6.0, 30°C, mutant E51A Saccharomyces cerevisiae
0.035
-
pyruvate per subunit, pH 6.0, 30°C, mutant E51Q Saccharomyces cerevisiae
0.049
-
pyruvate per subunit, pH 6.0, 30°C, mutant E51D Saccharomyces cerevisiae
0.066
-
pyruvate per subunit, pH 6.0, 30°C, mutant D28A Saccharomyces cerevisiae
0.086
-
pyruvate per subunit, pH 6.0, 30°C, mutant E477Q Saccharomyces cerevisiae
11
-
pyruvate per subunit, pH 6.0, 30°C, mutant E91D Saccharomyces cerevisiae
18.2
-
pyruvate per subunit, pH 6.0, 30°C, mutant C221E/C222A Saccharomyces cerevisiae
60
-
pyruvate per subunit, pH 6.0, 30°C, wild-type enzyme Saccharomyces cerevisiae

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
6
-
assay at Saccharomyces cerevisiae

Cofactor

Cofactor Comment Organism Structure
thiamine diphosphate bound in the V conformation in the active sites of the enzyme, side chains of residues Glu51, Glu477, Asp28, His114, and His 115 potentially participate in proton transfer steps Saccharomyces cerevisiae

General Information

General Information Comment Organism
evolution the enzyme is a member of the superfamily of thiamine diphosphate-dependent enzymes Saccharomyces cerevisiae