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Literature summary extracted from

  • Kutter, S.; Wille, G.; Relle, S.; Weiss, M.S.; Huebner, G.; Koenig, S.
    The crystal structure of pyruvate decarboxylase from Kluyveromyces lactis. Implications for the substrate activation mechanism of this enzyme (2006), FEBS J., 273, 4199-4209.
    View publication on PubMed

Activating Compound

EC Number Activating Compound Comment Organism Structure
4.1.1.1 Pyruvamide the activator pyruvamide arrests one of the flexible loops comprising residues 106-113 and 292-301, so that two of four active sites become closed, the loop of residues 105-113 remains flexible in the nonactivated enzyme, overview Saccharomyces cerevisiae
4.1.1.1 Pyruvamide the activator pyruvamide arrests the flexible loops comprising residues 106-113 and 292-301, so that two of four active sites become closed Kluyveromyces lactis
4.1.1.1 pyruvate allosteric substrate activation, binding of substrate at a regulatory site induces catalytic activity, accompanied by conformational changes and subunit rearrangements Saccharomyces cerevisiae
4.1.1.1 pyruvate allosteric substrate activation, binding of substrate at a regulatory site induces catalytic activity, accompanied by conformational changes and subunit rearrangements, the structuring of the flexible loop region 105-113 seems to be the crucial step during the substrate activation process Kluyveromyces lactis

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.1.1.1 recombinant expression Kluyveromyces lactis
4.1.1.1 recombinant expression Saccharomyces cerevisiae

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.1.1.1 purified recombinant enzyme, 2 mg/ml protein in 50 mM MES, pH 6.45, 5 mM thiamine diphosphate, 1 mM dithiothreitol, and 5 mM MgSO4, or 35 mM sodium citrate, pH 6.45, 1 mM dithiothreitol, 5 mM thiamine diphosphate, and 5 mM MgSO4, in absence of ammonium sulfate, hanging drop vapour diffusion method, 8°C, in a 1:1 mixture with reservoir solution containing 20% w/v PEG 2000/PEG 8000 in crystallization buffer, microcrystals within 3 days, larger crystals within 4 weeks, X-ray diffraction structure determination and analysis at 2.26 A resolution Kluyveromyces lactis

Inhibitors

EC Number Inhibitors Comment Organism Structure
4.1.1.1 glyoxylic acid
-
 Saccharomyces cerevisiae

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
4.1.1.1 Mg2+ dependent on, bound tightly, but not covalently, at the interface of two monomers Saccharomyces cerevisiae
4.1.1.1 Mg2+ dependent on, bound tightly, but not covalently, at the interface of two monomers, reversible dissociation of Mg2+ at pH above 8.0, leads to complete loss of activity Kluyveromyces lactis

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
4.1.1.1 240000
-
-
 Kluyveromyces lactis
4.1.1.1 240000
-
-
 Saccharomyces cerevisiae

Natural Substrates/ Products (Substrates)

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

Organism

EC Number Organism UniProt Comment Textmining
4.1.1.1 Kluyveromyces lactis Q12629 single gene
-
4.1.1.1 Saccharomyces cerevisiae P06169 more than one gene
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.1.1.1 native enzyme by acetone precipitation, ammonium sulfate fractionation, and gel filtration to over 95% homogeneity Saccharomyces cerevisiae
4.1.1.1 native enzyme by ammonium sulfate fractionation, gel filtration, and anion exchange chromatography to over 95% homogeneity Kluyveromyces lactis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.1.1.1 pyruvate
-
 Kluyveromyces lactis acetaldehyde + CO2
-
 ?
4.1.1.1 pyruvate
-
 Saccharomyces cerevisiae acetaldehyde + CO2
-
 ?
4.1.1.1 pyruvate catalytic cycle, overview Kluyveromyces lactis acetaldehyde + CO2
-
 ?
4.1.1.1 pyruvate catalytic cycle, overview Saccharomyces cerevisiae acetaldehyde + CO2
-
 ?

Subunits

EC Number Subunits Comment Organism
4.1.1.1 tetramer subunit crystal structure analysis, the subunits are each composed of three domains, the R domain, the PYR domain, and the PP domain, all three domains exhibit typical alpha/beta-topology, the enzyme contains flexible loops comprising residues 106-113 and 292-301 involved in catalysis via four active sites, open and closed conformation of the activate and nonactivated enzyme, respectively, the completely open enzyme state is favoured for Saccharomyces cerevisiae pyruvate decarboxylase, overview Saccharomyces cerevisiae
4.1.1.1 tetramer subunit crystal structure analysis, the subunits are each composed of three domains, the R domain, the PYR domain, and the PP domain, all three domains exhibit typical alpha/beta-topology, the enzyme shows a half-side closed tetramer in presence or absence of any activator, the half-side closed form is predominant for Kluyveromyces lactis pyruvate decarboxylase, the structuring of the flexible loop region 105-113 seems to be the crucial step during the substrate activation process, overview Kluyveromyces lactis

Synonyms

EC Number Synonyms Comment Organism
4.1.1.1 PDC
-
 Kluyveromyces lactis
4.1.1.1 PDC
-
 Saccharomyces cerevisiae

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.1.1.1 5.7 6.3
-
 Kluyveromyces lactis
4.1.1.1 5.7 6.3
-
 Saccharomyces cerevisiae

Cofactor

EC Number Cofactor Comment Organism Structure
4.1.1.1 thiamine diphosphate dependent on, bound tightly, but not covalently, at the interface of two monomers Saccharomyces cerevisiae
4.1.1.1 thiamine diphosphate dependent on, bound tightly, but not covalently, at the interface of two monomers, reversible dissociation of the cofactor at pH above 8.0, leads to complete loss of activity Kluyveromyces lactis