Literature summary for 4.1.1.1 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.

Activating Compound

Activating Compound	Comment	Organism
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
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
pyruvate	allosteric substrate activation, binding of substrate at a regulatory site induces catalytic activity, accompanied by conformational changes and subunit rearrangements	Saccharomyces cerevisiae
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)

Cloned (Comment)	Organism
recombinant expression	Kluyveromyces lactis
recombinant expression	Saccharomyces cerevisiae

Crystallization (Commentary)

Crystallization (Comment)	Organism
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

Crystallization (Comment)

Organism

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

Inhibitors	Comment	Organism	Structure
glyoxylic acid	-	Saccharomyces cerevisiae

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	dependent on, bound tightly, but not covalently, at the interface of two monomers	Saccharomyces cerevisiae
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]

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

Natural Substrates/ Products (Substrates)

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

Organism

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

Purification (Commentary)

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

Substrates and Products (Substrate)

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

Subunits

Subunits	Comment	Organism
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
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

Synonyms	Comment	Organism
PDC	-	Kluyveromyces lactis
PDC	-	Saccharomyces cerevisiae

pH Optimum

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

Cofactor

Cofactor	Comment	Organism	Structure
thiamine diphosphate	dependent on, bound tightly, but not covalently, at the interface of two monomers	Saccharomyces cerevisiae
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